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  • 2015-2019
  • 2005-2009  (34)
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  • 1
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    Barrier methods for a control problem from hyperthermia treatment planning (2009)
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    Publication Date: 2019-01-29
    Description: We consider an optimal control problem from hyperthermia treatment planning and its barrier regularization. We derive basic results, which lay the groundwork for the computation of optimal solutions via an interior point path-following method. Further, we report on a numerical implementation of such a method and its performance at an example problem.
    Keywords: ddc:510
    Language: English
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  • 2
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    Transparent boundary conditions for Maxwell's equations: Numerical concepts beyond the PML method (2009)
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    Publication Date: 2016-06-09
    Description: Optical technologies are ubiquitously used in hi-tech devices. As a common feature of such devices one finds structures with dimensions in the order of the wavelength of the used light. To design and produce such devices, the wave nature of light must be taken into account. Accordingly, robust simulation tools are required which are based on rigorously solving Maxwell's equations, the governing equations of light propagation within macroscopic media. This thesis contributes to the modeling and the numerical computation of light scattering problems: Light scattering problems are typically posed on the entire space. The Perfectly-Matched -Layer method (PML) is widely used to restrict the simulation problem onto a bounded computational domain. We propose an adaptive PML method which exhibits a good convergence even for critical problems where standard PML implementations fail. Besides the computation of the near field, that is the electromagnetic field within the computational domain, it is of major interest to evaluate the electromagnetic field in the exterior domain and to compute the far field. So far, this was numerically only possible for simple geometries such as homogeneous exterior domains or layered media. To deal with more complicated devices, for example with waveguide inhomogeneities, we develop an evaluation formula based on the PML solution which allows for an exterior domain field evaluation in a half space above the device. Finally, we generalize the PML method to problems with multiply structured exterior domains. The term “multiply structured exterior domain” is defined in this thesis and means that the exterior domain exhibits several half-infinite structures. Mathematically, this gives rise to various complications. For example, no analytical solutions to Maxwell's equations for standard light sources are available in the exterior domain, which are needed to describe the incoming field in a light scattering problem. To tackle this we propose a new light scattering problem formulation which fits well into the PML method framework and which may be regarded as an extension of classical contributions by Sommerfeld, Wiener and Hopf. An exterior domain evaluation formula for multiply structured exterior domains with an extended illumination is derived as well.
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 3
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    The Coolest Path Problem (2009)
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    Publication Date: 2020-08-05
    Description: We introduce the coolest path problem, which is a mixture of two well-known problems from distinct mathematical fields. One of them is the shortest path problem from combinatorial optimization. The other is the heat conduction problem from the field of partial differential equations. Together, they make up a control problem, where some geometrical object traverses a digraph in an optimal way, with constraints on intermediate or the final state. We discuss some properties of the problem and present numerical solution techniques. We demonstrate that the problem can be formulated as a linear mixed-integer program. Numerical solutions can thus be achieved within one hour for instances with up to 70 nodes in the graph.
    Keywords: ddc:510
    Language: English
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  • 4
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    The MCF-Separator -- Detecting and Exploiting Multi-Commodity Flow Structures in MIPs (2009)
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    Publication Date: 2021-08-05
    Description: Given a general mixed integer program (MIP), we automatically detect block structures in the constraint matrix together with the coupling by capacity constraints arising from multi-commodity-flow formulations. We identify the underlying graph and generate cutting planes based on cuts in the detected network. Our implementation adds a separator to the branch-and-cut libraries of SCIP and CPLEX. We make use of the complemented mixed integer rounding framework (cMIR) but provide a special purpose aggregation heuristic that exploits the network structure. Our separation scheme speeds-up the computation for a large set of MIPs coming from network design problems by a factor of two on average.
    Keywords: ddc:510
    Language: English
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  • 5
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    Nonlinear pseudo-Boolean optimization: relaxation or propagation? (2009)
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    Publication Date: 2022-03-14
    Description: Pseudo-Boolean problems lie on the border between satisfiability problems, constraint programming, and integer programming. In particular, nonlinear constraints in pseudo-Boolean optimization can be handled by methods arising in these different fields: One can either linearize them and work on a linear programming relaxation or one can treat them directly by propagation. In this paper, we investigate the individual strengths of these approaches and compare their computational performance. Furthermore, we integrate these techniques into a branch-and-cut-and-propagate framework, resulting in an efficient nonlinear pseudo-Boolean solver.
    Keywords: ddc:510
    Language: English
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  • 6
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    Planning Problems in Public Transit (2009)
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    Publication Date: 2020-08-05
    Description: Every day, millions of people are transported by buses, trains, and airplanes in Germany. Public transit (PT) is of major importance for the quality of life of individuals as well as the productivity of entire regions. Quality and efficiency of PT systems depend on the political framework (state-run, market oriented) and the suitability of the infrastructure (railway tracks, airport locations), the existing level of service (timetable, flight schedule), the use of adequate technologies (information, control, and booking systems), and the best possible deployment of equipment and resources (energy, vehicles, crews). The decision, planning, and optimization problems arising in this context are often gigantic and “scream” for mathematical support because of their complexity. This article sketches the state and the relevance of mathematics in planning and operating public transit, describes today’s challenges, and suggests a number of innovative actions. The current contribution of mathematics to public transit is — depending on the transportation mode — of varying depth. Air traffic is already well supported by mathematics. Bus traffic made significant advances in recent years, while rail traffic still bears significant opportunities for improvements. In all areas of public transit, the existing potentials are far from being exhausted. For some PT problems, such as vehicle and crew scheduling in bus and air traffic, excellent mathematical tools are not only available, but used in many places. In other areas, such as rolling stock rostering in rail traffic, the performance of the existing mathematical algorithms is not yet sufficient. Some topics are essentially untouched from a mathematical point of view; e.g., there are (except for air traffic) no network design or fare planning models of practical relevance. PT infrastructure construction is essentially devoid of mathematics, even though enormous capital investments are made in this area. These problems lead to questions that can only be tackled by engineers, economists, politicians, and mathematicians in a joint effort. Among other things, the authors propose to investigate two specific topics, which can be addressed at short notice, are of fundamental importance not only for the area of traffic planning, should lead to a significant improvement in the collaboration of all involved parties, and, if successful, will be of real value for companies and customers: • discrete optimal control: real-time re-planning of traffic systems in case of disruptions, • model integration: service design in bus and rail traffic. Work on these topics in interdisciplinary research projects could be funded by the German ministry of research and education (BMBF), the German ministry of economics (BMWi), or the German science foundation (DFG).
    Keywords: ddc:510
    Language: English
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  • 7
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    Solving Steel Mill Slab Problems with Branch and Price (2009)
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    Publication Date: 2020-08-05
    Description: The steel mill slab design problem from the CSPLib is a binpacking problem that is motivated by an application of the steel industry and that has been widely studied in the constraint programming community. Recently, several people proposed new models and methods to solve this problem. A steel mill slab library was created which contains 380 instances. A closely related binpacking problem called multiple knapsack problem with color constraints, originated from the same industrial problem, were discussed in the integer programming community. In particular, a simple integer programming for this problem has been given by Forrest et al. [3]. The aim of this paper is to bring these different studies together. Moreover, we adopt the model of [3] for the steel mill slab problem. Using a state of the art integer program solver, this model is capable to solve all instances of the steel mill slab library, mostly in less than one second, to optimality. We improved, thereby, the solution value of 76 instances.
    Keywords: ddc:510
    Language: English
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  • 8
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    On the Hardness of Finding Small Shortest Path Routing Conflicts (2009)
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    Publication Date: 2020-08-05
    Description: Nowadays most data networks use shortest path protocols such as OSPF or IS-IS to route traffic. Given administrative routing lengths for the links of a network, all data packets are sent along shortest paths with respect to these lengths from their source to their destination. One of the most fundamental problems in planning shortest path networks is to decide whether a given set of routing paths forms a valid routing and, if this is not the case, to find a small subset of the given paths that cannot be shortest paths simultaneously for any routing lengths. In this paper we show that it is NP-hard to approximate the size of the smallest shortest path conflict by a factor less than 7/6.
    Keywords: ddc:510
    Language: English
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  • 9
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    A Binary Quadratic Programming Approach to the Vehicle Positioning Problem (2009)
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    Publication Date: 2020-08-05
    Description: The Vehicle Positioning Problem (VPP) consists of the assignment of vehicles (buses, trams or trains) of a public transport or railway company to parking positions in a depot and to timetabled trips. Such companies have many different types of vehicles, and each trip can be performed only by vehicles of some of these types. These assignments are non-trivial due to the topology of depots. The parking positions are organized in tracks, which work as one- or two-sided stacks or queues. If a required type of vehicle is not available in the front of any track, shunting movements must be performed in order to change vehicles' positions, which is undesirable and should be avoided. In this text we present integer linear and non-linear programming formulations for some versions of the problem and compare them from a theoretical and a computational point of view.
    Keywords: ddc:510
    Language: English
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  • 10
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    Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics (2009)
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    Publication Date: 2020-03-11
    Description: The understanding of geometric structures and dynamical properties of molecular conformations gives insight into molecular long-term behavior. The identification of metastable conformations together with their life times and transition patterns is the intention of conformation dynamics. Conformation dynamics is a multi-scale approach that leads to a reduced description of the dynamical system in terms of a stochastic transition probability matrix. The present thesis deals with the error analysis of computed matrices and the resulting matrix functions. Since conformational membership vectors, as they are computed by the Robust Perron Cluster Analysis (PCCA+), form an invariant subspace of the transition matrix, subspace-based error estimators are of particular interest. The decomposition of the state space into basis functions and the approximation of integrals by Monte-Carlo quadrature give rise to row-wise correlated random matrices, for which stochastic norms are computed. Together with an appropriate statistical model for the distribution of matrix rows, this allows for the calculation of error bounds and error distributions of the invariant subspace and other variables of interest. Equilibration of errors among the basis functions can be achieved by enhanced sampling in regions where the trajectories are mixing slowly. Hierarchical refinement of such basis functions systematically improves the clustering into metastable conformations by reducing the error in the corresponding invariant subspace. These techniques allow for an evaluation of simulation results and pave the way for the analysis of larger molecules. Moreover, the extension of PCCA+ to non-reversible Markov chains, verified by the corresponding perturbation theory, and the modification of the objective function for the case of soft membership vectors represent a further generalization of the clustering method, thus continuing the development from PCCA over PCCA+ to PCCA++. The methods developed in this thesis are useful for but not limited to conformation dynamics. In fact, they are applicable to a broader class of problems which combine domain decomposition with Monte-Carlo quadrature. Possible application areas may include the chemical master equation or quantum dynamical systems.
