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  • 1
    Publication Date: 2020-08-05
    Description: This article is about the optimal track allocation problem (OPTRA) to find, in a given railway network, a conflict free set of train routes of maximum value. We study two types of integer programming formulations: a standard formulation that models block conflicts in terms of packing constraints, and a new extended formulation that is based on additional configuration' variables. We show that the packing constraints in the standard formulation stem from an interval graph, and that they can be separated in polynomial time. It follows that the LP relaxation of a strong version of this model, including all clique inequalities from block conflicts, can be solved in polynomial time. We prove that the extended formulation produces the same LP bound, and that it can also be computed with this model in polynomial time. Albeit the two formulations are in this sense equivalent, the extended formulation has advantages from a computational point of view, because it features a constant number of rows and is therefore amenable to standard column generation techniques. Results of an empirical model comparison on mesoscopic data for the Hannover-Fulda-Kassel region of the German long distance railway network are reported.
    Keywords: ddc:000
    Language: English
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  • 2
    Publication Date: 2016-06-09
    Description: We study barrier methods for state constrained optimal control problems with PDEs. In the focus of our analysis is the path of minimizers of the barrier subproblems with the aim to provide a solid theoretical basis for function space oriented path-following algorithms. We establish results on existence, continuity and convergence of this path. Moreover, we consider the structure of barrier subdifferentials, which play the role of dual variables.
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    Language: English
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  • 3
    Publication Date: 2016-06-09
    Description: For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator ${\cal P}^\tau$ does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of the operator and can be interpreted as a decomposition of the state space into (fuzzy) sets. The conformation-based transition state theory presented here can be seen as a first step in conformation dynamics towards the computation of essential dynamical properties of molecular systems without time-consuming molecular dynamics simulations.
    Keywords: ddc:000
    Language: English
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  • 4
    Publication Date: 2021-01-22
    Description: We present a middleware to store multidimensional data sets on Internet-scale distributed systems and to efficiently perform range queries on them. Our structured overlay network \emph{SONAR (Structured Overlay Network with Arbitrary Range queries)} puts keys which are adjacent in the key space on logically adjacent nodes in the overlay and is thereby able to process multidimensional range queries with a single logarithmic data lookup and local forwarding. The specified ranges may have arbitrary shapes like rectangles, circles, spheres or polygons. Empirical results demonstrate the routing performance of SONAR on several data sets, ranging from real-world data to artificially constructed worst case distributions. We study the quality of SONAR's routing information which is based on local knowledge only and measure the indegree of the overlay nodes to find potential hot spots in the routing process. We show that SONAR's routing table is self-adjusting, even under extreme situations, keeping always a maximum of $\lceil \log N \rceil$ routing entries.
    Keywords: ddc:000
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  • 5
    Publication Date: 2016-06-09
    Description: \begin{abstract} In systems biology, the stochastic description of biochemical reaction kinetics is increasingly being employed to model gene regulatory networks and signalling pathways. Mathematically speaking, such models require the numerical solution of the underlying evolution equat ion, also known as the chemical master equation (CME). Up to now, the CME has almost exclusively been treated by Monte-Carlo techniques, the most prominent of which is the simulation algorithm suggest ed by Gillespie in 1976. Since this algorithm requires an update for each single reaction event, realizations can be computationally very costly. As an alternative, we here propose a novel approach, which focuses on the discrete partial differential equation (PDE) structure of the CME and thus allows to adopt ideas from adaptive discrete Galerkin methods (as designed by two of the present authors in 1989), which have proven to be highly efficient in the mathematical modelling of polyreaction kinetics. Among the two different options of discretizing the CME as a discrete PDE, the method of lines approach (first space, then time) and the Rothe method (first time, then space), we select the latter one for clear theoretical and algorithmic reasons. First numeric al experiments at a challenging model problem illustrate the promising features of the proposed method and, at the same time, indicate lines of necessary further research. \end{abstract}
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  • 6
    Publication Date: 2014-02-26
    Description: Chvatal-Gomory cuts are among the most well-known classes of cutting planes for general integer linear programs (ILPs). In case the constraint multipliers are either 0 or $\frac{1}{2}$, such cuts are known as $\{0,\frac{1}{2}\}$-cuts. It has been proven by Caprara and Fischetti (1996) that separation of $\{0,\frac{1}{2}\}$-cuts is NP-hard. In this paper, we study ways to separate $\{0,\frac{1}{2}\}$-cuts effectively in practice. We propose a range of preprocessing rules to reduce the size of the separation problem. The core of the preprocessing builds a Gaussian elimination-like procedure. To separate the most violated $\{0,\frac{1}{2}\}$-cut, we formulate the (reduced) problem as integer linear program. Some simple heuristic separation routines complete the algorithmic framework. Computational experiments on benchmark instances show that the combination of preprocessing with exact and/or heuristic separation is a very vital idea to generate strong generic cutting planes for integer linear programs and to reduce the overall computation times of state-of-the-art ILP-solvers.
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  • 7
    Publication Date: 2014-02-26
    Description: In this paper a Godunov-type projection method for computing approximate solutions of the zero Froude number (incompressible) shallow water equations is presented. It is second-order accurate and locally conserves height (mass) and momentum. To enforce the underlying divergence constraint on the velocity field, the predicted numerical fluxes, computed with a standard second order method for hyperbolic conservation laws, are corrected in two steps. First, a MAC-type projection adjusts the advective velocity divergence. In a second projection step, additional momentum flux corrections are computed to obtain new time level cell-centered velocities, which satisfy another discrete version of the divergence constraint. The scheme features an exact and stable second projection. It is obtained by a Petrov-Galerkin finite element ansatz with piecewise bilinear trial functions for the unknown incompressible height and piecewise constant test functions. The stability of the projection is proved using the theory of generalized mixed finite elements, which goes back to Nicola{\"i}des (1982). In order to do so, the validity of three different inf-sup conditions has to be shown. Since the zero Froude number shallow water equations have the same mathematical structure as the incompressible Euler equations of isentropic gas dynamics, the method can be easily transfered to the computation of incompressible variable density flow problems.
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  • 8
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    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
    Type: annualzib , doc-type:report
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  • 9
    Publication Date: 2020-12-15
    Description: We provide information on the Survivable Network Design Library (SNDlib), a data library for fixed telecommunication network design that can be accessed at http://sndlib.zib.de. In version 1.0, the library contains data related to 22 networks which, combined with a set of selected planning parameters, leads to 830 network planning problem instances. In this paper, we provide a mathematical model for each planning problem considered in the library and describe the data concepts of the SNDlib. Furthermore, we provide statistical information and details about the origin of the data sets.
