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  • 2000-2004  (57)
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  • 2004  (57)
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  • 2000-2004  (57)
  • 1985-1989  (1,744)
  • 1975-1979
  • 1950-1954
  • 1890-1899
Year
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  • 1
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    Vorhaben: Offene Navigation und Suchmaschinen in Verbünden, Konsortien und den Wissenschaften; Schlussbericht zumTeilprojekt des BMBF-Vorhabens: Kompetenznetzwerk NeueDienste, Standardisierung, Metadaten. (2004)
    Details
    Publication Date: 2020-03-23
    Description: Die harmonische Integration der Navigation und Suche in lizenzierten Journalen und gleichzeitig in freien digitalen Dokumenten unter einer einheitlichen konsistenten Nutzeroberflache ist eines der ungelösten F&E-Probleme der Fachinformation. Hierfür sollen Elemente des Invisible Web und des Visible Web unter Berücksichtigung offener Standards nahtlos #I miteinander verbunden werden. Dem Projekt liegt ein Modell mit Internet-Index, Metasuche und Open Linking über verteilten heterogenen Speichern #I zu Grunde: Verschiedenste Server, digitale Referenzen in Artikeln und Dokumenten, Links in Datenbanken und auf Bestelldienste sollen unter Berücksichtigung von Standort-, Studien- und Lernbedingungen kooperativ miteinander vernetzt werden. Die Leistungsfähigkeit des Modells soll in Pilotimplementierungen getestet und für eine breite Anwendung vorbereitet werden. Auf dieser Basis soll das Vorhaben Verteilter Zeitschriftenserver der AG der Verbundsysteme in eigenen Teilprojekten kooperativ initiiert werden, das jetzt in das Vorhaben Verteilter Dokumentenserver von vascoda integriert ist.
    Keywords: ddc:000
    Language: German
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  • 2
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    Parameter Estimation and Accuracy Matching Strategies for 2-D Reactor Models (2004)
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    Publication Date: 2014-02-26
    Description: The mathematical modeling of a special modular catalytic reactor kit leads to a system of partial differential equation in two space dimensions. As customary, this model contains unconfident physical parameters, which may be adapted to fit experimental data. To solve this nonlinear least squares problem we apply a damped Gauss-Newton method. A method of lines approach is used to evaluate the associated model equations. By an a priori spatial discretization a large DAE system is derived and integrated with an adaptive, linearly-implicit extrapolation method. For sensitivity evaluation we apply an internal numerical differentiation technique, which reuses linear algebra information from the model integration. In order not to interfere the control of the Gauss-Newton iteration these computations are done usually very accurately and, therefore, very costly. To overcome this difficulty, we discuss several accuracy adaptation strategies, e.g., a master-slave mode. Finally, we present some numerical experiments.
    Keywords: ddc:000
    Language: English
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  • 3
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    Finding All Maximal Cliques of a Family of Induced Subgraphs (2004)
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    Publication Date: 2020-03-06
    Description: Many real world problems can be mapped onto graphs and solved with well-established efficient algorithms studied in graph theory. One such problem is to find large sets of points satisfying some mutual relationship. This problem can be transformed to the problem of finding all cliques of an undirected graph by mapping each point onto a vertex of the graph and connecting any two vertices by an edge whose corresponding points satisfy our desired relationship. Clique detection has been widely studied and there exist efficient algorithms. In this paper we study a related problem, where all points have a set of binary attributes, each of which is either 0 or 1. This is only a small limitation, since all discrete properties can be mapped onto binary attributes. In our case, we want to find large sets of points not only satisfying some mutual relationship; but, in addition, all points of a set also need to have at least one common attribute with value 1. The problem we described can be mapped onto a set of induced subgraphs, where each subgraph represents a single attribute. For attribute $i$, its associated subgraph contains those vertices corresponding to the points with attribute $i$ set to 1. We introduce the notion of a maximal clique of a family, $\mathcal{G}$, of induced subgraphs of an undirected graph, and show that determining all maximal cliques of $\mathcal{G}$ solves our problem. Furthermore, we present an efficient algorithm to compute all maximal cliques of $\mathcal{G}$. The algorithm we propose is an extension of the widely used Bron-Kerbosch algorithm.
    Keywords: ddc:000
    Language: English
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  • 4
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    An Integer Programming Model for Multi-Layer Network Design (2004)
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    Publication Date: 2014-02-26
    Description: We present an integer linear programming model for the design of multi-layer telecommunication networks. The formulation integrates hardware, capacity, routing, and grooming decisions in \emph{any} n umber of network layers. Practical hardware restrictions and cost can accurately be taken into account for technologies based on connection-oriented routing protocols.
    Keywords: ddc:000
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  • 5
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    Compressing Triangle Meshes using Geometric Infomation (2004)
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    Publication Date: 2014-02-26
    Description: We introduce FreeLence, a lossless single-rate connectivity compression algorithm for triangle surface meshes. Based upon a geometry-driven traversal scheme we present two novel and simple concepts: free-valence connectivity encoding and entropy coding based on geometric context. Together these techniques yield significantly smaller rates for connectivity compression than current state of the art approaches - valence-based algorithms and Angle- Analyzer, with an average of $36\%$ improvement over the former and an average of $18\%$ over the latter on benchmark 3D models, combined with the ability to well adapt to the regularity of meshes. We also prove that our algorithm exhibits a smaller worst case entropy for a class of "'well-behaved"' triangle meshes than valence-driven connectivity encoding approaches.
    Keywords: ddc:000
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  • 6
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    Jahresbericht 2003 (2004)
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    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
    Type: annualzib , doc-type:report
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  • 7
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    Large-scale hierarchical networks: How to compute an optimal architecture? (2004)
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    Publication Date: 2020-02-11
    Description: In this article, we present a mathematical model and an algorithm to support one of the central strategic planning decisions of network operators: How to organize a large number of locations into a hierarchical network? We propose a solution approach that is based on mixed-integer programming and Lagrangian relaxation techniques. As major advantage, our approach provides not only solutions but also worst-case quality guarantees. Real-world scenarios with more than 750 locations have been solved within 30 minutes to less than 1\% off optimality.
    Keywords: ddc:000
    Language: English
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  • 8
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    UMTS Radio Network Evaluation and Optimization beyond Snapshots (2004)
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    Publication Date: 2020-02-11
    Description: This paper is concerned with UMTS radio network design. Our task is to reconfigure antennas and the related cells as to improve network quality. In contrast to second generation GSM networks, \emph{interference} plays a paramount role when designing third generation radio networks. A known compact formulation for assessing the interference characteristics of a radio network as coupling relations between cells based on user snapshots is generalized to statistical average load. This enables us to overcome the notorious difficulties of snapshot-based network optimization approaches. We recall a mixed-integer programming model for the network design problem that is based on user snapshots and contrast it with a new network design model based on the average coupling formulation. Exemplarily focusing on the important problem of optimizing antenna tilts, we give computational results for a fast local search algorithm and the application of a MIP solver to both models. These results demonstrate that our new average-based approaches outperform state-of-the-art snapshot models for UMTS radio network optimization.
    Keywords: ddc:000
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  • 9
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    SCIP - a framework to integrate Constraint and Mixed Integer Programming (2004)
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    Publication Date: 2021-08-05
    Description: Constraint Programs and Mixed Integer Programs are closely related optimization problems originating from different scientific areas. Today's state-of-the-art algorithms of both fields have several strategies in common, in particular the branch-and-bound process to recursively divide the problem into smaller sub problems. On the other hand, the main techniques to process each sub problem are different, and it was observed that they have complementary strenghts. We propose a programming framework {\sffamily SCIP} that integrates techniques from both fields in order to exploit the strenghts of both, Constraint Programming and Mixed Integer Programming. In contrast to other proposals of recent years to combine both fields, {\sffamily SCIP} does not focus on easy implementation and rapid prototyping, but is tailored towards expert users in need of full, in-depth control and high performance.