    Description: Das Verständnis von geometrischen Strukturen und dynamischen Eigenschaften molekularer Konformationen ist essentiell für die Vorhersage des Langzeitverhaltens von Molekülen. Die Identifikation metastabiler Konformationen sowie die Bestimmung von Übergangswahrscheinlichkeiten und Haltezeiten sind Bestandteil der Konformationdynamik. Dabei handelt es sich um eine Mehrskalenmethode, die auf eine reduzierte Beschreibung des Systems mittels einer stochastischen Übergangsmatrix führt. In der vorliegenden Dissertation wurde untersucht, wie man die Genauigkeit der Matrizen sowie der daraus berechneten Größen quantifizieren kann. Im Mittelpunkt stehen dabei Fehlerschätzer für den invarianten Unterraum, da die rechten Eigenvektoren als Grundlage der Robusten Perron Cluster Analyse (PCCA+) zur Identifizierung der metastabilen Konformationen dienen. Die Zerlegung des Zustandsraumes in Basisfunktionen sowie die Approximation der Matrixeinträge mittels Monte-Carlo-Quadratur führen zu zeilenweise korrelierten Zufallsmatrizen. Mit Hilfe einer stochastischen Norm sowie einem geeigneten statistischen Modell für die Verteilung der Matrixzeilen können u.a. Fehlerschranken und -verteilungen für den invarianten Unterraum brechnet werden. Eine Equilibrierung des Fehlers zwischen den Basisfunktionen kann durch erweitertes Sampling in solchen Regionen erreicht werden, in denen die Trajektorien nur langsam mischen.Eine hierarchische Zerlegung dieser Basisfunktionen verbessert systematisch die Zerlegung in metastabile Konformationen, indem sie den Fehler im invarianten Unterraum reduziert. Diese Techniken gestatten eine Evaluierung der Simulationsergebnisse und ebnen den Weg zur Behandlung komplexerer Moleküle. Desweiteren wurden Verallgemeinerungen der PCCA+ untersucht. Die Erweiterung der PCCA+ auf nicht-reversible Markov-Ketten sowie die Modifizierung der Zielfunktion für den Fall der weichen Clusterung setzen die Entwicklung von der PCCA über PCCA+ zu PCCA++ fort. Somit können neue Anwendungsfelder für dieses Cluster-Verfahren erschlossen werden. Die Methoden wurden zwar in Rahmen der Konformationsdynamik entwickelt, jedoch lassen sie sich auf eine weite Problemklasse anwenden, in der Gebietszerlegungsverfahren mit Monte-Carlo-Quadratur kombiniert werden. Mögliche Anwendungsgebiete umfassen die chemische Master-Gleichung oder quantenchemische Systeme.
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 11
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    A Set Partitioning Approach to Shunting (2009)
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    Publication Date: 2020-08-05
    Description: The Vehicle Positioning Problem (VPP) is a classical combinatorial optimization problem in public transport planning. A number of models and approaches have been suggested in the literature, which work for small problems, but not for large ones. We propose in this article a novel set partitioning model and an associated column generation solution approach for the VPP. The model provides a tight linear description of the problem. The pricing problem, and hence the LP relaxation itself, can be solved in polynomial resp. pseudo-polynomial time for some versions of the problems.
    Keywords: ddc:510
    Language: English
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  • 12
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    Solving Large-scale Open Pit Mining Production Scheduling Problems by Integer Programming (2009)
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    Publication Date: 2020-08-05
    Description: Since the initial application of mathematical optimisation methods to mine planning in 1965, the Lerchs-Grossmann algorithm for computing the ultimate pit limit, operations researchers have worked on a variety of challenging problems in the area of open pit mining. This thesis focuses on the open pit mining production scheduling problem: Given the discretisation of an orebody as a block model, determine the sequence in which the blocks should be removed from the pit, over the lifespan of the mine, such that the net present value of the mining operation is maximised. In practise, when some material has been removed from the pit, it must be processed further in order to extract the valuable elements contained therein. If the concentration of valuable elements is not sufficiently high, the material is discarded as waste or stockpiled. Realistically-sized block models can contain hundreds of thousands of blocks. A common approach to render these problem instances computationally tractable is the aggregation of blocks to larger scheduling units. The thrust of this thesis is the investigation of a new mixed-integer programming formulation for the open pit mining production scheduling problem, which allows for processing decisions to be made at block level, while the actual mining schedule is still computed at aggregate level. A drawback of this model in its full form is the large number of additional variables needed to model the processing decisions. One main result of this thesis shows how these processing variables can be aggregated efficiently to reduce the problem size significantly, while practically incurring no loss in net present value. The second focus is on the application of lagrangean relaxation to the resource constraints. Using a result of Möhring et al. (2003) for project scheduling, the lagrangean relaxation can be solved efficiently via minimum cut computations in a weighted digraph. Experiments with a bundle algorithm implementation by Helmberg showed how the lagrangean dual can be solved within a small fraction of the time required by standard linear programming algorithms, while yielding practically the same dual bound. Finally, several problem-specific heuristics are presented together with computational results: two greedy sub-MIP start heuristics and a large neighbourhood search heuristic. A combination of a lagrangean-based start heuristic followed by a large neighbourhood search proved to be effective in generating solutions with objective values within a 0.05% gap of the optimum.
    Keywords: ddc:510
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 13
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    1D-Reduktion thermal signifikanter Aderstränge in der Hyperthermie-Modellierung (2009)
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    Publication Date: 2019-01-29
    Description: In dieser Arbeit wird ein neuer Ansatz zur Modellierung von thermal signifikanten Gefäßsträngen im Hyperthermie-Kontext betrachtet. Ausgehend von einer Konvektions-Diffusions-Gleichung wird durch Reskalierung des Massenflussterms eine Reduktion des Adergebietes auf eine 1D-Struktur erreicht. Nach numerischen Vorbetrachtungen wird die Grenzgleichung innerhalb einer verallgemeinerten Sobolev-Algebra formuliert. Die Untersuchung der Lösungsfamilie in klassischen Funktionenräumen zeigt, dass deren schwacher Grenzwert die Lösung der korrespondierenden Diffusions-Gleichung ist. Die Diskretisierung einer formalen Grenzgleichung mit Linienstromanteil stellt jedoch eine gute Approximation an die Diskretisierung des ursprünglichen Problems dar, wenn man die lokale Maschenweite an die Gefäßradien koppelt und bei erhöhtem Genauigkeitsbedarf auf ein vollständiges 3D-Modell umschaltet.
    Keywords: ddc:510
    Language: German
    Type: masterthesis , doc-type:masterThesis
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  • 14
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    Undercover – a primal heuristic for MINLP based on sub-MIPs generated by set covering (2009)
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    Publication Date: 2022-03-14
    Description: We present Undercover, a primal heuristic for mixed-integer nonlinear programming (MINLP). The heuristic constructs a mixed-integer linear subproblem (sub-MIP) of a given MINLP by fixing a subset of the variables. We solve a set covering problem to identify a minimal set of variables which need to be fixed in order to linearise each constraint. Subsequently, these variables are fixed to approximate values, e.g. obtained from a linear outer approximation. The resulting sub-MIP is solved by a mixed-integer linear programming solver. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. Although general in nature, the heuristic seems most promising for mixed-integer quadratically constrained programmes (MIQCPs). We present computational results on a general test set of MIQCPs selected from the MINLPLib.
    Keywords: ddc:510
    Language: English
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  • 15
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    On sojourn times in M/GI systems under state-dependent processor sharing (2009)
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    Publication Date: 2020-08-05
    Description: We consider a system with Poisson arrivals and i.i.d. service times. The requests are served according to the state-dependent processor sharing discipline, where each request receives a service capacity which depends on the actual number of requests in the system. The linear systems of PDEs describing the residual and attained sojourn times coincide for this system, which provides time reversibility including sojourn times for this system, and their minimal non negative solution gives the LST of the sojourn time $V(\tau)$ of a request with required service time $\tau$. For the case that the service time distribution is exponential in a neighborhood of zero, we derive a linear system of ODEs, whose minimal non negative solution gives the LST of $V(\tau)$, and which yields linear systems of ODEs for the moments of $V(\tau)$ in the considered neighborhood of zero. Numerical results are presented for the variance of $V(\tau)$. In case of an M/GI/2-PS system, the LST of $V(\tau)$ is given in terms of the solution of a convolution equation in the considered neighborhood of zero. For bounded from below service times, surprisingly simple expressions for the LST and variance of $V(\tau)$ in this neighborhood of zero are derived, which yield in particular the LST and variance of $V(\tau)$ in M/D/2-PS.
    Keywords: ddc:510
    Language: English
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  • 16
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    E-Learning and the Working Mathematician (2009)
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    Publication Date: 2020-12-11
    Description: Eigentlich war der erste Autor nur zu einem Grußwort zur Tagung „GML² 2009 - Grundfragen Multi¬medialen Lehrens und Lernens“ eingeladen. Daraus wurde ein E-Learning-bezogener Vortrag, der – basierend auf Erfahrungen im Fach Mathematik – einen kritischen Blick auf die E-Learning-Szene in Deutschland wirft und diese mit entsprechenden Aktivitäten weltweit vergleicht. Dies ist die in seinen mathematischen Teilen gekürzte, in den E-Learning-Anteilen ein wenig erweiterte schriftliche Fassung des Vortrags. Der Artikel stammt nicht von E-Learning-Spezialisten sondern von Personen, die sich seit fast zwanzig Jahren mit elektronischer Information und Kommunikation (kurz: IuK) – insbesondere in der Mathematik – beschäftigen. Nach einer Definition von Michael Kerres kennzeichnet der Begriff E-Learning (electronic learning – elektronisch unterstütztes Lernen) alle Formen von Lernen, bei denen digitale Medien für die Präsentation und Distribution von Lernmaterialien und/oder zur Unterstützung zwischenmenschlicher Kommunikation zum Einsatz kommen, siehe z.B. http://de.wikipedia.org/wiki/E-Learning. IuK und E-Learning haben nach dieser Begriffsbildung viele Berührungspunkte. Deswegen wagen wir es, unsere positiven und negativen Erfahrungen im Bereich IuK in diesem Eröffnungsvortrag zu berichten, einige Entwicklungslinien zu vergleichen und eine eigene Kurzversion der Definition von E-Learning (besser E-Teaching and -Learning) voranzustellen: „Lehren und Lernen mit Unterstützung elektronischer Hilfsmittel“.
    Keywords: ddc:510
    Language: German
    Type: reportzib , doc-type:preprint
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  • 17
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    Optimal Design of Survivable Multi-layer Telecommunication Networks (2009)
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    Publication Date: 2020-08-05
    Description: Telecommunication transport networks consist of a stack of technologically different subnetworks, so-called layers, which are strongly interdependent. For example, one layer may correspond to an Internet (IP) backbone network whose links are realized by lightpath connections in an underlying optical fiber layer. To ensure that the network can fulfill its task of routing all communication requests, the inter-layer dependencies have to be taken into account already in the planning phase of the network. This is particularly important with survivability constraints, where connections in one layer have to be protected against cable cuts or equipment failures in another layer. The traditional sequential planning approach where one layer is optimized after the other cannot properly take care of the inter-layer dependencies; this can only be achieved with an integrated planning of several network layers at the same time. This thesis provides mathematical models and algorithmic techniques for the integrated optimization of two network layers with survivability constraints. We describe a multi-layer network design problem which occurs in various technologies, and model it mathematically using mixed-integer programming (MIP) formulations. The presented models cover many important practical side constraints from different technological contexts. In contrast to previous models from the literature, they can be used to design large two-layer networks with survivability requirements. We discuss modeling alternatives for various aspects of a multi-layer network and compare different routing formulations under multi-layer survivability constraints. We solve our models using a branch-and-cut-and-price approach with various problemspecific enhancements. This includes a presolving technique based on linear programming to reduce the problem size, combinatorial and sub-MIP-based primal heuristics to compute feasible network configurations, cutting planes which take the multi-layer survivability constraints into account to improve the lower bound on the optimal network cost, and column generation to generate flow variables dynamically during the algorithm. We develop techniques to speed up computations in a Benders decomposition approach and compare this approach to the standard formulation with a single MIP. We use the developed techniques to design large survivable two-layer networks by means of linear and integer programming methods. On realistic test instances with up to 67 network nodes and survivability constraints, we investigate the algorithmic impact of our techniques and show how to use them to compute good network configurations with quality guarantees. Most of the smaller test instances with up to 17 nodes can be solved to near-optimality. Moreover, we can compute feasible solutions and dual bounds even for large networks with survivability constraints, which has not been possible before.
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 18
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    On the Factorization of Simplex Basis Matrices (2009)
    Details
    Publication Date: 2020-08-05
    Description: In the simplex algorithm, solving linear systems with the basis matrix and its transpose accounts for a large part of the total computation time. We investigate various methods from modern numerical linear algebra to improve the computation speed of the basis updates arising in LPs. The experiments are executed on a large real-world test set. The most widely used solution technique is sparse LU factorization, paired with an updating scheme that allows to use the factors over several iterations. Clearly, small number of fill-in elements in the LU factors is critical for the overall performance. Using a wide range of LPs we show numerically that after a simple permutation the non-triangular part of the basis matrix is so small, that the whole matrix can be factorized with (relative) fill-in close to the optimum. This permutation has been exploited by simplex practitioners for many years. But to our knowledge no systematic numerical study has been published that demonstrates the effective reduction to a surprisingly small non-triangular problem, even for large scale LPs. For the factorization of the non-triangular part most existing simplex codes use some variant of dynamic Markowitz pivoting, which originated in the late 1950s. We also show numerically that, in terms of fill-in and in the simplex context, dynamic Markowitz is quite consistently superior to other, more recently developed techniques.