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  • 10
    Publication Date: 2020-08-05
    Description: The \emph{optimal track allocation problem} (\textsc{OPTRA}), also known as the train routing problem or the train timetabling problem, is to find, in a given railway network, a conflict-free set of train routes of maximum value. We propose a novel integer programming formulation for this problem that is based on additional configuration' variables. Its LP-relaxation can be solved in polynomial time. These results are the theoretical basis for a column generation algorithm to solve large-scale track allocation problems. Computational results for the Hanover-Kassel-Fulda area of the German long distance railway network involving up to 570 trains are reported.
    Keywords: ddc:000
    Language: English
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  • 11
    Publication Date: 2020-12-15
    Description: We consider a multicommodity routing problem, where demands are released \emph{online} and have to be routed in a network during specified time windows. The objective is to minimize a time and load dependent convex cost function of the aggregate arc flow. First, we study the fractional routing variant. We present two online algorithms, called Seq and Seq$^2$. Our first main result states that, for cost functions defined by polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of Seq and Seq$^2$ is at most $(d+1)^{d+1}$, which is tight. We also present lower bounds of $(0.265\,(d+1))^{d+1}$ for any online algorithm. In the case of a network with two nodes and parallel arcs, we prove a lower bound of $(2-\frac{1}{2} \sqrt{3})$ on the competitive ratio for Seq and Seq$^2$, even for affine linear price functions. Furthermore, we study resource augmentation, where the online algorithm has to route less demand than the offline adversary. Second, we consider unsplittable routings. For this setting, we present two online algorithms, called U-Seq and U-Seq$^2$. We prove that for polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of U-Seq and U-Seq$^2$ is bounded by $O{1.77^d\,d^{d+1}}$. We present lower bounds of $(0.5307\,(d+1))^{d+1}$ for any online algorithm and $(d+1)^{d+1}$ for our algorithms. Third, we consider a special case of our framework: online load balancing in the $\ell_p$-norm. For the fractional and unsplittable variant of this problem, we show that our online algorithms are $p$ and $O{p}$ competitive, respectively. Such results where previously known only for scheduling jobs on restricted (un)related parallel machines.
    Keywords: ddc:000
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  • 12
    Publication Date: 2014-02-26
    Description: Die Zentrale des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV) betreibt seit Januar 2004 das KOBV-Portal, in dem u.a. vielfältige Open-Linking-Dienste eingebunden sind. Dieser Beitrag erläutert Open-Linking allgemein und stellt die KOBV spezifischen Dienste im Detail vor. Dabei wird auch die Zugriffsentwicklung auf die KOBV-Open-Linking-Dienste evaluiert. Ein Ergebnis ist, dass signifikante Steigerungen der Nutzung erst dann bewirkt werden, wenn Maßnahmen durchgeführt werden, die erstens die Open-Linking-Dienste stärker ins Bewusstsein der NutzerInnen rücken und zweitens den Weg dorthin im KOBV-Portal verkürzen. Vor allem muss ein schneller Weg zu den Open-Linking-Diensten gewährleistet sein, um die Nutzung deutlich zu steigern. Um zusätzlich den Bekanntheitsgrad der Open-Linking-Dienste bundesweit zu erhöhen, regt die KOBV-Zentrale andere Bibliotheken und Verbünde dazu an, analoge Open-Linking-Dienste einzurichten. Auf diese Weise wird die Handhabung von Open-Linking selbstverständlicher.
    Keywords: ddc:000
    Language: German
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  • 13
    Publication Date: 2014-02-26
    Description: Dieser Artikel berichtet über eine erfolgreiche Schüleraktivität, die seit Jahren am Zuse-Institut Berlin (ZIB) bei Besuchen von Schülergruppen erprobt und verfeinert worden ist. Das hier zusammengestellte Material ist gedacht als Basis für eine Unterrichtseinheit in Leistungskursen Mathematik an Gymnasien. Inhaltlich wird von einem zwar für Schüler (wie auch Lehrer) neuen, aber leicht fasslichen Gegenstand ausgegangen: der Drei-Term-Rekursion für Besselfunktionen. Die Struktur wird erklärt und in ein kleines Programm umgesetzt. Dazu teilen sich die Schüler selbstorganisierend in Gruppen ein, die mit unterschiedlichen Taschenrechnern "um die Wette" rechnen. Die Schüler und Schülerinnen erfahren unmittelbar die katastrophale Wirkung von an sich kleinen'' Rundungsfehlern, sie landen -- ebenso wie der Supercomputer des ZIB -- im Bessel'schen Irrgarten''. Die auftretenden Phänomene werden mathematisch elementar erklärt, wobei lediglich auf das Konzept der linearen Unabhängigkeit zurückgegriffen wird. Das dabei gewonnene vertiefte Verständnis fließt ein in die Konstruktion eines klassischen Algorithmus sowie eines wesentlich verbesserten Horner-artigen Algorithmus.
    Keywords: ddc:000
    Language: German
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  • 14
    Publication Date: 2017-08-01
    Description: In this paper we study capacitated network design problems, differentiating directed, bidirected and undirected link capacity models. We complement existing polyhedral results for the three variants by new classes of facet-defining valid inequalities and unified lifting results. For this, we study the restriction of the problems to a cut of the network. First, we show that facets of the resulting cutset polyhedra translate into facets of the original network design polyhedra if the two subgraphs defined by the network cut are (strongly) connected. Second, we provide an analysis of the facial structure of cutset polyhedra, elaborating the differences caused by the three different types of capacity constraints. We present flow-cutset inequalities for all three models and show under which conditions these are facet-defining. We also state a new class of facets for the bidirected and undirected case and it is shown how to handle multiple capacity modules by Mixed Integer Rounding (MIR).
    Keywords: ddc:000
    Language: English
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  • 15
    Publication Date: 2020-12-15
    Description: In this paper we study online multicommodity routing problems in networks, in which commodities have to be routed sequentially. The flow of each commodity can be split on several paths. Arcs are equipped with load dependent price functions defining routing costs, which have to be minimized. We discuss a greedy online algorithm that routes each commodity by minimizing a convex cost function that only depends on the demands previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is 4K2 (1+K)2 -competitive, where K is the number of commodities. For the single-source single-destination case, this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably.
    Keywords: ddc:000
    Language: English
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  • 16
    Publication Date: 2020-12-15
    Description: In this paper, we empirically investigate the NP-hard problem of finding sparse solutions to linear equation systems, i.e., solutions with as few nonzeros as possible. This problem has received considerable interest in the sparse approximation and signal processing literature, recently. We use a branch-and-cut approach via the maximum feasible subsystem problem to compute optimal solutions for small instances and investigate the uniqueness of the optimal solutions. We furthermore discuss five (modifications of) heuristics for this problem that appear in different parts of the literature. For small instances, the exact optimal solutions allow us to evaluate the quality of the heuristics, while for larger instances we compare their relative performance. One outcome is that the basis pursuit heuristic performs worse, compared to the other methods. Among the best heuristics are a method due to Mangasarian and a bilinear approach.