    Keywords: ddc:000
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  • 10
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    Searching and Classifying Differential Equations on the Web (2004)
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    Publication Date: 2018-12-06
    Description: In this paper we describe the semantic analysis of differential equations given in the ubiquitous semi-structured formats MathML and OpenMath. The analysis is integrated in a deployed Web indexing framework. Starting from basic classifications for differential equations the proposed system architecture is amenable to extensions for further reconstruction of mathematical content on the Web. The syntactic analysis of mathematical formulae given in the considered formats must overcome ambiguities that stem from the fact that formula particles may have different encodings, which are in principle completely arbitrary. However, it turns out that the syntactic analysis can be done straightforward given some natural heuristic assumptions.
    Keywords: ddc:000
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  • 11
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    Anisotropic Filtering of Non-Linear Surface Features (2004)
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    Publication Date: 2014-02-26
    Description: A new method for noise removal of arbitrary surfaces meshes is presented which focuses on the preservation and sharpening of non-linear geometric features such as curved surface regions and feature lines. Our method uses a prescribed mean curvature flow (PMC) for simplicial surfaces which is based on three new contributions: 1. the definition and efficient calculation of a discrete shape operator and principal curvature properties on simplicial surfaces that is fully consistent with the well-known discrete mean curvature formula, 2. an anisotropic discrete mean curvature vector that combines the advantages of the mean curvature normal with the special anisotropic behaviour along feature lines of a surface, and 3. an anisotropic prescribed mean curvature flow which converges to surfaces with an estimated mean curvature distribution and with preserved non-linear features. Additionally, the PMC flow prevents boundary shrinkage at constrained and free boundary segments.
    Keywords: ddc:000
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  • 12
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    Function space interior point methods for PDE constrained optimization (2004)
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    Publication Date: 2019-01-29
    Description: A primal-dual interior point method for optimal control problems with PDE constraints is considered. The algorithm is directly applied to the infinite dimensional problem. Existence and convergence of the central path are analyzed. Numerical results from an inexact continuation method applied to a model problem are shown.
    Keywords: ddc:000
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  • 13
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    Zusammenarbeit mit vascoda im Rahmen des Verteilten Dokumentenservers (VDS) (2004)
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    Publication Date: 2014-02-26
    Description: Die in der Arbeitsgemeinschaft der Verbundsysteme zusammengeschlossenen deutschen Verbundsysteme kooperieren zur Realisierung eines die Länder und Verbundregionen übergreifenden offenen Netzwerkes einer offenen digitalen Bibliothek, dem Verteilten Dokumentenserver (VDS). Wesentliche Bestandteile des VDS sind die in den lokalen Bibliotheken und Verbundsystemen verteilten Dokumentenspeicher. Beim Aufbau des VDS verfolgen die deutschen Verbundsysteme für ihre digitalen Ressourcen, Zeitschriften und Dokumente, folgende Ziele [AGV03]: \begin{itemize} \item{Erhalt und dauerhafte Sicherung einmal erworbener Rechte} \item{Bessere Erschließung und Integration in das eigene Angebot} \item{Nahtlose Navigation in lokalen Zeitschriften- und Dokumentenservern und zwischen digitalen Artikeln und Zeitschriften, Dokumenten und Servern} \item{Dauerhafte Sicherung des Zugriffs und perspektivisch Langzeitverfügbarkeit} \end{itemize} Die Verbundsysteme streben an, die Speicherung, Erschließung und das Angebot ihrer digitalen Materialien in einer nationalen Kooperation durchzuführen. Sie entwickeln und betreiben zu diesem Zweck Portal- und Querschnittstechnologien zur Integration ihrer dezentral gespeicherten digitalen Ressourcen mittels Internet-Technologien.
    Keywords: ddc:000
    Language: German
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  • 14
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    Utility Proportional Fair Bandwidth Allocation - An Optimization Oriented Approach (2004)
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    Publication Date: 2014-02-26
    Description: In this paper, we present a novel approach to the congestion control and resource allocation problem of elastic and real-time traffic in telecommunication networks. With the concept of utility functions, where each source uses a utility function to evaluate the benefit from achieving a transmission rate, we interpret the resource allocation problem as a global optimization problem. The solution to this problem is characterized by a new fairness criterion, \e{utility proportional fairness}. We argue that it is an application level performance measure, i.e. the utility that should be shared fairly among users. As a result of our analysis, we obtain congestion control laws at links and sources that are globally stable and provide a utility proportional fair resource allocation in equilibrium. We show that a utility proportional fair resource allocation also ensures utility max-min fairness for all users sharing a single path in the network. As a special case of our framework, we incorporate utility max-min fairness for the entire network. To implement our approach, neither per-flow state at the routers nor explicit feedback beside ECN (Explicit Congestion Notification) from the routers to the end-systems is required.
    Keywords: ddc:000
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  • 15
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    Die Mathematik der kürzesten Wege. Inhalte und Methoden für den Unterricht (2004)
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    Publication Date: 2014-02-26
    Description: Wie findet man den optimalen Weg im U-Bahnnetz? Das Problem wird als Graph modelliert und dann eine Breitensuche durchgeführt. Will man Weglängen oder Fahrzeiten mitberücksichtigen, so braucht man den Algorithmus von Dijkstra für gewichtige Graphen. Beim Nachdenken über diese Algorithmen werden auch Fragestellungen der Graphentheorie berührt. In einem zweiten Abschnitt werden methodische Hinweise für den Unterricht in der Sekundarstufe I und II gegeben, insbesondere, wie man Lernende dazu bringen kann, ihre Ideen für Algorithmen präzise zu analysieren und zu Papier zu bringen.
    Keywords: ddc:000
    Language: German
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  • 16
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    Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data (2004)
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    Publication Date: 2014-02-26
    Description: The problem of clustering data can be formulated as a graph partitioning problem. Spectral methods for obtaining optimal solutions have reveceived a lot of attention recently. We describe Perron Cluster Cluster Analysis (PCCA) and, for the first time, establish a connection to spectral graph partitioning. We show that in our approach a clustering can be efficiently computed using a simple linear map of the eigenvector data. To deal with the prevalent problem of noisy and possibly overlapping data we introduce the min Chi indicator which helps in selecting the number of clusters and confirming the existence of a partition of the data. This gives a non-probabilistic alternative to statistical mixture-models. We close with showing favorable results on the analysis of gene expressi on data for two different cancer types.
    Keywords: ddc:000
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  • 17
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    Linear Programming Lower Bounds for Minimum Converter Wavelength Assignment in Optical Networks (2004)
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    Publication Date: 2014-02-26
    Description: In this paper, we study the conflict-free assignment of wavelengths to lightpaths in an optical network with the opportunity to place wavelength converters. To benchmark heuristics for the problem, we develop integer programming formulations and study their properties. Moreover, we study the computational performance of the column generation algorithm for solving the linear relaxation of the most promising formulation. In many cases, a non-zero lower bound on the number of required converters is generated this way. For several instances, we in fact prove optimality since the lower bound equals the best known solution value.
    Keywords: ddc:000
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  • 18
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    On PDE Solution in Transient Optimization of Gas Networks (2004)
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    Publication Date: 2021-02-01
    Description: Operative planning in gas distribution networks leads to large-scale mixed-integer optimization problems involving a hyperbolic PDE defined on a graph. We consider the NLP obtained under prescribed combinatorial decisions---or as relaxation in a branch and bound framework, addressing in particular the KKT systems arising in primal-dual interior methods. We propose a custom solution algorithm using sparse local projections, based on the KKT systems' structual properties induced by the discretized gas flow equations in combination with the underlying network topology. The numerical efficiency and accuracy of the algorithm are investigated, and detailed computational comparisons with a control space method and with the multifrontal solver MA27 are provided.
    Keywords: ddc:000
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  • 19
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    Optimization Models for Operative Planning in Drinking Water Networks (2004)
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    Publication Date: 2021-02-01
    Description: The topic of this paper is minimum cost operative planning of pressurized water supply networks over a finite horizon and under reliable demand forecast. Since this is a very hard problem, it is desirable to employ sophisticated mathematical algorithms, which in turn calls for carefully designed models with suitable properties. The paper develops a nonlinear mixed integer model and a nonlinear programming model with favorable properties for gradient-based optimization methods, based on smooth component models for the network elements. In combination with further nonlinear programming techniques (to be reported elsewhere), practically satisfactory near-optimum solutions even for large networks can be generated in acceptable time using standard optimization software on a PC workstation. Such an optimization system is in operation at Berliner Wasserbetriebe.