    Keywords: ddc:510
    Language: English
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    Computing expectation values for molecular quantum dynamics (2009)
    Details
    Publication Date: 2020-03-11
    Description: We compute expectation values for the solution of the nuclear Schrödinger equation. The proposed particle method consists of three steps: sampling of the initial Wigner function, classical transport of the sampling points, weighted phase space summation for the final computation of the expectation values. The Egorov theorem guarantees that the algorithm is second order accurate with respect to the semiclassical parameter. We present numerical experiments for a two-dimensional torsional potential with three different sets of initial data and for a six-dimensional Henon-Heiles potential. By construction, the computing times scale linearly with the number of initial sampling points and range between three seconds and one hour.
    Keywords: ddc:510
    Language: English
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  • 20
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    Extending a CIP framework to solve MIQCPs (2009)
    Details
    Publication Date: 2022-03-14
    Description: This paper discusses how to build a solver for mixed integer quadratically constrained programs (MIQCPs) by extending a framework for constraint integer programming (CIP). The advantage of this approach is that we can utilize the full power of advanced MIP and CP technologies. In particular, this addresses the linear relaxation and the discrete components of the problem. For relaxation, we use an outer approximation generated by linearization of convex constraints and linear underestimation of nonconvex constraints. Further, we give an overview of the reformulation, separation, and propagation techniques that are used to handle the quadratic constraints efficiently. We implemented these methods in the branch-cut-and-price framework SCIP. Computational experiments indicates the potential of the approach.
    Keywords: ddc:510
    Language: English
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    A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator (2009)
    Details
    Publication Date: 2016-06-09
    Description: Supercomputers can simulate complex molecular systems. However, there is a very large gap between the fastest oscillations of covalent bonds of a molecule and the time-scale of the dominant processes. In order to extract the dominant time-scales and to identify the dominant processes, a clustering of information is needed. This thesis shows that only the subspace-based Robust Perron Cluster Analysis (PCCA+) can solve this problem correctly by the construction of a Markov State Model. PCCA+ allows for time-extrapolation in molecular kinetics. This thesis shows the difference between molecular dynamics and molecular kinetics. Only in the molecular kinetics framework a definition of transition rates is possible. In this context, the existence of an infinitesimal generator of the dynamical processes is discussed. If the existence is assumed, the Theorem of Gauß can be applied in order to compute transition rates efficiently. Molecular dynamics, however, is not able to provide a suitable statistical basis for the determination of the transition pattern.
    Keywords: ddc:510
    Language: English
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    Approximations for the second moments of sojourn times in M/GI systems under state-dependent processor sharing (2009)
    Details
    Publication Date: 2020-08-05
    Description: We consider a system with Poisson arrivals and general service times, where the requests are served according to the State-Dependent Processor Sharing (SDPS) discipline (Cohen's generalized processor sharing discipline), where each request receives a service capacity which depends on the actual number of requests in the system. For this system, denoted by $M/GI/SDPS$, we derive approximations for the squared coefficients of variation of the conditional sojourn time of a request given its service time and of the unconditional sojourn time by means of two-moment fittings of the service times. The approximations are given in terms of the squared coefficients of variation of the conditional and unconditional sojourn time in related $M/D/SDPS$ and $M/M/SDPS$ systems, respectively. The numerical results presented for $M/GI/m-PS$ systems illustrate that the proposed approximations work well.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 23
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    Insensitivity bounds for the moments of the sojourn times in M/GI systems under state-dependent processor sharing (2009)
    Details
    Publication Date: 2020-08-05
    Description: We consider a system with Poisson arrivals and i.i.d. service times and where the requests are served according to the state-dependent (Cohen's generalized) processor sharing discipline, where each request in the system receives a service capacity which depends on the actual number of requests in the system. For this system we derive asymptotically tight upper bounds for the moments of the conditional sojourn time of a request with given required service time. The bounds generalize corresponding results, recently given for the single-server processor sharing system by Cheung et al. and for the state-dependent processor sharing system with exponential service times by the authors. Analogous results hold for the waiting times.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 24
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    Randomized Online Algorithms for Dynamic Multi-Period Routing Problems (2009)
    Details
    Publication Date: 2020-11-13
    Description: The Dynamic Multi-Period Routing Problem DMPRP introduced by Angelelli et al. gives a model for a two-stage online-offline routing problem. At the beginning of each time period a set of customers becomes known. The customers need to be served either in the current time period or in the following. Postponed customers have to be served in the next time period. The decision whether to postpone a customer has to be done online. At the end of each time period, an optimal tour for the customers assigned to this period has to be computed and this computation can be done offline. The objective of the problem is to minimize the distance traveled over all planning periods assuming optimal routes for the customers selected in each period. We provide the first randomized online algorithms for the DMPRP which beat the known lower bounds for deterministic algorithms. For the special case of two planning periods we provide lower bounds on the competitive ratio of any randomized online algorithm against the oblivious adversary. We identify a randomized algorithm that achieves the optimal competitive ratio of $\frac{1+\sqrt{2}}{2}$ for two time periods on the real line. For three time periods, we give a randomized algorithm that is strictly better than any deterministic algorithm.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 25
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    Constraint Integer Programming (2009)
    Details
    Publication Date: 2021-08-05
    Description: This thesis introduces the novel paradigm of "constraint integer programming" (CIP), which integrates constraint programming (CP) and mixed integer programming (MIP) modeling and solving techniques. It is supplemented by the software SCIP, which is a solver and framework for constraint integer programming that also features SAT solving techniques. SCIP is freely available in source code for academic and non-commercial purposes. Our constraint integer programming approach is a generalization of MIP that allows for the inclusion of arbitrary constraints, as long as they turn into linear constraints on the continuous variables after all integer variables have been fixed. The constraints, may they be linear or more complex, are treated by any combination of CP and MIP techniques: the propagation of the domains by constraint specific algorithms, the generation of a linear relaxation and its solving by LP methods, and the strengthening of the LP by cutting plane separation. The current version of SCIP comes with all of the necessary components to solve mixed integer programs. In the thesis, we cover most of these ingredients and present extensive computational results to compare different variants for the individual building blocks of a MIP solver. We focus on the algorithms and their impact on the overall performance of the solver. In addition to mixed integer programming, the thesis deals with chip design verification, which is an important topic of electronic design automation. Chip manufacturers have to make sure that the logic design of a circuit conforms to the specification of the chip. Otherwise, the chip would show an erroneous behavior that may cause failures in the device where it is employed. An important subproblem of chip design verification is the property checking problem, which is to verify whether a circuit satisfies a specified property. We show how this problem can be modeled as constraint integer program and provide a number of problem-specific algorithms that exploit the structure of the individual constraints and the circuit as a whole. Another set of extensive computational benchmarks compares our CIP approach to the current state-of-the-art SAT methodology and documents the success of our method.
    Description: Diese Arbeit stellt einen integrierten Ansatz aus "Constraint Programming" (CP) und Gemischt-Ganzzahliger Programmierung ("Mixed Integer Programming", MIP) vor, den wir "Constraint Integer Programming" (CIP) nennen. Sowohl Modellierungs- als auch Lösungstechniken beider Felder fließen in den neuen integrierten Ansatz ein, um die unterschiedlichen Stärken der beiden Gebiete zu kombinieren. Als weiteren Beitrag stellen wir der wissenschaftlichen Gemeinschaft die Software SCIP zur Verfügung, die ein Framework für Constraint Integer Programming darstellt und zusätzlich Techniken des SAT-Lösens beinhaltet. SCIP ist im Source Code für akademische und nicht-kommerzielle Zwecke frei erhältlich. Unser Ansatz des Constraint Integer Programming ist eine Verallgemeinerung von MIP, die zusätzlich die Verwendung beliebiger Constraints erlaubt, solange sich diese durch lineare Bedingungen ausdrücken lassen falls alle ganzzahligen Variablen auf feste Werte eingestellt sind. Die Constraints werden von einer beliebigen Kombination aus CP- und MIP-Techniken behandelt. Dies beinhaltet insbesondere die "Domain Propagation", die Relaxierung der Constraints durch lineare Ungleichungen, sowie die Verstärkung der Relaxierung durch dynamisch generierte Schnittebenen. Die derzeitige Version von SCIP enthält alle Komponenten, die für das effiziente Lösen von Gemischt-Ganzzahligen Programmen benötigt werden. Die vorliegende Arbeit liefert eine ausführliche Beschreibung dieser Komponenten und bewertet verschiedene Varianten in Hinblick auf ihren Einfluß auf das Gesamt-Lösungsverhalten anhand von aufwendigen praktischen Experimenten. Dabei wird besonders auf die algorithmischen Aspekte eingegangen. Ein weiterer Hauptteil der Arbeit befasst sich mit der Chip-Design-Verifikation, die ein wichtiges Thema innerhalb des Fachgebiets der "Electronic Design Automation" darstellt. Chip-Hersteller müssen sicherstellen, dass der logische Entwurf einer Schaltung der gegebenen Spezifikation entspricht. Andernfalls würde der Chip fehlerhaftes Verhalten aufweisen, dass zu Fehlfunktionen innerhalb des Gerätes führen kann, in dem der Chip verwendet wird. Ein wichtiges Teilproblem in diesem Feld ist das Eigenschafts-Verifikations-Problem, bei dem geprüft wird, ob der gegebene Schaltkreisentwurf eine gewünschte Eigenschaft aufweist. Wir zeigen, wie dieses Problem als Constraint Integer Program modelliert werden kann und geben eine Reihe von problemspezifischen Algorithmen an, die die Struktur der einzelnen Constraints und der Gesamtschaltung ausnutzen. Testrechnungen auf Industrie-Beispielen vergleichen unseren Ansatz mit den bisher verwendeten SAT-Techniken und belegen den Erfolg unserer Methode.
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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    Fare Planning for Public Transport (2009)
    Details
    Publication Date: 2020-08-05
    Description: In this paper we investigate the fare planning model for public transport, which consists in designing a system of fares maximizing the revenue. We discuss a discrete choice model in which passengers choose between different travel alternatives to express the demand as a function of fares. Furthermore, we give a computational example for the city of Potsdam and discuss some theoretical aspects.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 27
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    Improving the performance of elevator systems using exact reoptimization algorithms (2009)
    Details
    Publication Date: 2020-08-05
    Description: This extended abstract is about algorithms for controlling elevator systems employing destination hall calls, i.e. the passenger provides his destination floor when calling an elevator. We present the first exact algorithm for controlling a group of elevators and report on simulation results indicating that destination hall call systems outperform conventional systems.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 28
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    On goal-oriented adaptivity for elliptic optimal control problems (2009)
    Details
    Publication Date: 2019-01-29
    Description: The paper proposes goal-oriented error estimation and mesh refinement for optimal control problems with elliptic PDE constraints using the value of the reduced cost functional as quantity of interest. Error representation, hierarchical error estimators, and greedy-style error indicators are derived and compared to their counterparts when using the all-at-once cost functional as quantity of interest. Finally, the efficiency of the error estimator and generated meshes are demonstrated on numerical examples.