    Keywords: ddc:000
    Language: English
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  • 17
    Publication Date: 2014-02-26
    Description: The performance evaluation of W-CDMA networks is intricate as cells are strongly coupled through interference. Pole equations have been developed as a simple tool to analyze cell capacity. Numerous scientific contributions have been made on their basis. In the established forms, the pole equations rely on strong assumptions such as homogeneous traffic, uniform users, and constant downlink orthogonality factor. These assumptions are not met in realistic scenarios. Hence, the pole equations are typically used during initial network dimensioning only. Actual network (fine-) planning requires a more faithful analysis of each individual cell's capacity. Complex analytical analysis or Monte-Carlo simulations are used for this purposes. In this paper, we generalize the pole equations to include inhomogeneous data. We show how the equations can be parametrized in a cell-specific way provided the transmit powers are known. This allows to carry over prior results to realistic settings. This is illustrated with an example: Based on the pole equation, we investigate the accuracy of average snapshot'' approximations for downlink transmit powers used in state-of-the-art network optimization schemes. We confirm that the analytical insights apply to practice-relevant settings on the basis of results from detailed Monte-Carlo simulation on realistic datasets.
    Keywords: ddc:000
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  • 18
    Publication Date: 2017-08-01
    Description: This paper deals with directed, bidirected, and undirected capacitated network design problems. Using mixed integer rounding (MIR), we generalize flow-cutset inequalities to these three link types and to an arbitrary modular link capacity structure, and propose a generic separation algorithm. In an extensive computational study on 54 instances from the Survivable Network Design Library (SNDlib), we show that the performance of cplex can significantly be enhanced by this class of cutting planes. The computations reveal the particular importance of the subclass of cutset-inequalities.
    Keywords: ddc:000
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  • 19
    Publication Date: 2020-02-04
    Description: Wigner transformation provides a one-to-one correspondence between functions on position space (wave functions) and functions on phase space (Wigner functions). Weighted integrals of Wigner functions yield quadratic quantities of wave functions like position and momentum densities or expectation values. For molecular quantum systems, suitably modified classical transport of Wigner functions provides an asymptotic approximation of the dynamics in the high energy regime. The article addresses the computation of Wigner functions by Monte Carlo quadrature. An ad aption of the Metropolis algorithm for the approximation of signed measures with disconnected support is systematically tested in combination with a surface hopping algorithm for non-adiabatic quantum dynamics. The numerical experiments give expectation values and level populations with an error of two to three percent, which agrees with the theoretically expected accuracy.
    Keywords: ddc:000
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  • 20
    Publication Date: 2020-11-13
    Description: We study a planning problem arising in SDH/WDM multi-layer telecommunication network design. The goal is to find a minimum cost installation of link and node hardware of both network layers such that traffic demands can be realized via grooming and a survivable routing. We present a mixed-integer programming formulation that takes many practical side constraints into account, including node hardware, several bitrates, and survivability against single physical node or link failures. This model is solved using a branch-and-cut approach with problem-specific preprocessing and cutting planes based on either of the two layers. On several realistic two-layer planning scenarios, we show that these cutting planes are still useful in the multi-layer context, helping to increase the dual bound and to reduce the optimality gaps.
    Keywords: ddc:000
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  • 21
    Publication Date: 2020-08-05
    Description: In \emph{classical optimization} it is assumed that full information about the problem to be solved is given. This, in particular, includes that all data are at hand. The real world may not be so nice'' to optimizers. Some problem constraints may not be known, the data may be corrupted, or some data may not be available at the moments when decisions have to be made. The last issue is the subject of \emph{online optimization} which will be addressed here. We explain some theory that has been developed to cope with such situations and provide examples from practice where unavailable information is not the result of bad data handling but an inevitable phenomenon.
    Keywords: ddc:000
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  • 22
    Publication Date: 2020-12-11
    Description: Die Intention ist der kooperative Aufbau einer Infrastruktur durch die Bibliotheksverbünde, um den Nutzern Volltext-Angebote dauerhaft und komfortabel zur Verfügung zu stellen: Zeitschriftenartikel und elektronische Dokumente werden mittels Suchmaschinentechnologie indexiert und unter Berücksichtigung von Zugriffsrechten zugänglich gemacht. Realisiert ist dies bereits im KOBV-Volltextserver, der seit Ende 2005 im Routinebetrieb läuft. Vorstellbar ist ein überregionales Netz von Volltextservern der Verbünde, die mittels Suchmaschinentechnologie indiziert und nahtlos in das regionale und lokale Literaturangebot integriert werden. Bei den lizenzierten Materialien sind insbesondere auch die Rechte der Verlage zu wahren und entsprechende Rechtemanagement-Verfahren einzusetzen. Es gilt, transparente Verfahren zu konzipieren und umzusetzen, um für die Verlage die notwendige Vertrauensbasis zu schaffen und gleichzeitig den Einrichtungen ihren berechtigten Zugriff auf die Volltexte zu sichern. Der vorliegende Text ist die schriftliche Fassung eines Vortrages auf dem 3. Leipziger Kongress für Information und Bibliothek "Information und Ethik", der vom 19.-22. März 2007 im Congress Center Leipzig stattfand.
    Keywords: ddc:000
    Language: German
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  • 23
    Publication Date: 2020-12-11
    Description: Zur Unterstützung der Bibliotheken bei ihren Open-Access-Aktivitäten betreibt die KOBV-Zentrale seit Anfang 2005 den Service "Opus- und Archivierungsdienste". Die KOBV-Zentrale agiert als Application Service Provider (ASP) für sämtliche technischen Komponenten des Publikationsprozesses, indem sie die gesamte technische Infrastruktur bereitstellt und betreibt – angefangen bei den lokalen Publikationsservern bis hin zu lokalen Repositories zur Archivierung der elektronischen Dokumente. Der vorliegende Text ist die schriftliche Fassung eines gleichnamigen Vortrages auf der 31. ASpB-Tagung "Kooperation versus Eigenprofil?" der Arbeitsgemeinschaft der Spezialbibliotheken, die vom 25.-28. September 2007 in der Technischen Universität Berlin stattfand.
    Keywords: ddc:000
    Language: German
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  • 24
    Publication Date: 2022-07-07
    Description: A new approach to derive transparent boundary conditions (TBCs) for wave, Schrödinger, heat and drift-diffusion equations is presented. It relies on the pole condition and distinguishes between physical reasonable and unreasonable solutions by the location of the singularities of the spatial Laplace transform of the exterior solution. To obtain a numerical algorithm, a Möbius transform is applied to map the Laplace transform onto the unit disc. In the transformed coordinate the solution is expanded into a power series. Finally, equations for the coefficients of the power series are derived. These are coupled to the equation in the interior, and yield transparent boundary conditions. Numerical results are presented in the last section, showing that the error introduced by the new approximate TBCs decays exponentially in the number of coefficients.