    Keywords: ddc:000
    Language: English
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  • 20
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    Unterrichtsideen zu Algorithmen der kombinatorischen Optimierung (2004)
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    Publication Date: 2014-02-26
    Description: Im Rahmen von Problemstellungen der kombinatorischen Optimierung können Schülerinnen und Schüler lernen, Algorithmen selber zu entwickeln. Gleichzeitig lernen sie dabei moderne Mathematik in ihren Anwendungen kennen und erleben die Mathematik als lebendige Wissenschaft.
    Keywords: ddc:000
    Language: German
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  • 21
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    Computing Optimal Morse Matchings (2004)
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    Publication Date: 2020-12-15
    Description: Morse matchings capture the essential structural information of discrete Morse functions. We show that computing optimal Morse matchings is NP-hard and give an integer programming formulation for the problem. Then we present polyhedral results for the corresponding polytope and report on computational results.
    Keywords: ddc:000
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  • 22
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    Provably Good Solutions for Wavelength Assignment in Optical Networks (2004)
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    Publication Date: 2014-02-26
    Description: In this paper, we study the minimum converter wavelength assignment problem in optical networks. To benchmark the quality of solutions obtained by heuristics, we derive an integer programming formula tion by generalizing the formulation of Mehrotra and Trick (1996) for the vertex coloring problem. To handle the exponential number of variables, we propose a column generation approach. Computational experiments show that the value of the linear relaxation states a good lower bound and can often prove optimality of the best solution generated heuristically.
    Keywords: ddc:000
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  • 23
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    A Note on Contraction Degeneracy (2004)
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    Publication Date: 2014-11-10
    Description: The parameter contraction degeneracy -- the maximum minimum degree over all minors of a graph -- is a treewidth lower bound and was first defined in (Bodlaender, Koster, Wolle, 2004). In experiments it was shown that this lower bound improves upon other treewidth lower bounds. In this note, we examine some relationships between the contraction degeneracy and connected components of a graph, block s of a graph and the genus of a graph. We also look at chordal graphs, and we study an upper bound on the contraction degeneracy and another lower bound for treewidth. A data structure that can be used for algorithms computing the degeneracy and similar parameters, is also described.
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  • 24
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    On the Maximum Cardinality Search Lower Bound for Treewidth (2004)
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    Publication Date: 2014-11-10
    Description: The Maximum Cardinality Search algorithm visits the vertices of a graph in some order, such that at each step, an unvisited vertex that has the largest number of visited neighbors becomes visited. An MCS-ordering of a graph is an ordering of the vertices that can be generated by the Maximum Cardinality Search algorithm. The visited degree of a vertex $v$ in an MCS-ordering is the number of neighbors of $v$ that are before $v$ in the ordering. The visited degree of an MCS-ordering $\psi$ of $G$ is the maximum visited degree over all vertices $v$ in $\psi$. The maximum visited degree over all MCS-orderings of graph $G$ is called its {\em maximum visited degree}. Lucena (2003) showed that the treewidth of a graph $G$ is at least its maximum visited degree. We show that the maximum visited degree is of size $O(\log n)$ for planar graphs, and give examples of planar graphs $G$ with maximum visited degree $k$ with $O(k!)$ vertices, for all $k\in \Bbb{N}$. Given a graph $G$, it is NP-complete to determine if its maximum visited degree is at least $k$, for any fixed $k\geq 7$. Also, this problem does not have a polynomial time approximation algorithm with constant ratio, unless P=NP. Variants of the problem are also shown to be NP-complete. We also propose and experimentally analyses some heuristics for the problem. Several tiebreakers for the MCS algorithm are proposed and evaluated. We also give heuristics that give upper bounds on the value of the maximum visited degree of a graph, which appear to give results close to optimal on many graphs from real life applications.
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  • 25
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    A new Model for the Free Energy of Solvation and its Application in Protein Ligand Scoring (2004)
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    Publication Date: 2014-02-26
    Description: A new and time efficient model to evaluate the free energy of solvation has been developed. The solvation free energy is separated into an electrostatic term, a hydrogen bond term, and a rest-term, combining both entropic and van der Waals effects. The electrostatic contribution is evaluated with a simplified boundary element method using the partial charges of the MMFF94 force field. The number of hydrogen bonds and the solvent excluded surface area over the surface atoms are used in a linear model to estimate the non-electrostatic contribution. This model is applied to a set of 213 small and mostly organic molecules, yielding an rmsd of 0.87kcal/mol and a correlation with experimental data of r=0.951. The model is applied as a supplementary component of the free energy of binding to estimate binding constants of protein ligand complexes. The intermolecular interaction energy is evaluated by using the MMFF94 force field.
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  • 26
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    Multiple Semi-flexible 3D Superposition of Drug-sized Molecules (2004)
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    Publication Date: 2020-03-06
    Description: In this paper we describe a new algorithm for multiple semi-flexible superpositioning of drug-sized molecules. The algorithm identifies structural similarities of two or more molecules. When comparing a set of molecules on the basis of their three-dimensional structures, one is faced with two main problems. (1) Molecular structures are not fixed but flexible, i.e., a molecule adopts different forms. To address this problem, we consider a set of conformers per molecule. As conformers we use representatives of conformational ensembles, generated by the program ZIBMol. (2) The degree of similarity may vary considerably among the molecules. This problem is addressed by searching for similar substructures present in arbitrary subsets of the given set of molecules. The algorithm requires to preselect a reference molecule. All molecules are compared to this reference molecule. For this pairwise comparison we use a two-step approach. Clique detection on the correspondence graph of the molecular structures is used to generate start transformations, which are then iteratively improved to compute large common substructures. The results of the pairwise comparisons are efficiently merged using binary matching trees. All common substructures that were found, whether they are common to all or only a few molecules, are ranked according to different criteria, such as number of molecules containing the substructure, size of substructure, and geometric fit. For evaluating the geometric fit, we extend a known scoring function by introducing weights which allow to favor potential pharmacophore points. Despite considering the full atomic information for identifying multiple structural similarities, our algorithm is quite fast. Thus it is well suited as an interactive tool for the exploration of structural similarities of drug-sized molecules.
    Keywords: ddc:000
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    Data Management for Processing Molecules (2004)
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    Publication Date: 2014-02-26
    Description: Molecular dynamics simulations of possible ligands for proteins yield large amounts of data in the form of trajectories which are further processed in order to find metastable conformations. These conformations can then be used for docking between ligand and protein. Around this core computation procedure lots of other data have to be managed. It should also be possible for external users not involved in program development to perform computations. As a paradigm for other fields where a similar constitution of program usage and data processing is found we present a software architecture for data generation, access and management. Requirements for this system include: Ease of use, graphical user interface, persistent storage of data concerning molecules, users, programs, program parameters, metadata, and results. A mere storage in the file system would render a quick overview of data more or less impossible. On the other hand, storing large amounts of binary data in a database doesn't yield any advantage concerning speed of access. Therefore, a hybrid approach combining file system and database is appropriate. The system should be easily extensible by inserting new applications which can be controlled and whose results can be collected and stored. The software system described here consists of different components, the presentation layer (graphical user interface), the business logic, the persistence layer (relational database plus file system), and an interface to the compute cluster (batch system for parallel processing). We will discuss the alternatives and take a closer look at the components.
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    Visual Analysis of Molecular Conformations by Means of a Dynamic Density Mixture Model (2004)
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    Publication Date: 2020-03-09
    Description: We propose an approach for transforming the sampling of a molecular conformation distribution into an analytical model based on Hidden Markov Models. The model describes the sampled shape density as a mixture of multivariate unimodal densities. Thus, it delivers an interpretation of the sampled density as a set of typical shapes that appear with different probabilities and are characterized by their geometry, their variability and transition probabilities between the shapes. The gained model is used to identify atom groups of constant shape that are connected by metastable torsion angles. Based on this description an alignment for the original sampling is computed. As it takes into account the different shapes contained in the sampled set, this alignment allows to compute reasonable average shapes and meaningful shape density plots. Furthermore, it enables us to visualize typical conformations.