    Keywords: ddc:510
    Language: English
    Type: reportzib , doc-type:preprint
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  • 29
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    Consistency Results for the Contact-Stabilized Newmark Method (2009)
    Details
    Publication Date: 2016-06-09
    Description: The paper considers the time integration of frictionless dynamical contact problems between viscoelastic bodies in the frame of the Signorini condition. Among the numerical integrators, interest focuses on the contact-stabilized Newmark method recently suggested by Deuflhard et al., which is compared to the classical Newmark method and an improved energy dissipative version due to Kane et al. In the absence of contact, any such variant is equivalent to the Störmer-Verlet scheme, which is well-known to have consistency order 2. In the presence of contact, however, the classical approach to discretization errors would not show consistency at all because of the discontinuity at the contact. Surprisingly, the question of consistency in the constrained situation has not been solved yet. The present paper fills this gap by means of a novel proof technique using specific norms based on earlier perturbation results due to the authors. The corresponding estimation of the local discretization error requires the bounded total variation of the solution. The results have consequences for the construction of an adaptive timestep control, which will be worked out subsequently in a forthcoming paper.
    Keywords: ddc:510
    Language: English
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    Discrete Optimization in Public Transportation (2009)
    Details
    Publication Date: 2020-08-05
    Description: The mathematical treatment of planning problems in public transit has made significant advances in the last decade. Among others, the classical problems of vehicle and crew scheduling can nowadays be solved on a routine basis using combinatorial optimization methods. This is not yet the case for problems that pertain to the design of public transit networks, and for the problems of operations control that address the implementation of a schedule in the presence of disturbances. The article gives a sketch of the state and important developments in these areas, and it addresses important challenges. The vision is that mathematical tools of computer aided scheduling (CAS) will soon play a similar role in the design and operation of public transport systems as CAD systems in manufacturing.
    Description: Die mathematische Behandlung von Planungsproblemen im öffentlichen Verkehr hat im letzten Jahrzehnt große Fortschritte gemacht. Klassische Probleme wie die Umlauf- und die Dienstplanung können heutzutage routinemäßig mit kombinatorischen Optimierungsmethoden gelöst werden. Die Behandlung von Problemen der Angebotsplanung und der Betriebssteuerung sind dagegen noch nicht ganz auf diesem Stand. Dieser Artikel gibt einen Überblick über den Stand der Forschung, über wichtige Entwicklungen und einige Herausforderungen in diesem Gebiet. Die Vision ist, dass mathematische Planungswerkzeuge im öffentlichen Verkehr (Computer Aided Scheduling, CAS) in Zukunft eine ähnliche Rolle spielen werden wie CAD-Systeme in der industriellen Fertigung.
    Keywords: ddc:510
    Language: English
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  • 31
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    Variational and statistical shape modeling for 3D geometry reconstruction (2009)
    Details
    Publication Date: 2022-07-19
    Description: The reconstruction of geometric shapes plays an important role in many biomedical applications. One example is the patient-specific, computer-aided planning of complex interventions, which requires the generation of explicitly represented geometric models of anatomical structures from medical image data. Only solutions that require minimal interaction by medical personnel are likely to enter clinical routine. Another example is the planning of surgical corrections of deformities where the target shape is unknown. Surgeons are often forced to resort to subjective criteria. These applications still pose highly challenging reconstruction problems, which are addressed in this thesis. The fundamental hypothesis, pursued in this thesis, is that the problems can be solved by incorporating a-priori knowledge about shape and other application-specific characteristics. Here, we focus mainly on the aspect of geometric shape analysis. The basic idea is to capture the most essential variations of a certain class of geometric objects via statistical shape models, which model typical features contained in a given population, and restrict the outcome of a reconstruction algorithm (more or less) to the space spanned by such models. A fundamental prerequisite for performing statistical shape analysis on a set of different objects is the identification of corresponding points on their associated surfaces. This problem is particularly difficult to solve if the shapes stem from different individuals. The reason lies in the basic difficulty of defining suitable measures of similarity. In this thesis, we divide the correspondence problem into feature and non-feature matching. The feature part depends on the application, while the non-feature part can be characterized by a purely geometric description. We propose two different approaches. The first approach has proved useful in many applications. Yet, it suffers from some practical limitations and does not yield a measure of similarity. Our second, variational, approach is designed to overcome these limitations. In it, we propose to minimize an invariant stretching measure, constrained by previously computed features. An important property, which sets our method apart from previous work, is that it does not require the computation of a global surface parameterization.
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 32
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    Meshless Methods in Confirmation Dynamics (2006)
    Details
    Publication Date: 2016-06-09
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 33
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    Kombinatorische Optimierung –Inhalte und Methoden für einen authentischen Mathematikunterricht (2006)
    Details
    Publication Date: 2020-08-05
    Description: wird nachgereicht
    Keywords: ddc:510
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 34
    Electronic Resource
    Electronic Resource
    Impacts of Bioremediation Schemes on Bacterial Population in Naphthalene-Contaminated Marine Sediments (2006)
    Springer
    Biodegradation 17 (2006), S. 227-235 
    Details
    ISSN: 1572-9729
    Keywords: community fingerprint ; polycyclic aromatic hydrocarbon ; 16S rRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Microcosm experiments were conduced in which the surface of marine sediment was contaminated with naphthalene and subjected to either of three different bioremediation schemes, i.e., biostimulation (BS) by supplementing with slow-release nitrogen and phosphorus fertilizers, bioaugmentation (BA) by inoculating with Cycloclasticus sp. E2, an aromatics-degrading bacterium identified to play an important role for aromatic-hydrocarbon degradation in marine environments and combination (CB) of BS and BA. These three schemes were found to be similarly effective for removing naphthalene, while naphthalene disappearance in sediment without any treatment (WT) was slower than those in the treated sediments. Shifts in bacterial populations during and after bioremediation were analyzed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. It was found that the Cycloclasticus rRNA type occurred as the strongest bands in the course of naphthalene degradation. Clustering analysis of DGGE profiles showed that bacterial populations in the WT, BS and CB sediments differed consistently from those in the uncontaminated control, while the profile for the BA sediment was finally included in the cluster for uncontaminated control sediments after a 150-day treatment. The results suggest that bioaugmentation with ecologically competent pollutant-degrading bacteria is an ecologically promising bioremediation scheme.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s10532-005-5018-9
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  • 35
    Electronic Resource
    Electronic Resource
    Cladistic analysis of 5S rRNA and 16S rRNA secondary and primary structure—The evolution of eukaryotes and their relation to archaebacteria (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 152-166 
    Details
    ISSN: 1432-1432
    Keywords: 5S rRNA ; 16S rRNA ; Archaebacteria ; Cladistics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The secondary structure of 5S rRNA has been elucidated by a cladistic analysis resulting in minimal models for eukaryotes, eubacteria, and halophilic-methanogenic archaebacteria, as well as for an ur-5S rRNA. This ancestor of all present-day 5S rRNA molecules is compared with an ur-tRNA and can be fitted into a tRNA-like structure allowing tertiary-structure interactions at the equivalent positions. A phylogenetic analysis of eukaryotic 5SrRNA and 16S rRNA sequences confirms particular monophyletic taxa: rhodophytes (red algae), chlorobionts (green algae and plants), metazoans (multicellular animals), euglenozoans (euglenids and trypanosomatids), a group of zygomycetes (excluding Kickxellales), a group of ascomycetes (excluding Protomycetales), two distinct groups of basidiomycetes, and a group consisting of phaeophyceans (brown algae) and oomycetes (water molds). The Euglenozoa show a distinct relation to the Eumycota (true fungi) and Metazoa. An analysis of archaebacterial sequences substantiates the paraphyletic nature of this third urkingdom defining the eubacteria as a sister group of the halophile-methanogens and defining the eukaryotes as a sister group of a particular lineage of the eocytes/sulfur-dependents. The latter fact implies that even the eocytes/sulfur-dependent archaebacteria are paraphyletic.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099963
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  • 36
    Electronic Resource
    Electronic Resource
    Eupatorium cannabinum L. (1986)
    Springer
    Pharmacy world & science 8 (1986), S. 245-251 
    Details
    ISSN: 1573-739X
    Keywords: Analysis ; Antineoplastic agents ; Biosynthesis ; Botany ; Chemistry ; Cytotoxins ; Eupatorium cannabium ; Sesquiterpenes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A review onEupatorium cannabinum L. is given, including botany, history and constituents. The sesquiterpene lactones are discussed in more detail, covering their biosynthesis, isolation, analysis and biological activity. Special attention is paid to the cytotoxic and antitumour activities of the sesquiterpene lactones.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01960068
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  • 37
    Electronic Resource
    Electronic Resource
    α-Helical oligopeptides with hydrophobic side chains soluble in lipophilic solvents (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1-4 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250102
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  • 38
    Electronic Resource
    Electronic Resource
    Conformations of dinucleoside monophosphates in relation to duplex DNA structures (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 17-30 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Mononucleotide conformations are important in understanding the structural aspects of nucleic acids and polynucleotides. In order to study the influence of stacking interactions between adjacent bases in a polynucleotide on the preferred conformations of mononucleotides, conformational energy calculations have been carried out on dinucleoside monophosphate fragments. Four base sequences - d(ApT), d(TpA), d(CpG), and d(GpC) -  have been analyzed in the framework of helical structures. Flexibility of the furanose ring has been incorporated in the investigations. Energetically favored conformers of the four compounds correspond to a variety of left- and right-handed uniform helical structures, similar to those of the commonly observed polymorphous forms. Implications of these investigations on the further understanding of double-helical polynucleotide conformations are briefly discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250104
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  • 39
    Electronic Resource
    Electronic Resource
    Vibrational circular dichroism of polypeptides, V. A study of 310-helical-octapeptides (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 79-89 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured vibrational CD spectra in the 3600-1250 cm-1 region of two monodisperse, protected octapeptides, which form right-handed 310-helices in CDC13 solution. The spectra are similar in sign pattern to those obtained for right-handed α-helices in solution but are smaller in magnitude and, additionally, provide evidence of some line-shape differences. The delineation of this type of ordered conformation was accomplished by means of 1H-nmr. Such a solution structure is consistent with the x-ray crystal structure of one of these molecules.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250107
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  • 40
    Electronic Resource
    Electronic Resource
    Interaction of calcium ions with gastrin fragments of increasing chain length (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 135-152 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of a series of biologically active gastrin fragments with calcium ions has been investigated by CD in trifluoroethanol. It was found that the gastrin octapeptide pGlu10,Nle15-HG[10-17] binds one calcium ion per molecule. The hypothesis is made that the binding involves the C-terminal, biologically important tetrapeptide. When the chain is elongated to the gastrin nonamer pGlu9,Nle15-HG[9-17], a second binding site is available, which is most likely situated at the N-terminal part of the molecule. Further elongation of the peptide chain up to the dodecapeptide pGlu6,Nle15-HG[6-17] does not provide any additional binding site. Saturation of the two sites in the shorter peptides produces different changes in the chiroptical properties in the near- and far-uv. As the chain is elongated, this difference tends to disappear. This result is consistent with an increased conformational order of the longer peptides. In the shorter fragments, the strength of this second binding is appreciably lower than that of the first, while in the longer peptides, the strength of the two bindings is comparable. On the assumption that the variation of the CD properties is proportional to the extent of binding, the constant for the binding of the second ion was determined to be of the order of 5 × 105 L/mol for the nonapeptide.
    Additional Material: 10 Ill.