    Keywords: ddc:000
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  • 25
    Publication Date: 2022-07-19
    Description: We present a unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines, which together form a feature skeleton. Our method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature skeleton and the input mesh.
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  • 26
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
    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
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  • 27
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 15-25 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long-range interactions between different regions, incorporating all these interactions in a single Ising-like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α- and β-structures for different residues in synthetic polypeptides, while long-range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x-ray structural data became available.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 28
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 27-31 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To increase our understanding of peptide-water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x-ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
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  • 29
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    Biopolymers 22 (1983), S. 49-58 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
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  • 30
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    Biopolymers 22 (1983), S. 87-91 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Near- and far-uv CD spectra of microtubule protein preparations have been examined to study the possible role of protein conformation in relation to the kinetics of the self-assembly of these proteins into microtubules in vitro. Although tubulin can form conformations with high helical content under apolar solution conditions, this transformation is apparently not involved in self-assembly. There is no major perturbation of tubulin near-uv CD by reagents and solution conditions favoring assembly. Thus, in these preparations, tubulin, as dimer and as oligomer with MAPs, is effectively in the conformation in which it undergoes self-assembly. This conclusion is consistent with a hybrid model of assembly of microtubule protein involving direct incorporation of oligomeric species as an alternative to the condensation polymerization of tubulin dimer as the exclusive assembly mechanism.
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  • 31
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    Biopolymers 22 (1983), S. 101-105 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ligand-modulated kinetics of the autoproteolysis of thermolysin and the high-molecular-weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
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  • 32
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    Biopolymers 22 (1983), S. 125-129 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature-sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature-sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
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  • 33
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    Biopolymers 22 (1983), S. 1677-1696 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of O2 release by oxyhemoglobin caused by sodium dithionite, in the presence and in the absence of organic cosolvents (monohydric alcohols and formamide) at 10°C. This study was performed by using standard stopped-flow techniques coupled with microprocessor-based data acquisition. We have fitted the experimental data to a mathematical expression obtained on the basis of a two-state model that takes into account the kinetic heterogeneity between α- and β-chains and the presence of αβ-dimers in oxyhemoglobin solutions. Results indicate that the cosolvents mainly affect the allosteric parameter L, i.e., the T ⇄ R conformational equilibrium of hemoglobin, leaving the intrinsic deoxygenation rates of both R and T states almost unaltered. The L values obtained in the present work are in excellent agreement with analogous values previously estimated from oxygen equilibrium measurements.
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  • 34
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    Biopolymers 22 (1983), S. 1657-1675 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Porcine submaxillary mucin (PSM) is a glycoprotein composed of a protein core and frequent, short oligosaccharide side chains. We report static and dynamic light scattering experiments and intrinsic viscosities for PSM in aqueous solvent systems. In 0.1M NaCl solution, the data suggest PSM exists as large, internally branched, highly hydrated, polydisperse aggregates that slowly dissociate to give a stable species of weight-average molecular weight (Mw) 7.4 × 106. In 6M GdnHCl solution, the noncovalent bonds between PSM molecules are broken, giving a highly elongated molecule of Mw = 2.0 × 106. The irreversible nature of this dissociation suggests that the forces that stabilize the native aggregates of PSM in 0.1M NaCl are specific in nature. On reduction of PSM with mercaptoethanol, the polydispersity decreases and Mw also decreases to 9 × 105. A discrete change is observed in the solution properties of PSM in 0.1M NaCl at a concentration of 2mg/mL, manifested by a sudden decrease in the translational diffusion coefficient, an increase in viscosity number, and a decrease in slope of the osmotic compressibility. We tentatively propose that a weak and reversible secondary association process occurs at this concentration, although a purely hydrodynamic interaction cannot be ruled out.
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  • 35
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow-oriented ethanol-water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LDR) curves in the region 250-290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A- and B-forms of DNA, based on the fiber structures and the π-π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A-form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LDR is explained in terms of an out-of-plane polarized n-π* transition.
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  • 36
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    Biopolymers 22 (1983), S. 1759-1767 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A vibrational analysis has been performed for a double-helix-single-strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen-bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)-poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.
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  • 37
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 38
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Nmr studies of the protected and free tetrapeptide Gly-Pro-Gly-Gly were carried out in β-turn-supporting solvents, that is, in CDCl3 for Z-Gly-Pro-Gly-Gly-OMe and in Me2SO-d6 for H-Gly-Pro-Gly-Gly-OH. Comparisons with specifically α-deuterated analogs gave complete assignments of the NH and methylene regions. Analysis of chemical shifts, coupling constants, and the temperature dependence of chemical shifts show that the peptide adopts a type II β-turn conformation. This turn is stabilized for the protected tetrapeptide by two hydrogen bonds between (i) C=O (Gly1) and NH(Gly4), and (ii) urethane function NH and methyl ester C=O.
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  • 39
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio minimal and split-valence basis set calculations have been performed on compounds that are involved in retro-inverso modifications, i.e., gem-diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem-diaminoalkyl and malonyl derivatives of residues found in the retro-inverso modified peptides is 5-8 kcal/mol lower than the Ceq7 conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.
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  • 40
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 41
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 42
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    Biopolymers 22 (1983), S. 1449-1460 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: SCF-LCAO-MO ab initio calculations were carried out for the interaction between a charged amino acid and a water molecule. The results obtained were fitted by an analytical potential function of the atom-atom type, and the corresponding potential surfaces were examined by means of orientationally optimized isoenergy contour maps. Monte Carlo simulations were also carried out on a few selected solute-water clusters at T = 300 K, in order to obtain insight into the solvation structure.
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  • 43
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An improved cube method has been developed for calculating the intensity of diffuse x-ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55, 374-400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6, 151-176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein-“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.
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  • 44
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 45
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    Biopolymers 22 (1983), S. 2501-2506 
    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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  • 46
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    Biopolymers 22 (1983), S. 2523-2538 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended retro-inverso modification was introduced at the central six residues of the somatostatin molecule, the region of internal enzymatic degradations. The synthesis of the analog [Ala4,g-Phe6-r-D-Phe7-r-D-Trp8-r-D-Lys9-r-D-Thr10-m-R,S-Phe11]-somatostatin required a unique strategy accommodating the unusual structure. Side-chain protection based on the t-butyl group in combination with Fmoc and Nps α-amino protection was employed. The key component containing the gem-diaminoalkyl residue was generated by an iodobenzene bistrifluoroacetate-mediated reaction. The separation of diastereomers of the cyclic tetradecapeptide in highly pure form was accomplished by high-performance liguid chromatography on a semipreparative scale. The analogs exhibited very low potency in the growth hormone inhibition test in vitro. This is interpreted as the consequence of the complex structural changes created by the extended retro-inverso modification.