    Keywords: ddc:000
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    MOMENTUM Data Scenarios for Radio Network Planning and Simulation (Extended Abstract) (2004)
    Details
    Publication Date: 2020-02-11
    Description: We present publicly available data sets related to research on wireless networks. The scenarios contain a wide range of data and are detailed in all aspects. To our knowledge, this is the most realistic, comprehensive, and detailed \emph{public} data collection on mobile networking. We indicate example uses of this data collection in applications related tu UMTS.
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    Models for Line Planning in Public Transport (2004)
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    Publication Date: 2020-12-15
    Description: The \emph{line planning problem} is one of the fundamental problems in strategic planning of public and rail transport. It consists of finding lines and corresponding frequencies in a public transport network such that a given travel demand can be satisfied. There are (at least) two objectives. The transport company wishes to minimize its operating cost; the passengers request short travel times. We propose two new multi-commodity flow models for line planning. Their main features, in comparison to existing models, are that the passenger paths can be freely routed and that the lines are generated dynamically.
    Keywords: ddc:000
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    Triangulated Manifolds with Few Vertices: Centrally Symmetric Spheres and Products of Spheres (2004)
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    Publication Date: 2014-02-26
    Description: The aim of this paper is to give a survey of the known results concerning centrally symmetric polytopes, spheres, and manifolds. We further enumerate nearly neighborly centrally symmetric spheres and centrally symmetric products of spheres with dihedral or cyclic symmetry on few vertices, and we present an infinite series of vertex-transitive nearly neighborly centrally symmetric 3-spheres.
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    Anisotropic Simulation of the Human Mandible (2004)
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    Publication Date: 2019-05-10
    Description: We focus on the role of anisotropic elasticity in the simulation of the load distribution in a human mandible due to a lateral bite on the leftmost premolar. Based on experimental evidence, we adopt ``local''" orthotropy of the elastic properties of the bone tissue. Since the trajectories of anisotropic elasticity are not accessible from Computer Tomographic (CT) data, they will be reconstructed from (i) the organ's geometry and (ii) from coherent structures which can be recognized from the spatial distribution of the CT values. A sensitivity analysis comprising various 3D FE simulations reveals the relevance of elastic anisotropy for the load carrying behavior of a human mandible: Comparison of the load distributions in isotropic and anisotropic simulations indicates that anisotropy seems to ``spare''" the mandible from loading. Moreover, a maximum degree of anisotropy leads to kind of an load minimization of the mandible, expressed by a minimum of different norms of local strain, evaluated throughout the organ. Thus, we may suggest that anisotropy is not only relevant, but also in some sense ``optimal''.
    Keywords: ddc:000
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    Affine conjugate adaptive Newton methods for nonlinear elastomechanics (2004)
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    Publication Date: 2019-05-10
    Description: The paper extends affine conjugate Newton methods from convex to nonconvex minimization, with particular emphasis on PDE problems originating from compressible hyperelasticity. Based on well-known schemes from finite dimensional nonlinear optimization, three different algorithmic variants are worked out in a function space setting, which permits an adaptive multilevel finite element implementation. These algorithms are tested on two well-known 3D test problems and a real-life example from surgical operation planning.
    Keywords: ddc:000
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    A Geometrical Characterization of the Multidimensional Hausdorff and Dale Polytopes with Applications to Exit Time Problems (2004)
    Details
    Publication Date: 2014-02-26
    Description: We present formulae for the corner points of the multidimensional Hausdorff and Dale Polytopes and show how these results can be used to improve linear programming models for computing e.\,g.\ moments of exit distribution of diffusion processes. Specifically, we compute the mean exit time of twodimensional Brownian motion from the unit square and the unit triangle, as well as higher moments of the exit time of time space Brownian motion from a triangle.
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    The Normal Graph Conjecture is true for Circulants (2004)
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    Publication Date: 2014-11-10
    Description: Normal graphs are defined in terms of cross-intersecting set families: a graph is normal if it admits a clique cover $\cal Q$ and a stable set cover $\cal S$ s.t.~every clique in $\cal Q$ intersects every stable set in $\cal S$. Normal graphs can be considered as closure of perfect graphs by means of co-normal products (Körner 1973) and graph entropy (Czisz\'ar et al. 1990). Perfect graphs have been recently characterized as those graphs without odd holes and odd antiholes as induced subgraphs (Strong Perfect Graph Theorem, Chudnovsky et al. 2002). Körner and de Simone observed that $C_5$, $C_7$, and $\overline C_7$ are minimal not normal and conjectured, as generalization of the Strong Perfect Graph Theorem, that every $C_5$, $C_7$, $\overline C_7$- free graph is normal (Normal Graph Conjecture, Körner and de Simone 1999). We prove this conjecture for a first class of graphs that generalize both odd holes and odd antiholes, the circulants, by characterizing all the normal circulants.
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    One-Point Suspensions and Wreath Products of Polytopes and Spheres (2004)
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    Publication Date: 2014-02-26
    Description: It is known that the suspension of a simplicial complex can be realized with only one additional point. Suitable iterations of this construction generate highly symmetric simplicial complexes with a various interesting combinatorial and topological properties. In particular, infinitely many non-PL spheres as well as contactible simplicial complexes with a vertex-transitive group of automorphisms cab be contained in this way.
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    Segmentation of the Liver using a 3D Statistical Shape Model (2004)
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    Publication Date: 2020-03-10
    Description: This paper presents an automatic approach for segmentation of the liver from computer tomography (CT) images based on a 3D statistical shape model. Segmentation of the liver is an important prerequisite in liver surgery planning. One of the major challenges in building a 3D shape model from a training set of segmented instances of an object is the determination of the correspondence between different surfaces. We propose to use a geometric approach that is based on minimizing the distortion of the correspondence mapping between two different surfaces. For the adaption of the shape model to the image data a profile model based on the grey value appearance of the liver and its surrounding tissues in contrast enhanced CT data was developed. The robustness of this method results from a previous nonlinear diffusion filtering of the image data. Special focus is turned to the quantitative evaluation of the segmentation process. Several different error measures are discussed and implemented in a study involving more than 30 livers.
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    Branching rules revisited (2004)
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    Publication Date: 2021-08-05
    Description: Mixed integer programs are commonly solved with linear programming based branch-and-bound algorithms. The success of the algorithm strongly depends on the strategy used to select the variable to branch on. We present a new generalization called {\sl reliability branching} of today's state-of-the-art {\sl strong branching} and {\sl pseudocost branching} strategies for linear programming based branch-and-bound algorithms. After reviewing commonly used branching strategies and performing extensive computational studies we compare different parameter settings and show the superiority of our proposed newstrategy.
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    A Bundle Method for Integrated Multi-Depot Vehicle and Duty Scheduling in Public Transit (2004)
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    Publication Date: 2020-03-09
    Description: This article proposes a Lagrangean relaxation approach to solve integrated duty and vehicle scheduling problems arising in public transport. The approach is based on the proximal bundle method for the solution of concave decomposable functions, which is adapted for the approximate evaluation of the vehicle and duty scheduling components. The primal and dual information generated by the bundle method is used to guide a branch-and-bound type algorithm. Computational results for large-scale real-world integrated vehicle and duty scheduling problems with up to 1,500 timetabled trips are reported. Compared with the results of a classical sequential approach and with reference solutions, integrated scheduling offers remarkable potentials in savings and drivers' satisfaction.
    Keywords: ddc:000
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    Adaptive Finite Element Simulation of the Human Mandible Using a New Physiological Model of the Masticatory Muscles (2004)
    Details
    Publication Date: 2019-05-10
    Description: Structural mechanics simulation of bony organs is of general medical and biomechanical interest, because of the interdependence of the inner architecture of bone and its functional loading already stated by Wolff in 1892. This work is part of a detailed research project concerning the human mandible. By adaptive finite element techniques, stress/strain profiles occurring in the bony structure under biting were simulated. Estimates of the discretization errors, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. In general, our simulation requires a representation of the organ's geometry, an appropriate material description, and the load case due to teeth, muscle, or joint forces. In this paper, we want to focus on the influence of the masticatory system. Our goal is to capture the physiological situation as far as possible. By means of visualization techniques developed by the group, we are able to extract individual muscle fibres from computed tomography data. By a special algorithm, the fibres are expanded to fanlike (esp. for the musc. temporalis) coherent vector fields similar to the anatomical reality. The activity of the fibres can be adapted according to compartmentalisation of the muscles as measured by electromyological experiments. A refined sensitivity analysis proved remarkable impact of the presented approach on the simulation results.