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    Masthead (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250201
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  • 42
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    UV-induced reduction of Cu(II) in DNA complex studied by Cu-K-edge XANES (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 217-221 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250202
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  • 43
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    Conformational properties of gastrin peptides: Synthesis, biological activity, and preliminary CD characterization of the (Asp)5 analog of des-Trp1, Leu12-minigastrin (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 229-234 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250204
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  • 44
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    A molecular mechanical study of netropsin-DNA interactions (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 249-266 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present molecular mechanical calculations on the complexes of netropsin with dA6·dT6, d(TATATA)2, d(CGCGCG)2, and d(CGCGAATTCGCG)2. The complexes were model built using computer graphics and then completely energy refined. Our calculations are consistent with the observed AT preference for netropsin and suggest that mixed sugar pucker geometries should be more stable than uniform in netropsin complexes with poly[d(A-T)]·poly[d(A-T)] and poly(dA)·poly(dt). The netropsin·d(TATATA) and netropsin·dA6·dT6 complexes are significantly different in structure, leading to a possible reason why the observed thermodynamics of netropsin-association with poly[d(A-T)]·poly[d(A-T)] and with poly(dA)·poly(dT) are so different. We also model built and energy refined a structure of netropsin-d(CGCGAATTCGCG)2 using as a guide the nmr data of Patel [(1982) Proc. Natl. Acad. Sci. USA, 79, 6424-6428] and found a three-dimensional structure qualitatively consistent with the NOE enhancements observed by him. After our calculations were completed, we learned of an x-ray structure of a netropsin:d(CGCGAATTCGCG)2 complex, and we compared the structure found in our calculation with the x-ray structure.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250207
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  • 45
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    Dependence of oxygen quenching of intercalated methylene blue triplet lifetime on DNA base-pair composition (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 307-316 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We utilize the dynamic quenching of the triplet state of methylene blue by molecular oxygen to observe changes in the rate at which oxygen can penetrate the helix as a function of base-pair composition. The results indicate that the interior of the oligonucleotide dA-dT is more accessible than dG-dC to small molecules such as dioxygen.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250211
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  • 46
    Electronic Resource
    Electronic Resource
    Masthead (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250301
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  • 47
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    Spermine-nucleic acid interactions: A theoretical study (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 375-392 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of spermine with nucleic acids is simulated theoretically using refined semi-empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B-DNA, as well as a transfer RNA, tRNAPhe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base-pair sequence is analyzed.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250302
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  • 48
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    Temperature dependence of dielectric constant at 10 GHz of Na-DNA gels (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 241-247 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Permittivity ε′ and dielectric loss ε″ of aqueous Na-DNA gels have been measured at 10 GHz in the temperature interval -15 to + 45°C. The experimental results are analyzed in terms of a three-component equation (Na-DNA, interfacial water, bulk water) and yield a value of 35 water molecules/nucleotide interacting with DNA. According to theoretical and experimental data the presence of strongly bonded and weakly bonded water is considered. The modified water exhibits a mean dielectric relaxation time two-or threefold greater than that of bulk water.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250206
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  • 49
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    The effect of solvent viscosity and temperature on DNA viscoelastic behavior (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 291-306 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of solvent viscosity (ηs) and temperature (T) on the shape of the concentration dependence of the principal and total recoils in creep-recovery viscoelastometry experiments has been studied for T4 DNA solutions. The range of DNA concentration (c) was 2 - 40 μg/ml; glycerol, 70-80% v/v, sucrose, 60% v/v; NaCl, 5 mM - 1M; and T, 275 - 323 K. A linear proportionality between recoil and c was obtained at high ηs/T. At low ηs/T, the c-dependence was nonlinear, approaching saturation at higher c. At low c, the slope of both curves was the same. Transition between “linear” and “nonlinear” values occurred over a narrow range of ηs/T (a width of 1-5 K if ηs/T was changed by varying T). (ηs/T)tr, the midpoint of the transition, was independent of solvent properties other than viscosity. Also, (ηs/T)tr increased with c. For a given c, ηs/T values above this transitional value yield linear behavior; below this, nonlinear behavior. The ratio of linear to nonlinear recoil values is a linear function of c with Kc, the slope of this dependence, independent of ηs and T. A kinetic model for the observed nonlinearity of recoil with c is presented. It explains the independence of Kc on ηs and T. An attempt has been made to explain the linear-nonlinear transitions by comparison of τ1 and TR, the lifetime of the contact points of the polymer network in the de Gennes theory. The nonlinear values are consistent with a pseudogel that exists when τ1 〈 TR. At τ1 〉 TR, the DNA behavior is similar to that in dilute solutions (linear values). Thus, the condition for transition is τ1 = TR. However, some unsolved problems remain.
    Additional Material: 9 Ill.
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  • 50
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    The growth of large single crystals of lysozyme (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 337-350 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: If protein single crystals larger than those suitable for x-ray analysis are obtained, various spectroscopic, thermal, mechanical, and electrical measurements become possible. To understand the factors governing the crystal size, tetragonal lysozyme crystals were grown in batches at 15°C from solutions of different protein and salt concentrations between pH 4-7. The number and size of the crystals, and the protein concentration remaining in the supernatant, varied markedly with the initial salt amount, pH, and cation species, but large crystals always grew when the initial protein concentration (P) was in a narrow range of 2.5-3 times the crystal solubility (S). It was also shown (1) that the period before the first crystals appeared (D) varied as D ∝ (P/S)-n, where n ≃ 5, and (2) that many previous experiments used more supersaturated solutions than the optimal ones thus determined. The reason why large crystals grow only from moderately supersaturated solutions is discussed. The crystal size of the orthorhombic form grown at 40°C was less sensitive to pH and P than the tetragonal form. An effort to measure D and the solubility at 40°C revealed many differences between the two crystal forms, which we ascribe to different interactions to promote crystallization.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250213
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  • 51
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    Conformational changes of pinellin in solution using intrinsic fluorescence and CD as probes (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 393-405 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pinellin is a plant protein extracted from the rhizome of the Chinese herb Pinellia. It has the ability to abort early pregnancy in mice as well as in rabbits. Studies on the conformational changes of pinellin have been carried out in our laboratory using intrinsic fluorescence and CD. Experimental results show that some tryptophanyl side chains are buried more deeply than others, which results in the heterogeneity of tryptophanyl emission. CD data indicated a high content of β-pleated sheet and β-turn for the backbone conformation. The results of fluorescence and CD measurements both demonstrated the presence of intermediates along the path of denaturation. The following was proposed as the unfolding mechanism of pinellin in 6M guanidine hydrochloride: native state → first intermediate → second intermediate → fully unfolded state.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250303
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  • 52
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    Examination of the secondary structure of proteins by deconvolved FTIR spectra (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 469-487 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm-1 resolution from 1600 to 1700 cm-1 in deuterium oxide solution. Fourier self-deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well-defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm-1. The observed components are assigned to helical segments, extended beta-segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta-structure band can vary within a range of approximately 15 cm-1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss-Newton, iterative curve-fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta-structure for each of 21 globular proteins. The results are in good general agreement with values derived from x-ray data by Levitt and Greer. The RMS deviation between 22 values (alpha- and beta-content of 11 beta-rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250307
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  • 53
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    Fluorescence decay of ethidium bromide in the presence of the Z-conformation of poly-(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 507-518 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A time-resolved fluorescence study of ethidium bromide (EB) in the presence of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride is presented under solvent conditions in which these polymers adopt the Z-conformation (high ionic strength). It is shown that these polynucleotides can intercalate a very small quantity of EB. The binding parameters have been determined. The fluorescence lifetime of EB is slightly higher when bound to the Z-conformation (≃25 ns) than when bound to the B-conformation (≃23.7 ns). The nature of the salt has been checked. In the presence of 2.5M NaClO4, no transition from the Z-conformation to another conformation is observed when EB is added. On the contrary, in the presence of 4.25M NaCl, EB induces a cooperative transition from the Z-conformation to a conformation characterized by a much higher affinity for EB intercalation. In the case of poly(dG-dC) this last conformation is identical to the one observed at low ionic strength (B-conformation), but in the case of the platinated polymer this conformation is slightly different, as judged by the smaller value of the fluorescence lifetime of the intercalated EB.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250309
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  • 54
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    DNA orientation during gel electrophoresis and its relation to electrophoretic mobility (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 539-554 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intensities of polarized fluorescence from ethidium bound to phage λ DNA undergoing agarose gel electrophoresis were measured. The intensities were strongly field dependent at voltage gradients of 8 V/cm, consistent with a partial orientation of DNA helices in the direction of electrophoresis about 500 times larger than seen in the same field in solution. Such an orientation was predicted by a reptation model of gel electrophoresis advanced by Lumpkin et al. [(1985) Biopolymers, 24, 1573-1593]. The present results can be fit successfully to this theory with a single adjustable parameter, the gel-DNA contact distance. Also, λ DNA electrophoretic mobilities in the same concentration gel were determined using the same buffer system. Both orientation and mobility measurements can be fit to the reptation theory within a factor of two using the same values of two parameters, the gel-DNA contact distance and the ratio of DNA charge to frictional coefficient.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250403
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  • 55
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    Effect of NaCl on the association of thrombin with heparin (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 527-537 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The association of heparin with thrombin was investigated by fluorometric titration. A maximum of 25% of the fluorescence of fluorescein-labeled heparin (FTC-heparin) was quenched at thrombin saturation in the absence of NaCl. FTC-heparin (H) associated tightly with thrombin (T) and the association constant of the ternary complex, H2T, formed in the absence of NaCl, was calculated to be 1.7 × 108M-1. However, the association was strongly influenced by the NaCl concentration, and the association constant of the equimolar complex, HT, formed in 0.15M NaCl was found to be 1 × 106M-1. The first-order rate constant, kapp, for inactivation of thrombin by antithrombin III (AT III) and low-affinity heparin (LA-heparin) was comparable with that of high-affinity heparin (HA-heparin) in the absence of NaCl, but decreased with an increase in the concentration of NaCl. The decreased enhancement of the thrombin-AT III reaction by LA-heparin at high NaCl concentration appeared to result from a decreased association of thrombin with LA-heparin, thus reducing the formation of the ternary complex, thrombin-LA-heparin-AT III.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250402
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  • 56
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    Structural studies of poly(α-aminoisobutyric acid) (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 607-625 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electron-diffraction pattern of an oriented film of poly(α-aminoisobutyric acid) in the 310-helical conformation has been analyzed. The conformation was obtained by a linked-atom least-squares refinement of average values from crystal structures. Specimens treated with dichloracetic acid, to improve their crystallinity, conform to space group R3c with a = 21.8 Å, c = 5.95 Å. The structure contains channels that can accommodate molecules of dichloracetic acid. One molecule of acid per six residues fills the channels, and the R-factor then is 34% using 23 reflections. Ir evidence is presented to show that the acid may hydrogen bond to the peptide groups. Some reflections occasionally observed on the diffraction photographs are attributed to a 15/4 α-helix. The significance of the results is considered in relation to Aib-containing peptides.
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    URL: http://dx.doi.org/10.1002/bip.360250407
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  • 57
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    The relationship of bound water to the IR amide I bandwidth of albumin (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 639-654 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four different types of ir experiments, involving changes in pH, changes in pressure, and the use of nonaqueous solvents, and with either albumin molecules dissolved in saline or adsorbed albumin films, support the hypothesis that the bandwidth of the amide I vibration of albumin is directly related to the amount of bound water in this protein. From the amide I band narrowing and the amide I shift to higher frequencies, it is proposed that a more ordered helix structure results as the amount of bound water is decreased.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250409
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  • 58
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    Sequence-dependent recognition of DNA duplexes: Netropsin complexation to the TATA site of the d(G-G-T-A-T-A-C-C) duplex in aqueous solution (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 707-727 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have recorded one-dimensional exchangeable proton and two-dimensional nonexchangeable proton nmr spectra on the complex of netropsin with the self-complementary d(G-G-T-A-T-A-C-C) duplex in aqueous solution between 25° and 35°C. The antibiotic amide, pyrrole, and methylene protons, and the nucleic acid base and sugar H1′, H2′, H2″, and H3′ protons, have been assigned from an analysis of the two-dimensional nuclear Overhauser effect (NOESY) spectra of the complex. We observe intermolecular NOEs between the antibiotic concave face amide, pyrrole, and CH2 resonances, and the adenosine H2 and sugar H1′ protons of base-pairs T3·A6 and A4·T5 in the central TATA core of the d(G1-G2-T3-A4-T5-A6-C7-C8) duplex. We present a molecular model outlining these seven antibiotic-DNA contacts for the complex in solution. The observed line-broadening of several base and sugar protons at the TATA minor groove netropsin binding site in the complex at 35°C are interpreted in terms of intermediate exchange between two orientations of bound netropsin on the duplex.