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  • 47
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120-160 base pairs (bp) long is examined by molecular-dynamics modeling using 13C-nmr spin-relaxation data obtained over the frequency range of 37-125 MHz. The broad range of 13C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τx = ∼10-6 s;τZ = ∼1.8 × 10-8s), which is in good agreement with values calculated from hydrodynamic theory (τx = ∼1.8 × 10-6 s; τZ = ∼2.7 × 10-8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C—H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τw = ∼4 × 10-9 s, θcone = ∼21°) or as a bistable jump (τA = τB = ∼2 × 10-9 s, θ = ∼15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C—H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τW = ∼0.2 × 10-9 s, θcone = ∼50°), and overall motion is affected by becoming essentially isotropic (τx = τZ = ∼5 × 10-8 s) for the single-stranded molecules. Since 13C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.
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  • 48
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of methyl orange with poly(L-lysine) was studied kinetically by the stopped-flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer-to-dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped-flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L-lysine), the second and third process were ascribed to the intramolecular reaction of the polymer-dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer-dye complex. The origin of the stacking of methyl orange on poly(L-lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.
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  • 49
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Novel devices for the spectroscopic and chromatographic analysis of the denaturation curves of the protein are described. A multidimensional spectroscopic measuring system makes it possible to carry out simultaneous and continuous acquisition of a set of data of different spectroscopic dimensions at several wavelengths in the course of increasing or decreasing denaturational perturbation. GuHCl-gradient chromatography can provide information about the progressive change of the protein volume in the course of increasing GuHCl concentration. Thus, denaturation curves with a high data-point density can be obtained. The data-storing function by a magnetic disk memory provides enough precision for a rigorous investigation of the correlation among the curves that probe different aspects of denaturation. The GuHCl denaturation of RNase A, cytochrome c, and pepsinogen are studied to demonstrate the high performance of these devices. Three types of transitions are found in these three proteins and the multiphasic nature of the transitions is clearly detected in the last two proteins.
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  • 50
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 51
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    Biopolymers 22 (1983), S. 2169-2172 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 52
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    Biopolymers 22 (1983), S. 2207-2217 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A sufficiently long semiflexible filamentous macromolecule is theroretically expected to exhibit three different domains of behavior of its apparent diffusion coefficient Dapp(K) as a function of scattering vector K: (1) the small wave vector limit, where Dapp(K) = D0 is the translational diffusion coefficient of the center-of-mass; (2) the universal K3 region, where Dapp(K) = (kBT/6πη)K is a universal function of K independent of any property of the molecule itself; (c) the plateau region at large K2, where Dapp(K) approaches either a plateau, or gradually sloping quasiplateau, characteristic of local (elastic) rigid-body motions of the filament. The existence of each of these different domains has now been established experimentally for at least some polymers. The boundaries of the universal K3 region and the plateau region are determined theoretically here using precise quantitative criteria for universal or plateau behavior of Dapp(K) for a Rouse-Zimm model containing N + 1 subchains with rms subchain extension b. Allowing a maximum of 13% nonuniversal behavior, the domain of the universal K3 region is given by K2R2G = K2Nb2/6 ≥ 7 and K2b2 ≤ 0.54. Allowing as much as 10% nonplateau behavior, the boundary for onset of plateau behavior is K2b2 = 18.3. Dapp(K) is at least 50% nonuniversal when K2b2/6 = 6 ln 3. Extension of these results to DNA is examined theoretically, and good agreement of the pertinent predictions with published experimental data is demonstrated.It is concluded that no truly universal K3 region exists for DNA with Mr ≤ 107 and persistence length a ≥ 450 Å, although marginally (≤17% nonuniversal) universal behavior, is exhibited in a very narrow domain 0.64 × 1010 ≤ K2 ≤ 0.84 × 1010 cm-2 for φ29 DNA (Mr = 11.5 × 106). More than 50% of Dapp(K) is governed by local (elastic) rigid-body motions when K2 = 5.23 × 1010 cm-2. The existence of a very wide region of nonuniversal apparent K3 behavior extending up to very large K2, far into the plateau region, is demonstrated in a plot of Dapp(K)/K vs K2 for the Rouse-Zimm model. This is shown to stem in part from visual artifacts of plotting Dapp(K)/K vs K2, even for rigid species.
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  • 53
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 54
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    Biopolymers 22 (1983), S. 2353-2366 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rotational relaxation tiem τ3 of DNA molecules (Mw ≃ 5 × 106) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher-molecular-weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ3 increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10-3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M-13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45, 1891-1894]. These results may be discussed in terms of the Doi-Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36, 607-611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74, 918-932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ3 and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high-molecular-weight elongated molecules are studied.
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  • 55
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    Biopolymers 22 (1983), S. 2411-2421 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A thermodynamic treatment of the helix-coil transition of synthetic polypeptides in binary organic solvent mixtures is extended to describe isobaric heat-capacity increments associated with the phenomenon. This development resolves such increments into three components: two associated respectively with intrinsic differences between the ordered and disordered states of the macromolecule and between the coil-solvent complex and its components, and a third term derived from the temperature dependence in the fraction of coil residues bound to active solvent. Insights derived from this analysis are also applied to the discussion of some heat capacity increments associated with the denaturation of globular proteins.
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  • 56
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 57
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    Biopolymers 22 (1983), S. 2507-2511 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 58
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    Biopolymers 22 (1983), S. 2539-2547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The temperature dependence of the humidity-sensitive spacing, d, related to the lateral packing of collagen molecules was measured for fully hydrated collagen. In the vicinity of 0°C, a sudden change in d was observed, which was reversible with temperature. In the diffraction profile, below 0°C, a set of diffraction peaks identified with the hexagonal crystalline form of ice was observed. With the reduction in water content, the intensity of the set of diffraction peaks decreased and was found to be zero at a water content of 0.38 g/g collagen. These results were considered to be caused by the frozen water in collagen fibril below 0°C. According to the water content dependence of d, it was considered that up to a certain water content water absorbed would be stowed in the intermolecular space of collagen and above that water content water molecules would aggregate to make pools, i. e., extrafibrillar spaces. The unfreezable bound water was considered to be located in the intermolecular space of collagen. Size of the extrafibrillar space, determined from the intensity analysis of a smallangle x-ray scattering pattern, corroborates the speculation that the water showed in the extrafibrillar space is freezable and free. The formation of the hexagonal crystalline form of ice in the extrafibrillar space was considered to cause the sudden change in d at 0°C.