    Keywords: ddc:000
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    KKT Systems in Operative Planning for Gas Distribution Networks (2004)
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    Publication Date: 2021-02-01
    Description: Operative planning in gas networks with prescribed binary decisions yields large scale nonlinear programs defined on graphs. We study the structure of the KKT systems arising in interior methods and present a customized direct solution algorithm. Computational results indicate that the algorithm is suitable for optimization in small and medium-sized gas networks.
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    Indexierung von Online-Katalogen: Ein gemeinsames Konzept der ALEPH-Anwender in Berlin (2004)
    Details
    Publication Date: 2021-02-05
    Description: Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) verzichtet auf eine einheitliche zentrale Verbunddatenbank zugunsten einer dezentralen, verteilten Struktur. In dieser Architektur erhält die Art der Indexierung der angesprochenen Online-Kataloge eine besondere Bedeutung. So werden sowohl Bibliotheksmitarbeiter als auch Bibliotheksbenutzer immer wieder mit der Recherche in fremden Katalogen konfrontiert, in denen unterschiedliche Indexierungsverfahren realisiert sein können. Ein abgestimmtes Indexierungskonzept verfolgt zwei grundsätzliche Ziele. Einerseits soll durch eine vereinheitlichte Indexierung die Qualität und Zuverlässigkeit der Rechercheergebnisse in der parallelen Suche in mehreren Katalogen über die KOBV-Suchmaschine erhöht werden. Gleichzeitig soll durch eine vereinheitlichte Indexierung die Akzeptanz von Suchen in entfernten Katalogen prinzipiell gesteigert und damit die Bedingungen für die gegenseitige Übernahme von Titeldaten erleichtert werden. Für die Indexierung muss zunächst die Art und der Umfang der im OPAC aufzubauenden Indices festgelegt werden. Aus Sicht des Nutzers entspricht diese Definition den möglichen Sucheinstiegen. Hat man dann entschieden, welche Indexterme aus welchen Feldern in die jeweiligen Indices einfließen sollen, muss bestimmt werden, nach welchen Regeln die Terme behandelt werden. Hier stellt sich insbesondere das Problem der Sonderzeichen wie Bindestriche, Apostrophe und Punkte oder Ziffern in Zeichenketten. Das vorliegende Konzept entstand in Zusammenarbeit der großen Universitätsbibliotheken in Berlin (der Freien Universität, der Humboldt-Universität, der Technischen Universität, der Universität der Künste) mit der KOBV-Verbundzentrale am ZIB.
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    Language: German
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    Integrable quadratic Hamiltonians on so(4) and so(3,1) (2004)
    Details
    Publication Date: 2014-02-26
    Description: We investigate a special class of quadratic Hamiltonians on $so(4)$ and $so(3,1)$ and describe Hamiltonians that have additional polynomial integrals. One of the main results is a new integrable case with an integral of sixth degree.
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    Holes, Antiholes and Maximal Cliques in a Railway Model for a Single Track (2004)
    Details
    Publication Date: 2020-11-16
    Description: We present a graph theoretical model for scheduling trains on a single unidirectional track between two stations. The set of departures of all possible train types at all possible (discrete) points of time is turned into an undirected graph $\Gneu$ by joining two nodes if the corresponding departures are in conflict. This graph $\Gneu$ has no odd antiholes and no $k$-holes for any integer $k\geq 5$. In particular, any finite, node induced subgraph of $\Gneu$ is perfect. For any integer $r\geq 2$ we construct minimal headways for $r$ train types so that the resulting graph $\Gneu$ has $2r$-antiholes and $4$-holes at the same time. Hence, $\Gneu$ is neither a chordal graph nor the complement of a chordal graph, in general. At the end we analyse the maximal cliques in $G$.
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    Robust Process Control by Dynamic Stochastic Programming (2004)
    Details
    Publication Date: 2021-02-01
    Description: Unnecessarily conservative behavior of standard process control techniques can be avoided by stochastic programming models when the distribution of random disturbances is known. In an earlier study we have investigated such an approach for tank level constraints of a distillation process. Here we address techniques that have accelerated the numerical solution of the large and expensive stochastic programs by a factor of six, and then present a refined optimization model for the same application.
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    The Effect of Hop Limits on Optimal Cost in Survivable Network Design (2004)
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    Publication Date: 2014-02-26
    Description: We investigate the impact of hop-limited routing paths on the total cost of a telecommunication network. For different survivability settings (dedicated protection, link and path restoration), the optimal network cost without restrictions on the admissible path set is compared to the results obtained with two strategies to impose hop limits on routing paths. In a thorough computational study on optimal solutions for nine real-world based problem instances, we show that hop limits should be avoided if the technology allows it and network cost is a major planning issue. In this case, column generation should be employed to deal with all routing paths. If hop-limits are required, these should be defined for each demand individually and as large as possible.
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    Reoptimization Gaps versus Model Errors in Online-Dispatching of Service Units for ADAC (2004)
    Details
    Publication Date: 2020-11-13
    Description: Under high load, the automated dispatching of service vehicles for the German Automobile Association (ADAC) must reoptimize a dispatch for 100--150 vehicles and 400 requests in about ten seconds to near optimality. In the presence of service contractors, this can be achieved by the column generation algorithm ZIBDIP. In metropolitan areas, however, service contractors cannot be dispatched automatically because they may decline. The problem: a model without contractors yields larger optimality gaps within ten seconds. One way-out are simplified reoptimization models. These compute a short-term dispatch containing only some of the requests: unknown future requests will influence future service anyway. The simpler the models the better the gaps, but also the larger the model error. What is more significant: reoptimization gap or reoptimization model error? We answer this question in simulations on real-world ADAC data: only the new model ZIBDIP{\footnotesize dummy} can keep up with ZIBDIP.
    Keywords: ddc:000
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    Contraction and Treewidth Lower Bounds (2004)
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    Publication Date: 2020-11-13
    Description: Edge contraction is shown to be a useful mechanism to improve lower bound heuristics for treewidth. A successful lower bound for treewidth is the degeneracy: the maximum over all subgraphs of the minimum degree. The degeneracy is polynomial time computable. We introduce the notion of contraction degeneracy: the maximum over all minors of the minimum degree. We show that the contraction degeneracy problem is NP-complete, even for bipartite graphs, but for fixed $k$, it is polynomial time decidable if a given graph $G$ has contraction degeneracy at least $k$. Heuristics for computing the contraction degeneracy are proposed and evaluated. It is shown that these can lead in practice to considerable improvements of the lower bound for treewidth, but can perform arbitrarily bad on some examples. A study is also made for the combination of contraction with Lucena's lower bound based on Maximum Cardinality Search (Lucena, 2003). Finally, heuristics for the treewidth are proposed and! evaluated that combine contraction with a treewidth lower bound technique by Clautiaux et al (2003).