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    URL: http://dx.doi.org/10.1002/bip.360250413
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  • 59
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    Influence of different tripeptides on the stability of the collagen triple helix. I. Analysis of the collagen sequence and identification of typical tripeptides (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1069-1080 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The amino acid sequence of the collagen α1(I) chain (calf) is analyzed. Deviations of random tripeptide distribution leads to the definition of clusters. Inside these regions, collagen-typical tripeptides are located. Besides Gly-Pro-Hyp, Gly-Pro-Ala, and Gly-Ala-Hyp, the polar sequences Gly-Glu-Hyp, Gly-Ala-Arg, Gly-Glu-Arg, and Gly-Pro-Lys form typical sequences. The neighborhood of each tripeptide is analyzed and classified. The proximity to the collagen-typical tripeptides is registered. Cluster theory: Less-typical sequences also fold as members of the collagen triple helix and they are as reasonable as well as important for the collagen structure as the cluster tripeptides, but only the latter are important for the nucleation of the triple-helical folding.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250607
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  • 60
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    Peptide-bond distortions and the curvature of α-helices (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1087-1093 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvent accessible peptide bonds in proteins exhibit a 1-3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes are consistent with an increase in hydrogen bonding to the carbonyl oxygen accompanying solvent exposure (J. D. Dunitz and F. K. Winkler, (1975) Acta Cryst. B31, 251-263). For amphiphilic structures such as α-helices, systematic differences in peptide-bond geometry between solvent-exposed and buried residues will generate significant curvature. A decrease of 4° in the OCN bond angle between hydrophilic and hydrophobic sides of an amphiphilic helix will lead to smooth bending, with a radius of curvature of about 70 Å. This curvature is in the range observed for α-helices in proteins. Helix curvature is estimated to have only a small effect on the magnitude and direction of the helical dipole moment.
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    URL: http://dx.doi.org/10.1002/bip.360250609
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  • 61
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    SANS studies of concentrated protein solutions. I. Bovine serum albumin (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1157-1175 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small-angle neutron scattering (SANS) was used to examine concentrated bovine serum albumin solutions of up to 20% protein w/v. At higher protein concentrations, scattering data show distinct features that can be ascribed to strong intermolecular interactions. Differential scattering cross-sections are fitted to a theoretical model of interparticle potential consisting of a hard core plus an exponentially decaying “tail.” For moderate ionic strength (0.03M K Acetate, pH 5.9), the intermolecular interaction agrees with the double-layer repulsive part of the well-known DLVO (Derjaguin, Landau, Verwey, Overbeek) theory for interacting colloidal particles. We thus demonstrate that it is possible to determine size parameters and the surface charge of protein molecules in dense solutions. At high salt concentrations (≥0.2M NaCl) data can be fitted by the same potential model, although interpretation in terms of DLVO theory is not possible. Even in this case, however, “effective” molecular size and potential parameters can be determined.
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    Diffusion of DNA in a gel under an intermittent electric field (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1179-1184 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250702
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    Shape complementarity at the hemoglobin α1β1 subunit interface (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1229-1247 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A computational method for attempting to predict protein complexes from the coordinates of the individual proteins has been developed. It is based on matching complementary patterns of knobs and holes. The computer algorithm correctly and uniquely predicts the association of the alpha and beta subunits to form the αβ dimer corresponding to the α1β1 interface in the hemoglobin tetramer. It fails to correctly dock trypsin inhibitor onto trypsin. Nevertheless, this lone success is still a significant advance over previous protein-docking algorithms. The method is also important because it introduces several ways to measure the shape of protein surface regions.
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    Enantioselective interactions of inversion-labile trigonal iron(II) complexes upon binding to DNA (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1209-1228 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the interactions of the substitution-inert inversion-labile complexes Fe(bipy)32+ and Fe(phen)32+ [and the inversion-stable complex Ru(bipy)32+] with DNA. The association of these complexes to DNA is mainly electrostatic, and Fe(phen)32+ shows a more effective binding to DNA than the two bipyridyl complexes, possibly owing to a different binding mode. The interactions are enantioselective, leading to a Pfeiffer shift in the diastereomeric inversion equilibria and an excess of the Δ-enantiomer of Fe(phen)32+ and Fe(bipy)32+, which is directly monitorable through CD. The partition constants for the inversion equilibrium range from 1.3 to 2.0 for Fe(bipy)32+ and Fe(phen)32+, depending on ionic conditions. From flow LD information about the orientation of the complexes on DNA was obtained: it is consistent with a fit of the Δ-enantiomer in the major groove of the right-handed DNA helix. The mechanisms of interaction are discussed against equilibrium, spectroscopic, and kinetic data.
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    Distribution of Mn2+ ions around poly(rI)·poly(rC) (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1283-1297 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of bound Mn2+ ions about poly(rI)·poly(rC) has been studied by measuring the effect of this paramagnetic metal ion on the relaxation behavior of poly(rI)·poly(rC) protons. By combining selective spin - lattice and spin - spin relaxation rates for various protons, some of the principle regions of ion association can be identified. The relaxation data on the CH6 proton are consistent with a 〈 10% occupancy of phosphate inner-sphere binding sites. The broadening of the imino proton resonance requires a substantial occupancy of sites located in the major groove, possibly near IN7. This would also be consistent with the observation that IH8 resonance is the proton most susceptible to relaxation by Mn2+. The relaxation data for the IH2 proton indicate a relatively low occupancy of minor-groove binding sites (e.g., IN3).
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    URL: http://dx.doi.org/10.1002/bip.360250709
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    Adsorption of thionine on heparin studied by combining ultrafiltration and difference VIS spectroscopyThis paper is dedicated to Prof. Georg Manecke on the occasion of his 70th birthday. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1273-1281 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The combination of ultrafiltration and difference spectroscopy allows the quantitative determination of spectra of thionine bound to heparin. The spectra of the bound dye do not depend on the degree of coverage; this and the shape of the Scatchard plot show that “all-or-none” binding is valid. A calculus of variations based on a modification of the Hill plot shows that aggregates of seven thionine cations are bound. Tetrasaccharides with an average charge of two carboxylate and five sulfate groups are suggested to be the binding sites. The binding constant given for one mole thionine is 4.4 · 105 M-1. The Gibbs enthalpy for binding of one mole of thionine is -31.7 kJ·M-1 at 20°C.
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    URL: http://dx.doi.org/10.1002/bip.360250708
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    Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1345-1357 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first-order binding with two different rate constants, k1* (= k1 + k-1) and k2* (= k2 + k-2). The larger rate constant (k1*) was at least four orders of magnitude smaller than the comparable first-order forward rate constant for binding to DNA released from its capsid. At 25°C values of k1* decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA-containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of kM1* are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k1* s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.
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    Masthead (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360250801
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    Molecular structure of the cis-syn photodimer of d(TpT) (cyanoethyl ester) (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1399-1417 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by -29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer-Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); φ: 141° (86°). These represent half-chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche- conformation at C4′-C5′; the [p]T segment is anti, 3T4, trans. The C5′-O5′ torsion of the [p]T unit is -124.5°, and the C3′-O3′ torsion of the T[p] unit is -152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are -138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250804
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    Conformation of mucous glycoproteins in aqueous solvents (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1505-1517 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering techniques have been used to measure the z-average radius of gyration Rg z-average translational diffusion coefficient Dt and weight-average molecular weight Mw of porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has a Mw about twice as large as a sample prepared without these precautions. The former sample has a Mw of 17 × 106 in 0.1M NaCl, which decreases to 8 × 106 in 6M guanidine hydrochloride (GdnHCl) and then to 2 × 106 on addition of 0.1M mercaptoethanol to the 6M GdnHCl solution. The Rg or D-1t values obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log-log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligosaccharide chains.
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    Conformation and aggregation of melittin: Effect of pH and concentration of sodium dodecyl sulfate (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1493-1504 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of melittin, a surface-active polypeptide, in solution was studied by CD spectra between 190 and 240 nm. The molecule was essentially unordered (possibly with a trace of helix) in water without salt at neutral pH. Upon deprotonation of four of the six cationic groups at pH 12 the polypeptide became partially helical (about 35%). The addition of NaDodSO4 to an aqueous melittin solution first caused the solution to become turbid but it became clear again in excess surfactant solution. The conformational changes depended on the molar NaDodSO4/melittin ratio, R. With R from 2.34 to 23.4, the melittin solution was turbid and the polypeptide conformation was probably a mixture of α-helix and β-sheets. This was supported by the ir spectrum of the turbid solution, which indicated the presence of both conformations. With R = 46.8 or 468 (1 or 10 mM NaDodSO4) the polypeptide conformation was characteristic of an α-helix, about 70-80% of the molecule, regardless of whether the surfactant was above or below its critical micelle concentration. This compared well with the x-ray results of 92% helix in crystals. The lower helicity of melittin in NaDodSO4 solution might be attributed to the end effects that destabilize the first and last turn of an helix at its N- and C-terminus, respectively.
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    URL: http://dx.doi.org/10.1002/bip.360250808
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    Evolutionary similarity among peptide segments is a basis for prediction of protein folding (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1565-1577 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Short segments of polypeptide, from a protein for which the primary sequence but not the three-dimensional structure is known, are compared to a library of known structures. The basis of comparison is the probability with which residues in the unknown segment might substitute through evolution for residues in segments of known structure. In test cases, segments from known structures that are similar in sequence to those from a protein treated as unknown are often found to be similar in three-dimensional structure to one another and to the true structure of the “unknown” segment. This provides a basis for prediction of the local configuration (secondary structure) of polypeptides.
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    URL: http://dx.doi.org/10.1002/bip.360250813
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    Can the double helix be parallel? (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1603-1606 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250903
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    The crystal structure of the photosynthetic inhibitors DCMU and DTPU (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1615-1621 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: X-ray diffraction studies have been carried out on a single crystal of the photosynthetic inhibitors N-(3,4-dichlorophenyl)-N′-dimethylurea (DCMU) and its newly synthesized spin-labeled analog N-(3,4-dichlorophenyl)-N′-(3,3,5,5-tetramethylpiperidine-4-oxyl)-urea (DTPU). The synthesis of DTPU as well as its crystallographic data are reported. The crystal system of both compounds is monoclinic with a space group P21/c. The cell constants of DCMU are a = 7.759(1), b = 14.737(3), c = 9.233(2) Å, β = 100.99(6)°; of DTPU they are a = 6.976(1), b = 11.998(2), c = 23.585(3) Å, β = 91.38(5)°. Comparison of conformational parameters of DCMU and DTPU reveal differences in the dihedral angle between the aromatic ring and the ureido plane. The measured volumes of DCMU and DTPU are 259.1 and 493.3 Å3, respectively. These figures suggest the size of the binding site of the inhibitors in the photosynthetic membrane.
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    Stereochemistry of peptides containing 1-aminocyclopentanecarboxylic acid (Acc5): Solution and solid-state conformations of Boc-Acc5-Acc5-NHMe (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1635-1644 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a β-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III β-turn conformation in the solid state stabilized by a 4 → 1 hydrogen bond between the Boc CO and methylamide NH groups. The φ,ψ values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (φ≃ ± 60°, ψ∼ ±30°).
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    URL: http://dx.doi.org/10.1002/bip.360250907
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    Rate constants and activation parameters for the mobility of bulk and DNA-associated glycol-water solvents (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1685-1695 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The decrease in mobility of viscous glycol-water solvents when associated with native DNA is quantified from a study of the loss of the exciting-wavelength dependence of the phosphorescence spectrum of free and bound proflavin with increasing temperature. The data are interpreted in terms of a distribution of rate constants with an Arrhenius temperature dependence. Over the temperature range of the experiments a relative decrease of ∼ 104 in the average rate constant is observed for reorientation of the solvent when associated with DNA. The basis for this large reduction is found to derive from a large decrease in the pre-exponential factors (i.e., activation entropy) associated with the reorientation rate constants. The changes in the distribution of rate constants and the activation parameters for solvent mobility induced by DNA do not resemble the changes observed for any one of a number of small ion or molecule perturbations. The results suggest the presence of disorganized, relatively immobile solvent in association with DNA.