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  • 59
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    Weinheim : Wiley-Blackwell
    Chemie in unserer Zeit 17 (1983), S. 67-67 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 60
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    Weinheim : Wiley-Blackwell
    Chemie in unserer Zeit 17 (1983), S. 67-67 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 61
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    Weinheim : Wiley-Blackwell
    Chemie in unserer Zeit 17 (1983), S. 77-84 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 6 Ill.
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  • 62
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    Weinheim : Wiley-Blackwell
    Chemie in unserer Zeit 17 (1983) 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 63
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    Chemie in unserer Zeit 17 (1983), S. 202-202 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 64
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 65
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    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. xi 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 66
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    Biopolymers 22 (1983), S. 33-36 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Potential-energy calculations are reported on the interaction between two collagenlike triple-stranded poly(Gly-L-Pro-L-Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.
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  • 67
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    Biopolymers 22 (1983), S. 43-47 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix-coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix-coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.
    Additional Material: 2 Ill.
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  • 68
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The major unfolded form of ribonuclease A is known to show well-populated structural intermediates transiently during folding at 0°-10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H-nmr after folding is complete. The feasibility of using 1H-nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7-14 are in the 1H-form. All eight of these protected peptide protons are H-bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H-form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H-bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3-13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α-helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.
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  • 69
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    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 93-99 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Denaturation profiles of 17 globular proteins were studied by the spectroscopic and chromatographic methods with high-data-point density. The denaturational transitions are broadly classified into three types according to their multiphasic characteristics. In general, more or less complex internal cooperative events seem to take place in the conformation transition of globular proteins.
    Additional Material: 3 Ill.
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  • 70
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report on the effects that the presence of ethylene glycol or glycerol has on the oxygen affinity of hemoglobin. We attribute these effects to an altered equilibrium between T and R quaternary conformations of hemoglobin and separate them into bulk-electrostatic and non-bulk-electrostatic contributions to the standard free-energy difference between the R and T states.
    Additional Material: 3 Ill.
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  • 71
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    Biopolymers 22 (1983), S. 139-145 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 270-MHz proton-nmr spectra of short neurotoxins (erabutoxins from Laticauda semifasciata and cobrotoxin from Naja naja atra) and long neurotoxins (toxin B from Naja naja and α-bungarotoxin from Bungarus multicinctus) have been analyzed. The conformation of erabutoxin b in solution is largely consistent with the x-ray crystal analysis, although the environment of His-7 in solution is definitely different from that in the crystal. The pH-dependent transition has been found for toxin B, indicating that the conformation in neutral solution is different from that in the crystal as grown from acidic solution. The deuterium-exchange rates of the amide protons for the four neurotoxins have been measured. The order of structural rigidity is the same as the order of the irreversibility of neuromuscular block by neurotoxins.
    Additional Material: 4 Ill.
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  • 72
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    Biopolymers 22 (1983), S. 163-169 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational studies on poly(oxyethylene)-bound homo-, oligo-, guest-host, and sequential peptides synthesized according to the liquid-phase method were carried out by means of 1H-nmr spectroscopy. The solubilizing effect of the C-terminal polymeric support allowed a thorough investigation of the secondary structure in solution.
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  • 73
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    Biopolymers 22 (1983), S. 217-225 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A vibrational force field for the polypeptide chain has been developed for normal-mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm-1. We review the application of this technique to conformational problems in peptides (β-turns and their model compounds), polypeptides [the αII-helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).
    Additional Material: 4 Ill.
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  • 74
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    Biopolymers 22 (1983), S. 247-253 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-nmr studies of [pGlu6]SP6-11, [gpGlu6,mPhe7]SP6-11, and [pGlu6,N-CH3Phe7]SP6-11 in DMSO-d6 reveal characteristic chemical shifts, 3JNH-αCH, temperature dependence, as well as deuterium exchange half-times. Marked similarities are revealed for the two first analogs, whereas the N-methylated analog is clearly different. Possible conformations are considered.
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  • 75
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 36-amino acid avian pancreatic polypeptide has been studied by x-ray analysis at 0.98-Å resolution and refined using a restrained least-squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline-like helix (residues 2-8) and an α-helix (residues 14-32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high-resolution analysis defines sequence-dependent distortions in the α-helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C-terminal residues. For the first time, six-parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
    Additional Material: 11 Ill.
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  • 76
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have carried out a systematic analysis of the solid-state conformational preferences of a number of linear homo-oligoprolines (to the tetramer) by ir absorption and x-ray diffraction. The peptides present different chiral sequences (tacticities), various types (urethane and amide) of N-protecting groups, and free and blocked C-termini (which imply different capabilities of forming H-bonds). The following conclusions can be drawn: (i) values for the geometry of the prolyl residue and the peptide bond in the cis and in the trans conformations are proposed; (ii) in general the conformational angles ϕ and ψ in the linear homo-oligoprolines have values appropriate for the polyproline II structure (conformation F); (iii) the pyrrolidine ring shows various types of puckering with no apparent relation to the backbone conformation; (iv) Pro-Pro peptide bonds generally take the trans conformation, the few cases of cis conformation being formed by Pro residues of different chirality; (v) the single H-bond donor  -  OH, when present, is always bonded to H-acceptors, which can be either the urethane or the amide or the peptide carbonyl but never the carbonyl group of the  -  COOH moiety.
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  • 77
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    Biopolymers 22 (1983), S. 377-380 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Myelin basic protein isolated from bovine white matter is known to consist of a mixture of three or more “charge isomers”, which can be separated by cation-exchange chromatography. We are using 360-MHz 1H-nmr spectroscopy to establish the chemical and structural differences among them. Preliminary studies by difference spectroscopy between two of the isomers suggest (a) all aromatic residues, and probably their nearest-neighbors, are unchanged; (b) the less cationic isomer lacks one (or two) of its C-terminal Arg residues; and (c) a significant fraction of the two Met residues in the less cationic isomer is present as methionine sulfoxide.
    Additional Material: 1 Ill.
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  • 78
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A hydrophobic linear peptide has been synthesized and studied over a range of environments using several complementary spectroscopic approaches, including nmr, CD, and vibrational spectroscopies. The sequence of this model peptide, carbobenzoxy-L-Pro-D-Phe-D-Ala-L-Pro-NHCH3, was designed such that a small number of “folded” conformations, stabilized by intramolecular hydrogen bonding, would be accessible to it. Additionally, the extremely hydrophobic character of the peptide favors its interactions with hydrophobic regions of a membrane. The conformational impact of the membrane environment on the peptide, and the effect of the peptide on lipid organization have been explored both in micellar media and in vesicles. To facilitate nmr analysis, the peptide has been synthesized with one of the prolines perdeuterated. Results of these studies reveal that the peptide experiences a microenvironment of moderate polarity in micellar media and causes changes in lipid structure in a vesicle that are indicative of a hydrophobic peptide-lipid interaction.