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    Das KOBV-Portal, elektronische Ressourcen in Berlin-Brandenburg: Nachweis, parallele Suche und weiterführende Dienste (2004)
    Details
    Publication Date: 2020-11-13
    Description: \documentclass[12pt]{article} \usepackage{german} \parindent=0pt \begin{document} Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) hat in den Jahren 2001 bis 2003 im Rahmen des Entwicklungsprojektes ''KOBV-Informationsportal`` ein regionales Portal aufgebaut, in dem integrierte Informationsdienste fr die regionalen Bibliotheken zur Verfügung gestellt werden. Das ''KOBV-Portal - Digitale Bibliothek Berlin-Brandenburg`` wurde im Dezember 2003 in Betrieb genommen. Das KOBV-Portal bietet in seiner ersten Ausbaustufe den Nachweis über die in den großen Bibliotheken lizenzierten Ressourcen und elektronischen Zeitschriften, zudem die nahtlose Navigation mittels des Reference-Linking-Werkzeuges SFX zu verschiedenen Diensten wie Fernleihe, Subito und freien Volltexten im Internet sowie zu frei zugänglichen elektronischen Zeitschriften. Realisiert wurden ferner die Remote-Authentifizierung, mit der sich ein Nutzer, der online eine Fernleih-Bestellung aufgeben möchte, über das Internet in seiner Heimatbibliothek authentifizieren kann. Des weiteren ist der Zugriff auf lizenzierte Bestände im Campus einer Hochschule mittels IP-Checking möglich. Als weiteren wesentlichen Bestandteil des KOBV-Portals hat die KOBV-Zentrale mit den Bibliotheken einen Workflow für ein Metadata-Sharing abgestimmt und für die Adaption und Normalisierung lokaler Metadaten aus lokalen Bibliothekssystemen und -Portalen den KOBV-Metadaten-Austausch-Parser (KMA-Parser) entwickelt. Damit Bibliotheken, deren Metadaten bislang lediglich in unstrukturierter Form vorliegen, strukturierte Metadaten anlegen, liefern und nachnutzen können, hat die KOBV-Zentrale das mit einer Web-Katalogisierungsschnittstelle ausgestattete ''Metadata-Tool`` entwickelt. Die für das Metadata-Sharing entwickelten Komponenten und Module sollen den Bibliotheken die Mehrfacherfassung ersparen und ihnen die Möglichkeit der wechselseitigen Nachnutzung der Metadaten eröffnen. Der vorliegende Projekt-Abschlussbericht gibt einen Überblick über die während der Projektlaufzeit realisierten Dienste des KOBV-Portals. \end{document}
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    Wie komme ich optimal zum Ziel? Unterricht über kürzeste-Wege-Algorithmen für Graphen (2004)
    Details
    Publication Date: 2014-02-26
    Description: Kürzeste Wege tauchen fast überall im Alltag auf. Daher eignet sich dieses Optimierungsproblem gut für den Unterricht. Modellierung und heuristische Vorgehensweisen werden geübt, um schließlich die klassischen kürzesten Wege-Algorithmen selbst zu erfinden. In diesem Artikel werden die Inhalte vorgestellt und konkrete Hinweise zum Unterricht in der Schule gegeben.
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    Language: German
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    A Control Reduced Primal Interior Point Method for PDE Constrained Optimization (2004)
    Details
    Publication Date: 2019-01-29
    Description: A primal interior point method for control constrained optimal control problems with PDE constraints is considered. Pointwise elimination of the control leads to a homotopy in the remaining state and dual variables, which is addressed by a short step pathfollowing method. The algorithm is applied to the continuous, infinite dimensional problem, where discretization is performed only in the innermost loop when solving linear equations. The a priori elimination of the least regular control permits to obtain the required accuracy with comparable coarse meshes. Convergence of the method and discretization errors are studied, and the method is illustrated at two numerical examples.
    Keywords: ddc:000
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    Hierarchical Infrastructure Planning in Networks (2004)
    Details
    Publication Date: 2020-02-11
    Description: In this article, strategical infrastructure planning problems in the design of large-scale telecommunication networks are discussed based on experiences from three projects with industrial partners: The access network planning of the German Gigabit-Wissenschaftsnetz (G-WiN) for DFN (Verein zur Förderung eines Deutschen Forschungsnetzes e.V.), the mobile network switching center location planning project for E-Plus Mobilfunk, and the fixed network switching center location planning project for TELEKOM AUSTRIA. We introduce a mathematical model for a hierarchical multi-commodity capacitated facility location problem, present adaptions of this basic model to the specific requirements within the different projects and discuss the individual peculiarities and model decisions made. Eventually, we present and discuss computational results of three associated case studies, illustrating '"how we did the job`` with mathematical methods.
    Keywords: ddc:000
    Language: English
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    Degree-Based Treewidth Lower Bounds (2004)
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    Publication Date: 2014-11-10
    Description: Every lower bound for treewidth can be extended by taking the maximum of the lower bound over all subgraphs or minors. This extension is shown to be a very vital idea for improving treewidth lower bounds. In this paper, we investigate a total of nine graph parameters, providing lower bounds for treewidth. The parameters have in common that they all are the vertex-degree of some vertex in a subgra ph or minor of the input graph. We show relations between these graph parameters and study their computational complexity. To allow a practical comparison of the bounds, we developed heuristic algorithms for those parameters that are NP-hard to compute. Computational experiments show that combining the treewidth lower bounds with minors can considerably improve the lower bounds.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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    The convergence of an interior point method for an elliptic control problem with mixed control-state constraints (2004)
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    Publication Date: 2019-01-29
    Description: The paper addresses primal interior point method for state constrained PDE optimal control problems. By a Lavrentiev regularization, the state constraint is transformed to a mixed control-state constraint with bounded Lagrange multiplier. Existence and convergence of the central path are established, and linear convergence of a short-step pathfollowing method is shown. The behaviour of the regularizations are demonstrated by numerical examples.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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    Homogenization for a Nonlocal Coupling Model (2004)
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    Publication Date: 2014-02-26
    Description: In [7,8,12] homogenization techniques are applied to derive an anisotropic variant of the bio-heat transfer equation as asymptotic result of boundary value problems providing a microscopic description for microvascular tissue. In view of a future application on treatment planning in hyperthermia, we investigate here the homogenization limit for a coupling model, which takes additionally into account the influence of convective heat transfer in medium size blood vessels. This leads to second order elliptic boundary value problems with nonlocal boundary conditions on parts of the boundary. Moreover, we present asymptotic estimates for first order correctors.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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    Polynomial Inequalities Representing Polyhedra (2004)
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    Publication Date: 2014-02-26
    Description: Our main result is that every $n$-dimensional polytope can be described by at most $2n-1$ polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an $n$-dimensional pointed polyhedral cone we prove the bound $2n-2$ and for arbitrary polyhedra we get a constructible representation by $2n$ polynomial inequalities.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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    Das KOBV-Metadaten-Schema im KOBV-Portal (2004)
    Details
    Publication Date: 2023-10-05
    Description: Das KOBV-Metadaten-Schema ist von der KOBV-Zentrale entwickelt worden, um Ressourcen im Sinn von Informationskollektionen wie Datenbanken oder Fachportale zu beschreiben. Es ist ein wichtiger Bestandteil des KOBV-Portals, das die in der Region verf"ugbaren Ressourcen nachweist. Das KOBV-Metadaten-Schema dient den Bibliotheken zur Handreichung, um dem KOBV-Portal die Ressourcen mit den standardisierten und individuellen Angaben zu melden, so dass die Ressourcebeschreibungen einem austauschbaren Format entsprechen. Auf diese Weise k"onnen Ressourcebeschreibungen von anderen Bibliotheken mitgenutzt werden und ein Metadata-Sharing in der Region Berlin-Brandenburg praktiziert werden, um in diesem Bereich doppelte Arbeiten zu sparen.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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    Electronic Resource
    Electronic Resource
    Intermolecular localization of epitopes within an oligomeric protein by immunoelectron microscopy and image processing (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 161-183 
    Details
    ISSN: 0887-3585
    Keywords: hemocyanin ; correspondence analysis ; monoclonal antibodies ; electron microscopy ; images analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three epitopes have been localized by immunoelectron microscopy on subunits Aa6 of the 4 × 6-meric hemocyanin of the scorpion Androctonus australis. Soluble immunocomplexes composed of monoclonal antibodies and of native hemocyanin were purified, negatively stained with uranyle acetate by the single-layer technique, and examined under the electron microscope (EM). The molecule images were digitized, aligned, and submitted to correspondence analysis according to the method of Van Heel and Frank (Ultramicroscopy 6: 187-194, 1981). A high-precision localization of the attachment point of the Fab arm to the antigen was achieved through a careful analysis of the average images. This method easily allowed the discrimination of epitopes located in different domains (Mr 20 kDa) of the same subunit. Nonoverlapping epitopes located in the same structural domain of subunit Aa6 could be distinguished by the stain exclusion patterns of their Fab arms. The method is general and may be used for epitope mapping in any antigen producing definite EM views.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030305
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  • 59
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    Electronic Resource