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    Calculations on the effect of methylation on the electrostatic stability of the B- and Z-conformers of DNA (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1697-1715 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double-helical DNA has been solved for solutions of .01M, .10M, and .20M monovalent salt. The polymers, poly[d(CpGp)] and poly[d(m5CpGp)], were studied in the B- and the Z-conformations. The effect of methylation on the relative stabilities of these conformers in solutions of different ionic strengths is known to favor the Z-form. Accumulation of charge density around the B- and the Z-conformers is compared in detail. The relative electrostatic stabilities of the B- and Z-conformers in .01M, .10M, and .20M solutions are compared and discussed in terms of the ion-DNA interactions and the self-energy of the structured ionic environment. The ion-DNA interaction energies, termed “phosphate screening,” monotonically decrease with ionic strength and are consistent with a B-to-Z conformation change induced in either polymer by increased electrolyte concentration. However, these calculated energies alone do not account for the fact that the ionic strength at the midpoint of the transition of the methylated polymer is substantially lower than that of its unmethylated analogues. The phosphate screening effect is counterbalanced by changes in the self-energy required for the creation of the structured counterion environment. This self-energy of the electrolyte environment monotonically increases with ionic strength. Methylation-induced shifts in the overall conformational equilibria depend on the relative changes of these competing effects. Increasing salt concentration is calcualted to favor the Z-conformer. The effect of methylation, lowering the ionic strength of the transition midpoint, is proposed to originate in minor structural changes in the Z-form of the polymer, making the groove more accessible to counterions in the G(3′ - 5′)C region. This allows a redistribution of counterion density and a lowering of the self-energy of the ionic environment, conferring added stability to the Z-conformation, as indicated by calculations of relative entropies. The experimentally observed temperature dependence of the B-to-Z transition, however, cannot be explained without assuming the release of bound water. Maps of the calculated three-dimensional structure at the counterion distribution near the surface of these molecules in both the B- and the Z-forms are also presented.
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    Vibrational circular dichroism spectra of three conformationally distinct states and an unordered state of poly(L-lysine) in deuterated aqueous solution (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1751-1765 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L-lysine) in D2O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right-handed α-helix, the antiparallel β-sheet, an extended helix conformation previously referred to as the so-called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β-sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.
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    URL: http://dx.doi.org/10.1002/bip.360250915
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    The hinge-bending mode of a lysozyme-inhibitor complexSupported in part by a grant from the National Institutes of Health. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1767-1802 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hinge-bending mode of hen egg white lysozyme is studied by a constrained minimization technique. Results with and without a bound inhibitor, tri-N-acetyl-glucosamine, are obtained. The frequency of the mode with the inhibitor is found to be 4.3 cm-1, in contrast to 3.0 cm-1 for the free enzyme. Also, the hinge-bending angle with the lowest energy is shifted 10° towards a more closed cleft in the bound species. The main contribution to these differences arise from interactions with the residues lining the cleft and those on the back side of it. Structural details that account for the energetics are presented. The method of calculation is somewhat different from a previous study [J. A. McCammon, B. R. Gelin, M. Karplus & P. G. Wolynes, (1976) Nature 262, 325-326] to reduce the likelihood of artifacts in the results.
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    Pf1 virus particle dynamics (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1859-1864 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The overall dynamics of the Pf1 filamentous bacteriophage particle in solution are characterized by nmr experiments. The chemical-shift anisotropy powder-pattern lineshapes from both DNA and protein backbone sites of the virus are motionally averaged in the same way, indicating that the entire particle undergoes rapid (〈 104 Hz) reorientation about the long axis of the filament when the virus is in solution at high pH. In contrast, the virus particles in samples at low pH are immobile on this time scale.
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    Structure and internal mobility of proteins: A molecular dynamics study of hen egg white lysozymeSupported in part by a grant from the National Institutes of Health. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1909-1937 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high-resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root-mean-square deviations for backbone atoms of 2.3 Å and 1.1-1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root-mean-square deviations of 0.73-0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β-sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side-chain atoms have larger fluctuations than main-chain atoms. Moreover, the regions that have large deviations among the x-ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.
    Additional Material: 10 Ill.
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    The interaction of Ca2+-binding proteins with the carbocyanine dye stains-allThis study was supported by NIH Grant AM 30322-04. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1579-1595 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the carbocyanine dye Stains-all with the Ca2+-binding proteins calmodulin, troponin C, and parvalbumin has been monitored by means of absorption spectra and CD. In the absence of Ca2+, complexes with Stains-all of all three proteins exhibit at high dye: protein mole ratios an intense J absorption band at 600-650 nm, which is associated with a characteristic CD spectrum. In the cases of calmodulin and troponin C, the J-band is progressively lost as the dye: protein ratio decreases and is replaced by bands of the γ and β types at 450-550 nm, which likewise give rise to characteristic CD spectra. For parvalbumin, only the J-band is observed; its intensity is undiminished at the lowest dye: protein ratios examined. In the presence of excess Ca2+ the J-band is lost for all three proteins. For calmodulin and troponin C it is replaced by σ- and β-bands; in the case of parvalbumin the bound dye is released. A tentative model has been proposed to account for these observations.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250814
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  • 83
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    Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. II. average backbone structure of enkephalin (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1547-1563 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The average conformation of Met-enkephalin was determined by using an adaptive, importance-sampling Monte Carlo algorithm (SMAPPS - Statistical Mechanical Algorithm for Predicting Protein Structure). In the calculation, only the backbone dihedral angles (φ and ψ) were allowed to vary; i.e., all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to a low-energy structure of the pentapeptide. The total conformational energy for each randomly generated structure of the polypeptide was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP/2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The calculation was repeated until a total of 10 independent average conformations were established. The regions of conformational space occupied by the average structures were compared with the regions of low conditional free energy obtained by SMAPPS in the first paper of this series. Such a comparison provides an analysis of the capacity of SMAPPS to adjust the Monte Carlo search to regions of highest probability. The results demonstrate that the ability of SMAPPS to focus the Monte Carlo search is excellent. Finally, the 10 independent average conformations and the mean of the 10 average structures were utilized as the initial conformations for a direct energy minimization of the pentapeptide. Of the 11 final energy-minimized structures, three of the conformations were found to be equivalent to the conformation of lowest energy determined previously. In addition, all but two of the remaining energy-minimized structures were found to correspond to one of the two other conformations of high probability obtained in the first paper of this series. These results indicate that a set of independent average conformations can provide a rational, unbiased choice for the initial conformation, to be used in a direct energy minimization of a polypeptide. The final energy-minimized structures consequently constitute a set of low-energy conformations, which include the global energy minimum.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250812
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  • 84
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    Estimation of the stability of globular proteins (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1623-1633 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interpretation of ΔGDH2O (the free energy change for the reaction, globular conformation ⇋ randomly coiled conformation, in the absence of denaturant), in terms of the free energies of transfer of various parts of the protein molecule from water to denaturant solution, is unsatisfactory because the latter are assumed to be identical to the transfer-free energies of similar groups attached to smaller model compounds. We have made empirical adjustments to transfer-free energy theory that make possible linear extrapolation of the free energy of denaturation of a protein from transition region to zero denaturant concentration. The modified theory, used to analyze the denaturation of proteins by guanidine hydrochloride and urea, allowed us to calculate reasonable values for Δα, the average change in accessibility to solvent of the component groups of protein.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250906
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  • 85
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    Prediction of protein structural class from the amino acid sequenceNRCC No. 25459. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1659-1672 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The multidimensional statistical technique of discriminant analysis is used to allocate amino acid sequences to one of four secondary structural classes: high α content, high β content, mixed α and β, low content of ordered structure. Discrimination is based on four attributes: estimates of percentages of α and β structures, and regular variations in the hydrophobic values of residues along the sequence, occurring with periods of 2 and 3.6 residues. The reliability of the method, estimated by classifying 138 sequences from the Brookhaven Protein Data Bank, is 80%, with no misallocations between α-rich and β-rich classes. The reliability can be increased to 84% by making no allocation for proteins classified with odds close to 1. Classification using previously developed secondary structural prediction methods is considerably less reliable, the best result being 64% obtained using predictions based on the Delphi method.
    Additional Material: 6 Tab.
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    URL: http://dx.doi.org/10.1002/bip.360250909
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  • 86
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    The distribution of charged groups in proteins (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1717-1733 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distributions of charged groups in 32 proteins of known three-dimensional structure have been analyzed to determine how regularly the groups are spread over the molecule's surfaces, and to identify and to study those proteins where charge asymmetry would seem important for their function. The distributions have been analyzed in terms of charge “polarity,” surface “charge density,” and electric dipole moments. More detailed studies of the distributions for individual proteins are made using map projections specifically developed for this purpose. In the light of the results obtained we discuss the role of charged groups in relation to protein function.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250913
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  • 87
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    Masthead (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360251001
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  • 88
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    Phosphorus nmr spectra of natural DNA fragments in the course of the B-to-A conformational transition (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1803-1812 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Changes in the 31P-nmr spectra of sonicated natural DNA fragments were investigated in ethanol solutions where the fragments underwent, as checked by CD, the B-to-A conformational transition. The study produced the following conclusions: (1) The high DNA concentrations used for the 31P-nmr measurements promote the transition compared to dilute solutions that are commonly used for CD measurements. (2) The B-to-A transition was reflected in a cooperative downfield shift of the DNA 31P-nmr resonance, consistent with unwinding of the double helix. (3) Prior to the transition, the changes in chemical shift of double-and single-stranded DNAs were almost identical. It thus appears that the effect of ethanol on the geometry and hydration of phosphodiester linkages does not depend heavily on DNA base-base interactions. (4) The A-form resonances were 30-40% narrower than the B-form resonances, which is attributed to marked sequence-dependent variations in the latter conformation and to their reduction in the former. (5) The B-form DNA aggregated in the concentrated 31P-nmr samples in the presence of ethanol, judged from a milky opalescence of the solution and a substantial broadening of its 31P-nmr resonance. The broadening abruptly disappeared as soon as DNA adopted the A-form so that DNA, in dependence on the secondary structure, showed different tendencies to condense in the presence of ethanol. The condensation increased cooperativity of the B-to-A interconversion.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250917
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  • 89
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    Computer simulation of the folding-unfolding transition of island-model proteins - folding pathway, transition process, and fluctuations (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1815-1835 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monte Carlo computer simulations were performed to elucidate the dynamic aspects of the folding and unfolding transitions of island-model protein. Five different types of model proteins were designed, according to characteristics of backbone structure. The computer simulations clearly show that the unfolding and folding transitions are all-or-none processes between the N-and U-states. They are typical Poisson processes. From the Arrhenius plots of rate constants, the activation enthalpies of folding and unfolding were determined. In addition, the folding pathways were determined along the reaction coordinate. Formations of several local structures along a polypeptide chain are almost simultaneous, but the most probable time sequence of events exists at the moment of transition. That is the most probable folding pathway. The unfolding pathway was found to be just the reverse process of the most probable folding pathway. The relationship between the fluctuations in each equilibrium state and the transition process was considered. In contrast to the theory of absolute reaction rate, the transient states are widely distributed along the reaction coordinate. From analysis of the “transient process,” we tried to determine the critical states from which the transient process starts. As a result, we found that the unfolding transition occurs at the stage near the N-state. During the U-state, large joined blocks rarely appear, but they appear in the transient process towards the N-state. However, the “branch point” between the N- and U-states lies near the N-state, and joined blocks tend to unfold prior to passing over the branch point. We concluded that the stability of later folding intermediates is important for selection of the folding pathway, while preferential selection of an early folding intermediate is important in acceleration of the folding rate. The effects of intrachain cross-linking and peptide fragment binding on the rate constants were examined by using computer simulations of model proteins. In general, a small-sized loop formed by cross-linking accelerates the folding rate and a large-sized loop contributes much to the stabilization of the native conformation. We also found that peptide fragment binding contributes little to the acceleration of the folding rate of the residual protein.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360251002