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  • 79
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    Biopolymers 22 (1983), S. 425-440 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody-combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid-phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross-reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72-89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25-55) is also antigenic.
    Additional Material: 13 Ill.
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  • 80
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of novel, functionalized catecholamines (congeners) has been synthesized in which, formalistically, the N-isopropyl group of isoproterenol has been extended by a linear alkyl chain of varying length, terminated by a carboxyl group. Model amide derivatives have also been prepared in order to optimize the biological activity of these derivatives and also to aid in the design of appropriate peptides for the synthesis of conjugates. As a result of these studies, a series of amino acid and monodisperse peptide carriers, containing p-aminophenylalanine as the point of attachment for the drug, was prepared, together with the corresponding conjugates. In vitro and in vivo evaluation of the congeners, model amides, and conjugates has demonstrated that the biological activity of these derivatives is extremely sensitive to structural modifications at a point far-removed from the pharmacophore, in both the congener amide and conjugate series. A number of the model amides and conjugates have proven to be highly active when tested in both in vitro and in vivo test systems. The implications of these results in terms of a novel structure-activity approach to drug design are discussed.
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  • 81
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    Biopolymers 22 (1983), S. 557-567 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Antineoplastic drugs such as daunomycin, adriamycin, methotrexate, 5-fluorouridine, cytosine arabinoside, and platinate were bound to antibodies directly or via a polymeric bridge. The drug antibody conjugates retained most of their drug and antibody activities when tested in vitro. Daunomycin-antibody conjugates were shown to penetrate tumor cells in the conjugated form. In animals, daunomycin-antibody conjugates were at least as effective chemotherapeutically as the corresponding free drugs and considerably less toxic. In some tumor systems, the daunomycin-antibody conjugates represented an improvement over the free drug. This improvement was restricted in some tumors to a particular injection route of the tumor and the treatment.
    Additional Material: 6 Ill.
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  • 82
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a synthetic method aimed at specifically coupling poly(ethylene oxide) (PEO) to proteins without altering their spectroscopic properties. To do so, we have first modified the alcohol end group of PEO to an acid end group (PEO-COOH). Coupling of PEO-COOH to Gly A1 methylsulfonylethyloxycarbonyl (Msc) protected insulin yielded NαB1,N∊B29-(PEO)2-insulin. Conversely, coupling of PEO-COOH to insulin whose Gly A1 and Lys B29 amino groups were protected with Msc yielded NαB1-PEO-insulin. The products were obtained in a spectroscopically pure form and characterized by uv and CD spectroscopy. Conformational and biological studies are in progress.
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  • 83
    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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  • 84
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    Biopolymers 22 (1983), S. 633-641 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure and conformation of the synthetic cyclic tetrapeptide, cyclo(L-Pro-Sar)2, was determined by x-ray analysis. The peptide crystallizes in the orthorhombic space group P212121 with cell parameters a = 9.277(1), b = 12.884(1), and c = 15.581(2) Å. The crystal structure was solved by the symbolic addition procedure for direct phase determination and least-squares refinement using 1796 reflections, which led to the final R value of 0.043. This structure provides the first example observed in a crystal of a cyclic tetrapeptide in which all four peptide units have been found in the cis conformation with ω angles deviating slightly by 2°-10° from the ideal value of 0°. It was also found that the two Pro Cα-CO single bonds assumed a trans′ (ψ = 159.6° and 158.4°) conformation. Adjoining average planes of the peptide groups fall at nearly right angles to each other. The pyrrolidine ring conformations of the two prolyl residues are in the envelope form, with Cγ carbon out of the least-squares planes for the remaining four atoms.
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  • 85
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
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  • 86
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    Biopolymers 22 (1983), S. 879-893 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We examined three sonicated, specific-seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P-nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P-nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche--gauche- conformation and shifts upfield in all four monovalent salts used, relative to a single-stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans-gauche- conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly-(dAdT) from a presumed right-handed dinucleotide-repeat B-form to another conformation with a dinucleotide-repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans-gauche- conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly-(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right-handed regular B-form to a left-handed Z-form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B-form with a gauche--gauche- phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
    Additional Material: 7 Ill.
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  • 87
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Seven dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurine nucleoside residue, dAfl-U, dAcl-U, dAbr-U, dAio-U, dGfl-U, and dIfl-C, were chemically synthesized and investigated by 1H-nmr spectroscopy at 300 MHz. The sugar and backbone conformations of these compounds were analyzed by the spectral pattern of furanose proton resonances; and the extents of base-base interaction were estimated from chemical shifts and their temperature-dependent changes of base-proton resonances. It is found that the population of C3′-endo conformer and the extent of base-base interaction decrease as the electronegativity of 2′-substituent decreases in dAx-U (x = fl, cl, br, and io) series. The C3′-endo (3E) population and the base-base interaction in Nfl-U (N = A,G)-type dimers as well as dIfl-C are relatively higher than the corresponding natural ribo-dimers but can be recognized as grossly similar to the conformation of regular RNA dimers.
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  • 88
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 89
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    Biopolymers 22 (1983), S. 1267-1283 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the Raman spectra of the zwitterionic glycylglycine crystal (GG) and its N-deuterated analog. A normal coordinate analysis on its α-crystalline form was performed and the effects of intra-and intermolecular couplings are discussed. A modified Urey-Bradley potential was used as a model of the intramolecular force field. Factor group splittings are described by the use of intermolecular potentials consisting of nonbonded atom-atom interactions and dipole-dipole interactions. Effects of hydrogen bonds on the vibrational frequencies of amino and carboxylate groups are also analyzed.
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  • 90
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ir absorption and CD conformational analyses of solutions of the protected 2-9 fragment of the peptaibol antibiotics emerimicins III and IV \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - L - Leu\rlap{--} (Aib_2 \rlap{--} ) $\end{document} and related short sequences are consistent with the presence of a right-handed α-helix for the octapeptide, while the tri-, tetra-, and pentapeptides adopt a 310-helix, either right- or left-handed, depending on the amino acid sequences. The structural preferences of solid-state \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - OMe $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - OMe $\end{document} have been determined by x-ray diffraction. In accord with the solution data, incipient 310-helices, formed by two and three β-turns, have been found for the tetra- and pentapeptides, respectively. The tetrapeptide helix has the left-handed screw sense, while that of the pentapetide is right-handed, thus confirming the conclusions of the CD analysis of the solution.