    Crystallization and preliminary X-ray diffraction study of a protein with a high potential rubredoxin center and a hemerythrin-type Fe center (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 184-186 
    Details
    ISSN: 0887-3585
    Keywords: new Fe-protein ; rubredoxin ; hemerythrin ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A newly discovered iron-containing protein, isolated from the bacterium Desulfovibrio vulgaris (Hildenborough, NCIB 8303), has been crystallized. The molecule appears to be a dimer of mass 44kDa. This protein has iron centers with spectroscopic similarities to those in rubredoxins and in hemerythrins.The X-ray diffraction shows symmetry consistent with space group I222 or I212121. Cell parameters are a = 49.2 Å, b = 81.3 Å, c= 100.1 Å, and α, β, γ = 90°. X-ray diffraction data have been collected to 3.0 Å, and a search for useful heavy atom derivatives is in progress for the analysis of the crystal structure of this Fe-protein.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030306
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  • 60
    Electronic Resource
    Electronic Resource
    Lecithin: Cholesterol acyltransferase activation by synthetic amphipathic peptides (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 187-198 
    Details
    ISSN: 0887-3585
    Keywords: amphipathic peptide ; liposomes ; peptide ; serum apolipoproteins ; synthetic ; LCAT ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The amphipathic helical theory of Segrest and colleagues (FEBS Lett.: 38: 247-253, 1974) proposes that the lipid-binding segments of serum apolipoproteins are in an alpha helical conformation. Furthermore the helices have a hydrophobic face and a hydrophilic face with a specific distribution of positively and negatively charged residues. The importance of the pattern of the charged residues in the lipid binding and lecithin:cholesterol acyltransferase (LCAT) activation by the segments is still debated. We designed a 30-residue peptide, GALA, which in the alpha helical conformation hs a hydrophilic face composed of glutamic acid residues (Sabbarao et al.: Biochemistry 26: 2964-2972, 1987). GALA behaves like the serum apolipoproteins in its interaction with dimyristoylphospatidylcholine (DMPC) at neutral pH; the amino terminal tryptophan of GALA undergoes a blue shift in its fluorescence emission spectrum, and the circular dichroism (CD) spectrum indicates that GALA acquires alpha helical structure in the presence of DMPC. A DMPC-GALA:19/1 (molar ratio) complex can be isolated by gel-permeation chromatography. This complex has a discoidal structure with the approximate dimensions of 44-Å diameter. GALA edge thickness and a 170- to 350-Å diameter. GALA activates LCAT with DMPC but not with unsaturated phospholipids as the substrate. The apparent partition coefficient of GALA into DMPC vesicles is 100-fold larger than into egg phosphatidlylcholine vesicles. The interaction of GALA with unsaturated lipids at neutral pH is so weak that no detectable change in the spectroscopic properties of GALA or the structure of the liposomes can be detected under the conditions used here. The sequence of GALA differs from previously studied model Apo A1 peptides by the absence of positively charged residues on the hydrophilic face. This indicates that positive charges in Apo A1-like peptides are not required in order to form discoidal structures with saturated phospholipids or to activate LCAT with such lipid substrates.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030307
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    In memorium: Emil Thomas Kaiser, 1938-1988 (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040102
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  • 62
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    Photochemical crosslinking of bacteriophage T4 single-stranded DNA-binding protein (gp32) to oligo-p(dT)8: Identification of phenylalanine-183 as the site of crosslinking (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 1-6 
    Details
    ISSN: 0887-3585
    Keywords: single-standard DNA-binding protein ; protein-nucleic acid interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using ultraviolet light, both the 33,000-dalton single-standard DNA-binding protein from T4 bacteriophage (gp32)as well as a 25,000-dalton limited trypsin cleavage product of gp32 (core gp32*) that retains high affinity for single-stranded DNA can be crosslinked to an oligodeoxynucleotide, p(dT)8. After photolysis, a single tryptic peptide crosslinked to p(dT)8 was isolated by anion-exchange high-performance liquid chromatography. Gas-phase sequencing of this modified peptide gave the following sequence: Gln-Val-Ser-Gly-(X)-Ser-Asn-Tyr-Asp-Glu-Ser-Lys, which corresponds to residues 179-190 in gp32. Based on the absence of the expected phenylthiohydantoin derivative of phenylalanine 183 at cycle 5 (X) we infer that crosslinking has occurred at this position and that phenylalanine 183 is at the interface of the gp32:P(dT)8 complex in an orientation that allows covalent bond formation with the thymine radical produced by ultraviolet irradiation.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040103
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  • 63
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    Electronic Resource
    Structure-function relationships in 3-phosphoglycerate kinase: Role of the carboxy-terminal peptide (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 56-62 
    Details
    ISSN: 0887-3585
    Keywords: Protein engineering ; mutagenesis ; enzyme catalysis ; conformational changes ; domain movement ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Yeast 3-phosphoglycerate kinase (PGK) is a monomeric enzyme (Mr ∼ 45,000) composed of two globular domains. Each domain corresponds approximately to the amino- and carboxyterminal halves of the polypeptide chain. The carboxy-terminal end extends over the interdomain “hinge” region and packs against the amino-terminal domain. It has been proposed that domain movement, resulting in closure of the active site left, is essential for the catalytic of PGK. Large-scale conformational changes have also been postulated to explain activation of the enzyme by sulfate ions. Using site-specific mutagenesis, we have removed a 15-amino-acid carboxy-terminal fragment, in order to probe its role in the substrate- and sulfate-induced conformational changes. The truncated enzyme exhibited approximately 1% of the activity of native PGK and lost the ability to undergo sulfateinduced activation. The Km for ATP was essentially unchanged (Km = 0.23mM), whereas the Km value for 3-phosphoglycerate was increased about eightfold (Km = 3.85 mM and 0.50 mM, respectively). These results suggest that the carboxy-terminal segment is important for the mechanism of substrate- and specific-induced conformational transitions. CD spectra and sedimentation velocity measurements indicate that the carboxy-terminal peptide is essential for structural integrity of PGK. The increased susceptibility of the truncated enzyme to thermal inactivation implies that the carboxy-terminal peptide also contributes to the stability of PGK.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040108
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  • 64
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    Model of a complex between the tetrahemic cytochrome c3 and the ferredoxin I from Desulfovibrio desulfuricans (Norway strain) (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 63-70 
    Details
    ISSN: 0887-3585
    Keywords: molecular graphics ; protein complex ; electron transfer ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional model of an electron-transfer complex between the tetrahemic cytochrome c3 and the ferredoxin I from the sulfatereducing bacterium Desulfovibrio desulfuricans (Norway strain) has been generated through computer graphics methods. The model is based on the known X-ray structure of the cytochrome and on a model of the ferredoxin that has been derived through computer graphics modeling and energy minimization methods, from the X-ray structure of the homologous ferredoxin from Peptococcus aerogenes. Four possible models of interaction between the two molecules were examined by bringing in close proximity each of the four hemes and the redox center (4Fe-4S) of the ferredoxin and by optimizing the ion pairs interactions. One of these models shows by far the “best” structure in terms of charges, interactions, and complementary f the topology of the contact surfaces. In this complex, the distance between the iron atoms of the ferredoxin redox center and the hemic iron atom is 11.8 Å, which compares well with those found between redox centers in other complexes. The contact surface area between the two molecules is 170 Å2.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040109
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  • 65
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040201
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  • 66
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    Crystallization and preliminary investigation of single crystals of deoxyuidine triphosphate nucleotidohydrolase from Escherichia coli (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 71-75 
    Details
    ISSN: 0887-3585
    Keywords: dUTPase ; nucleotide binding enzyme ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase), an enzyme in the nucleotide metabolism that is a pyrophosphatase hydrolyzing dUTP, has been crystallized. The crystals belong to the trigonal space group R3 and diffract beyond 2 Å. The native dUTPase crystals and a mercury derivative are stable in the X-ray beam and are suitable for a high resolution X-ray structure analysis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040110
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  • 67