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  • 90
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    Multiple denaturational transitions in fibrillar collagen (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1875-1893 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The heat denaturation of pepsinized bovine nonfibrillar and fibrillar collagen was studied by differential scanning calorimetry. For fibrillar preparations that had been rapidly precipitated with stirring at low ionic strength, then resuspended at physiological ionic strength, multiple denaturational transitions were observed. At heating rates of 10°C/min, melting endotherms occurred at about 44, 50, 53, and 57°C. Fibrillar collagen that was slowly gelled without stirring at physiological ionic strength exhibited a similar series of endotherms, but the lower melting transitions were less conspicuous. In contrast, nonfibrillar bovine collagen in acidic solution showed only a single denaturational transition at 40°C. Nonfibrillar solutions at pH 7, to which inhibitors of fibrillogenesis were added, showed a major endotherm as high as 46°C. These results suggest that reconstituted fibrillar collagen contains a heterogeneous fibril population, possibly including molecules in a nonfibrillar state. It was proposed that the multiple melting endotherms of such preparations were due to sequential melting of molecular and fibril classes, each with a distinct melting temperature. The fibrillar classes may represent three or more types of banded and nonbanded species that differ from each other in packing order, collagen concentration, and possibly also in fibril width and level of cross-linking.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360251006
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  • 91
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    Gramicidin S analogs with a D-Ala, Gly, or L-Ala residue in place of the D-Phe residue: Molecular conformations and interactions with phospholipid membrane (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 2295-2307 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The proton nmr and CD spectra of gramicidin S (GS) cyclic-(Val1,1′-Orn2,2′-Leu3,3′-D-Phe4,4′-Pro5,5′)2 and of GS analogs - namely, [D-Ala4,4′]-GS, [Gly4,4′]-GS, and [L-Ala4,4′]-GS - were analyzed. The molecular conformation of [D-Ala4,4′]-GS is similar to that of GS, with the trans form about the D-Ala-Pro peptide bond. The molecular conformation of [Gly4,4′]-GS depends on the solvent composition of dimethylsulfoxide-d6/trifluoroethanol (DMSO)-d6/TFE and DMSO-d6/H2O as well as the solute concentration. In DMSO-d6 solution, [Gly4,4′]-GS forms the GS-type conformation of the monomer at lower concentration. At higher concentration, the GS-type conformer is converted to the other one that forms molecular aggregates. The cis form about the X-Pro peptide bonds is found for [Gly4,4′]-GS and [L-Ala4,4′]-GS in DMSO-d6 and for [L-Ala4,4′]-GS in TFE solution. The large temperature dependences of α-proton chemical shifts of [L-Ala4,4′]-GS in DMSO-d6 solution indicate that the conformer equilibrium changes with temperature. The GS-type conformation is not formed in [L-Ala4,4′]-GS. The two active peptide analogs, [D-Ala4,4′]-GS and [Gly4,4′]-GS, interact with the phospholipid membrane, taking the GS-type conformation. By contrast, an inactive analog, [L-Ala4,4′]-GS, does not interact with phospholipid membrane. The activities of GS analogs are found to correlate to the formation of the GS-type conformation upon binding with phospholipid membrane.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360251207
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  • 92
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    Lateral packing of protofibrils in fibrin fibers and fibrinogen polymers (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 2359-2373 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distinctive transverse banding pattern of fibrin fibers clearly indicates ordering of molecules in the longitudinal direction. In this study we examined the fibers of fibrin clots, as well as two types of fibrinogen polymers, by thin-section electron microscopy. The fibrinogen polymers have a transverse banding pattern identical to that of fibrin fibers - clearly indicating a regular longitudinal repeat - but they are larger in diameter, and show little or no branching. We therefore expected their overall ordering to be better than that of fibrin fibers. Several different fixation protocols were used. We readily observed the typical transverse banding seen previously by negative stain and metal replication techniques. However, only very rarely was any regular lateral lattice seen in any of the samples. X-ray diffraction was used to examine unfixed specimens of the two fibrinogen polymers and, once again, although a longitudinal repeat was evident, only rarely was evidence for lateral crystallinity seen. The electron-microscope and x-ray results showed that the needles and pellet fibers of fibrinogen have essentially the same internal architecture as thick fibrin fibers, and that all three types of polymer, although clearly transversely banded, have almost no crystallinity in their lateral protofibril packing.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360251213
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  • 93
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    Binding of porcine pancreatic secretory trypsin inhibitor to bovine β-trypsin: A kinetic study (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 2325-2333 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of the formation of the complex between bovine β-trypsin and the porcine pancreatic secretory trypsin inhibitor (PSTI; Kazal-type inhibitor) was investigated following the spectral changes associated with the displacement of proflavine from the enzyme, upon inhibitor binding, between pH 3.5 and 8.0 (I = 0.1M) at 21 ± 0.5°C. With inhibitor in excess over the enzyme ([PSTI] ≥ 5 × [bovine β-trypsin]), the time course of the reaction corresponds to a pseudo-first-order process. Over the whole pH range explored, the concentration dependence of the rate is second order at low PSTI concentrations but tends to first order at high inhibitor concentrations. This behavior may be explained by a relatively fast pre-equilibrium followed by a limiting first-order process. Values of kinetic parameters for PSTI binding to bovine β-trypsin depend, between pH 3.5 and 8.0, on the acid-base equilibrium of a single ionizing group (probably His-57 of bovine β-trypsin) that undergoes an acidic pKa shift from 7.0 in the free bovine β-trypsin to 5.5 in the enzyme:PSTI complex. Kinetics of the bovine β-trypsin:PSTI adduct formation has been analyzed and compared with that of other (pro)enzyme:inhibitor reactions. Considering the known molecular structures of free serine (pro)enzymes, of Kazal- and Kunitz-type inhibitors, as well as of their complexes, the binding behavior of PSTI to bovine β-trypsin has been related to the inferred stereochemistry of the proteinase:inhibitor contact region.
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    URL: http://dx.doi.org/10.1002/bip.360251210
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  • 94
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    Metallisch leitfähige Polymere ITeil II dieses Beitrags wird in Heft 2/86 erscheinen. (1986)
    Weinheim : Wiley-Blackwell
    Chemie in unserer Zeit 20 (1986), S. 1-10 
    Details
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/ciuz.19860200102
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  • 95
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    Masthead (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250101
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  • 96
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    The relation of ion pairs to protein hydration: An IR spectroscopic and X-ray crystallographic survey (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 317-335 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report here a novel ir technique that we use to determine the apparent van't Hoff's energy for the distillation of water from protein amide and acid groups. The method is used to study the hydration properties of ten different proteins. The results show that water removal from the environment of ion-paired acid groups (those ≤ 4 Å from a basic group on the protein surface) requires less energy than water removal from the environment of nonpaired acid groups. These observations are supported by an analysis of the solvent distributions in protein crystal structures. A model is proposed for the interaction between water and protein acid groups, and this model is used to account for the distributions and properties of certain eye-lens proteins.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250212
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  • 97
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    A polynucleotide CD probe: Interactions with oligomers of a polycationic amine that exhibit positive extrinsic bands at 〉 300 nm (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 407-429 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A set of large positive extrinsic CD bands ([θ]333 = 2.6 X 104 deg-cm2/decimole phosphate) in the 〉 300 nm region as well as diminution of the intrinsic signals (θ275) have been observed in the CD spectra of various nucleic acids complexed with the achiral compound, N-poly{α-[N-(4-pyridylethylene-4-pyridyl-N′-)α′-p-xylyl]dibromide}-4-pyridylethylene-4-pyridinium bromide, (polymer X).1,2,5 The signal changes are attributed to the binding of polymer X chromophores isogeometrically to the DNA helix in an ordered chiral arrangement. Fractionation of polymer X gives 10 well-separated oligomers. The oligomers were characterized by nmr. Their interactions with DNA have been investigated with respect to r(r = ratio of equivalents of polymer X charge/g-atoms DNA phosphorus) and n (oligomer chain length). In all cases where n ≥ 1, [θ]333 increases linearly with increasing r between 0 and 0.32, and is accompanied by a corresponding decrease in [θ]275, which becomes negative as r approaches .32. Extrinsic band intensities reveal a dependence on n up to n = 5, above which increases in nonspecific binding result in a reduction in normalized band intensities. Polymer X shows a strong preference for B-form nucleic acids and induces maximum extrinsic CD signal intensities with A-T homopolymers. Alterations in helix hydration are believed to accompany complex formation. Inversions in [θ]275 of the octamer X-poly(dA-dT) complex have been attributed to the “alternating B” conformation of poly(dA-dT).3 Similar inversions are not observed in other nucleic acid-octamer X complexes. Visible and CD spectrometry data from competition studies in the presence of the antibiotics actinomycin D (AMD), daunomycin (DM), and distamycin A (DST) are consistent with “nonclassical” intercalation as the mode of binding, and these data place the potential binding site in or near the hydrophobic region of the minor groove. Reductions in [θ]333 with increasing urea further implicate the involvement of hydrophobic interactions in the formation of an asymmetric complex. Stabilization of the helix results in all cases as evidenced by alterations in Tm; corresponding changes, however, in cooperativity are not clearly discernable. Viscosity and light-scattering data indicate no changes in molecular weight due to aggregation, and as such are not consistent with a transition to the ψ-DNA upon complex formation.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250304
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  • 98
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    Vacuum UV CD of the low-salt Z-forms of poly(rG-dC)·poly(rG-dC), and poly(dG-m5dC)·poly(dG-m5dC) (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 519-523 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The vacuum CD spectra of poly(rG-dC)·poly(rG-dC) and poly(dG-m5dC)·poly(dG-m5dC) have been obtained for the low-salt Z-conformations of both polymers. The spectra are very similar to those for the high-salt Z-forms. This behavior is consistent with the suggestion that the low- and high-salt Z-forms are comprised of different proportions of ZI- and ZII-conformations.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360250310
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  • 99
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    Chain association of pectic molecules during calcium-induced gelationPart of this work has been presented at the 7th European Polymer Network Group Meeting, September 10-14, 1984, Manchester, England. (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 455-468 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The chain association of pectic molecules with different levels and patterns of esterification during calcium-induced gelation was studied by methods such as light scattering, viscometry, and determination of calcium activity coefficient and of calcium transport parameter. A gel point can be determined, assuming a power law including a critical ratio (equivalent concentration of calcium ions/pectin carboxylic groups) and quasi-critical exponents varying in the range 0.50-1.26. The values of these critical parameters were discussed as a function of polymer concentration, of level and pattern of esterification, and of the nature of the divalent counterion. The lower these values are, the better, apparently, the gel-forming ability of the pectins is.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250306
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    Electronic Resource
    Models of thioredoxin hairpin structures: Conformational properties of β-turn containing sequences (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 555-570 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sequences 74-91 and 77-91 of E. coli thioredoxin, which according to x-ray structure contain an irregular β-turn, a hairpinlike structural element, have been synthesized and their conformational properties in solution have been investigated by means of CD spectroscopy. In addition, analogs of these sequences, containing the regular β-turn element Gly-Pro-(Gly)2, have also been prepared and investigated. These are BOC-Ile-Gly-Pro-(Gly)2-Val-OMe (III) and BOC-(Ile)3Gly-Pro-(Gly)2-(Val)5-OMe (IV) that on the basis of probability, should form hairpin structures stabilized by intramolecular interactions. While the natural sequences were shown to be unable to adopt structures characterized by an intrinsic conformational stability, the two analogs showed evidence of intramolecular folding in methanol and trifluoroethanol-water solution. In particular, the CD spectra are indicative of β-structure. The most interesting case was observed for compound IV, as the highest degree of conformational order was present in solutions containing a large proportion of water. In addition, the formation of this structure took place in a highly cooperative manner. The results are utilized to discuss whether and to what extent conformationally stable folding peptide units of small size can be formed in aqueous solution.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250404
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