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  • 91
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    Biopolymers 22 (1983), S. 1401-1407 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Isomeric oligopeptides composed of five methionyl residues and one glycyl residue or of five γ-methyl-L-glutamyl residues and one glycyl residue all exhibit marked differences in retention on normal-phase silica. When the glycyl residue is at internal positions of hexa or heptapeptides, the peptide elutes most rapidly form the μPorasil column. Comparison of the effect of positional isomerism on retention in short oligopeptides with the effect on retention of hexamers and heptamers suggests that a change in peptide conformation may be responsible for the change in oligopeptide mobility.
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  • 92
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    Biopolymers 22 (1983), S. 1319-1334 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of an enzymatically derived sodium hyaluronate (NaHA) segment preparation with chain length 18 ± 3 disaccharide units [NaHAseg, ( NaGlcUA GlcNAc)15-20°. NaGlcUA, sodium D-glucuronate; GlcNAc, 2-acetamido-2-deoxy-D-glucose] in H2O was recorded to 180 nm using a computer-controlled vacuum-uv CD instrument. Near 190 nm the spectrum is of low intensity, similar to the sum of the free monosaccharide contributios, attributed to the π-π* transitions of the acetamido and carboxylate substituents. In contrast, much smaller oligosaccharides, also derived from high-molecular-weight NaHA by enzymatic digestions, show CD spectra in H2O with prominent bands centered near 190 nm. The oligosaccharide spectra can be matched as linear combinations of interior sugar residue (= NaHAseg) and end sugar residue CD contributions. End residues from oligosaccharides of the type (NaGlcUA-GlcNAc)n show a negative CD band near 190 nm. End residues from oligosaccharides of the reverse sequence (GlcNAc-NaGlcUA)n show a positive CD band near 190 nm. Averaging of the two end-residue spectral contributions yields an approximate match for the spectrum of NAHAseg below 200 nm. It is proposed that the low intensity CD of NaHA in the π-π* region is the result of large-magnitude, oppositely signed contributions, which can be visulized by studying oligosaccharides.
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  • 93
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    Biopolymers 22 (1983), S. 1383-1399 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of a crystalline cellulose II-hydrazine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose-solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x-ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked-atom least-squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen-bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an N—H…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.
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  • 94
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    Biopolymers 22 (1983), S. 1445-1448 
    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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  • 95
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    Biopolymers 22 (1983), S. 1489-1498 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical force-field calculations and ir and 1H-nmr spectra indicate that five-membered (C5) and seven-membered (C7eq) hydrogen-bonded rings are the preferred conformations of acetyl-L-Phe p-acetyl and p-valeryl anilides in nonpolar media. The C5/C7eq ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational-energy calculations suggest that a molecule of water participates in the stabilization of the C7eq conformation.
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  • 96
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    Biopolymers 22 (1983), S. 333-339 
    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 amino terminal half-molecule of histone H4 with duplex DNA has been studied by fiber x-ray diffraction. Changes induced in the diffraction pattern of B-DNA by the presence of the bound peptide have been Fourier-analyzed and the results presented in terms of a deweighted radial projection of the electron density. We conclude that the peptide binds on the major groove side of the sugar-phosphate chain.
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  • 97
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    Biopolymers 22 (1983), S. 355-362 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recent studies of the neurophysins and associated neuropeptide hormones have addressed both the biosynthetic pathways by which these noncovalent protein-peptide complexes are derived in neurosecretory neurons and the nature of the noncovalent interactions likely to occur during transport and storage in neurosecretory granules within the neurons. In vitro translation of hypothalamic mRNA and sequencing of cDNA obtained from this mRNA have yielded chemical evidence that each complex of hormone and major neurophysin is made through a common precursor molecule. The mature complexes obtained upon proteolytic processing of precursors exhibit interdependent hormone binding and self-association interactions. Photoaffinity labeling and quantitative affinity chromatography have helped detect and define the binding surfaces involved. Further study of the structural nature of these surfaces is being carried out using large neurophysin fragments obtained by limited tryptic proteolysis.
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  • 98
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    Biopolymers 22 (1983), S. 397-402 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gramicidin A exists in distinctly different conformations in phospholipid vesicles and in organic solvents. These different folding motifs are also reflected in crystals of gramicidin formed in the presence and absence of lipid molecules.
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  • 99
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    Biopolymers 22 (1983), S. 409-414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Macrocyclic molecules can serve as ion carriers when their polar groups form an inner cage to capture ions while their hydrophobic groups form an outer layer to dissolve the molecule in lipid membranes. A “template method” has been developed for high-yield synthesis of a whole variety of macrocyclic esters, amides, and other families which may show ionophoric properties. In order to select the more promising compounds for synthesis, energetic and conformational characteristics of such molecules have been calculated from empirical energy functions. Calculations are examined using known structures and are employed to predict the properties of molecules not yet synthesized.
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  • 100
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    Biopolymers 22 (1983), S. 453-464 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For a better understanding of the molecular nature of the antigen-specific T-cell recognition system, continuous T-cell lines specific to the synthetic polypeptide antigen poly(Tyr,Glu)-poly(DLAla)--poly(Lys) [(T,G)-A--L] were established from C3H.SW (high-responder) activated T-cells, cloned, and characterized. These lines and their derived clones are also constitutive secretors of antigen-specific T-cell replacing helper factors. The secreted T-cell helper factor was shown to possess MHC determinants as well as V-region determinants, or more specifically, idiotypic determinants that are cross-reactive with those expressed on (T,G)-A--L-specific antibodies of the same mouse strain. Using the fluorescence-activated cell sorter (FACS II) and individual C57BL/6 anti-idiotypic sera produced against (T,G)-A--L-specific antibodies of C3H.SW origin, we have demonstrated the expression of the cross-reactive idiotypic markers on the monoclonal helper T-cells. Attempts were made to purify the active fraction of the T-cell factors secreted by the (T,G)-A--L continuous helper lines. Gel analysis of the twice affinity-purified eluate of a (T,G)-A--L column revealed the existence of iodinated bands with molecular weight of 17,000 and 15,000, in addition to a diffuse band of high molecular weight. The specific helper activity of the factors was associated with a 65-75% ammonium sulfate precipitate. Gel electrophoresis of the latter fraction, as well as of an eluate of a (T,G)-A--L-Sepharose column indicated that a high-molecular-weight (〈 67,000) and a low-molecular-weight (15,000-17,000) fraction contained the biological activity of the factor. Similar results were obtained following chromatography of the factor on Sephadex G-100 columns. The two fractions were shown to be synthesized by the T-cell lines, as indicated by internal labeling experiments using 35S-methionine. Thus, it is suggested that a fraction of an apparent molecular weight of 15,000-17,000 preserves both the antigen specificity and the helper activity of the factor produced by the (T,G)-A--L-specific T-cell lines.
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