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    Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: A pentacoordinated binding of the SCN- ion to the zinc at high pH (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 283-293 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; structure ; refinement ; sulfonamide ; thiocyanate ; mercury ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The binding of four inhibitors - mercuric ion, 3-acetoxymercuri-4-aminobenzenesulfonamide (AMS), acetazolamide (Diamox), and thiocyanate ion - to human carbonic anhydrase II (HCA II) has been studied with X-ray crystallography.The binding of mercury to HCA II at pH 7.0 has been investigated at 3.1 Å resolution. Mercuric ions are observed at both nitrogens in the His-64 ring. One of these sites is pointing toward the zinc ion. The only other binding site for mercury is at Cys-206.The binding of the two sulfonamide inhibitors AMS and Diamox, has been reinvestigated at 2.0 and 3.0 Å, respectively. Only the nitrogen of the sulfonamide group binds to the zinc ion replacing the hydroxyl ion. The sulfonamide oxygen closet to the zinc ion is 3.1 Å away. Thus the tetrahedral geometry of the zinc is retained, refuting earlier models of a pentacoordinated zinc.The structure of the thiocyanate complex has been investigated at pH 8.5 and the structure has been refined at 1.9 Å resolution using the least-squares refinement program PROLSQ. The crystallographic R factor is 17.6%. The zinc ion is pentacoordinated with the anion as well as a water molecule bound in addition to the three histidine residues. The nitrogen atom of the SCN- ion is 1.9 Å from the zinc ion but shifted 1.3 Å with respect to the hydroxyl ion in the native structure and at van der Waals' distance from the Oγl atom of Thr-199. This is due to the inability of the Oγl atom of Thr-199 to serve as a hydrogen bond donor, thus repelling the nonprotonated nitrogen. The SCN- molecule reaches into the deep end of the active site cavity where the sulfur atom has displaced the so-called “deep” water molecule of the native enzyme. The zinc-bound water molecule is 2.2 Å from the zinc ion and 2.4 Å from the SCN- nitrogen. In addition, this water is hydrogen bonded to the Oγl atom of Thr-199 and to another water molecule.We have observed that solvent and inhibitor molecules have three possible binding sites on the zinc ion and their significance for the catalysis and inhibition of HCA II will be discussed. All available crystallographic data are consistent with a proposed catalytic mechanism in which both the OH moiety and one oxygen of the substrate HCO3- ion are ligated to the zinc ion.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040407
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    Further experimental studies of the disulfide folding transition of ribonuclease A (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 251-261 
    Details
    ISSN: 0887-3585
    Keywords: protein folding kinetics ; disulfide bonds ; thiol-disulfide exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two very different mechanisms of folding have been proposed from experimental studies of disulfide formation in reduced ribonuclease A. (1) A pathway in which the rate-limiting step separates fully folded protein from all other disulfide intermediates and occurs solely in three-disulfide intermediates. (2) A multiple pathway mechanism with different rate-limiting steps for each pathway. The various rate-limiting steps involve disulfide breakage, formation, and rearrangement in intermediates with one, two, three, and four protein disulfides. To distinguish between these two mechanisms, we have carried out further studies of both unfolding and refolding.Refolding of reduced ribonuclease A requires three-disulfide intermediates to accumulate; negligible refolding occurs when only the nearly random one- and two-disulfide intermediate species are populated. Therefore, no rate-limiting steps of the type postulated in mechanism (2) occur in intermediates with one and two protein disulfides. Unfolding and disulfide reduction is an all-or-none process; no disulfide intermediates accumulate to detectable to detectable levels or precede the rate-limiting step. Mechanism (2) requires that such intermediates precede the rate-limiting step and accumulate to substantial levels.The different proposal were shown not to result from the use of different solution conditions or disulfide reagents; the two sets of data are not inconsistent. Instead, the inappropriate mechanism (2) resulted from an incorrect kinetic analysis and misinterpretation of the kinetics of disulfide formation are breakage.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040404
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  • 69
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030201
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  • 70
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    Conformational characteristics of the complete cequence of group A streptococcal M6 protein (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 60-69 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coli ; alpha-helix ; antiphagocytic ; heptad ; antigenic variation ; sequence repeats ; cell wall protein ; intermediate filaments ; myosin ; tropomyosin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: M protein is considered a virulence determinant on the streptococcal cell wall by virtue of its ability to allow the organism to resist attack by human neutrophils. The complete DNA sequence of the M6 gene from streptococcal strain D471 has allowed, for the first time, the study of the structural characteristics of the amino acid sequence of an entire M protein molecule. Predictive secondary structural analysis revealed that the majority of this fibrillar molecule exhibits strong alpha-helical potential and that, except for the ends, nonpolar residues in the central region of the molecule exhibit the 7-residue periodicity typical for coiled-coil proteins. Differences in this heptad pattern of nonpolar residues allow this central rod region to be divided into three subdomains which correlate essentially with the repeat regions A, B, and C/D in the M6 protein sequence. Alignment of the N-terminal half of the M6 sequence with PepM5, the N-terminal half of the M5 protein, revealed that 42% of the amino acids were identical. The majority of the identities were “core” nonpolar residues of the heptad periodicity which are necessary for the maintenance of the coiled coil. Thus, conservation of structure in a sequence-variable region of these molecules may be biologically significant. Results suggest that serologically different M proteins may be built according to a basic scheme: an extended central coiled-coil rod domain (which may vary in size among strains) flanked by functional end domains.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030106
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    Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure*A FORTRAN version of the program DEFINE_STRUCTURE, which defines the secondary structure and characterizes the first level of supersecondary structure, is available from the authors (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 71-84 
    Details
    ISSN: 0887-3585
    Keywords: Cα coordinates ; distance matrix ; difference distance matrix ; helix axes, strand axes ; interaxial angles ; turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer program is described that produces a description of the secondary structure and supersecondary structure of a polypeptide chain using the list of alpha carbon coordinates as input. Restricting the term “secondary structure” to the conformation of contiguous segments of the chain, the program determines the initial and final residues in helices, extended strands, sharp turns, and omega loops. This is accomplished through the use of difference distance matrices. The distances in idealized models of the segments are compared with the actual structure, and the differences are evaluated for agreement within preset limits. The program assigns 90-95% of the residues in most proteins to at least one type of secondary elementIn a second step the now-defined helices and strands are idealized as straight line segments, and the axial directions and locations are compiled from the input Cα coordinate list. These data are used to check for moderate curvature in strands and helices, and the secondary structure list is corrected where necessary. The geometric relations between these line segments are then calculated and output as the first level of supersecondary structure. A maximum of six parameters are required for a complete description of the relations between each pair. Frequently a less complete description will suffice, for example just the interaxial separation and angle. Both the secondary structure and one aspect of the supersecondary structure can be displayed in a character matrix analogous to the distance matrix format. This allows a quite accurate two-dimensional display of the three-dimensional structure, and several examples are presentedA procedure for searching for arbitrary substructures in proteins using distance matrices is also described. A search for the DNA binding helix-turnhelix motif in the Protein Data Bank serves as an exampleA further abstraction of the above data can be made in the form of a metamatrix where each diagonal element represents an entire secondary segment rather than a single atom, and the off-diagonal elements contain all the parameters describing their interrelations. Such matrices can be used in a straightforward search for higher levels of supersecondary structure or used in toto as a representation of the entire tertiary structure of the polypeptide chain.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030202
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    Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 97-101 
    Details
    ISSN: 0887-3585
    Keywords: URF ; nucleotide-binding sites ; pattern descriptor ; computer search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In an effort to identify the structural elements essential to a given protein function a new pattern-directed inference system has been developed. It has been employed to identify a potential dinucleotide-binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subunit.
    Additional Material: 2 Ill.
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    Lysine/fibrin binding sites of kringles modeled after the structure of kringle 1 of prothrombin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 85-96 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy minimization ; lysine/fibrin binding ; kringle structures ; plasminogen ; tissue plasminogen activator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Lys binding site of kringle 1 and 4 (K1 and K4) of plasminogen (PG) has been modeled on the basis of the three-dimensional structure of kringle 1 of prothrombin and 300- and 600-MHz proton nuclear magnetic resonance observations. These structures were then compared to the corresponding regions of modeled kringle 1 and 2 of tissue plasminogen activator (PA). The coordinates of the modeled structures have been refined by energy minimization in the presence and absence of ∊-aminocaproic acid ligand in order basically to remove unacceptable van der Waals contacts. The binding site is characterized by an apparent dipolar surface, the polar parts of which are separated by a hydrophobic region of highly conserved aromatic residues. Zwitterionic ligands such as Lys and ∊-aminocaproic acid form ion pair interactions with Asp55 and Asp57 located on the dipolar surface; the latter are also conserved in all the Lys binding kringles. The cationic center of the dipolar surface is Arg71, in the case of PGK4, and is composed of Arg34 and Arg71 in PGK1. The doubly charged anionic/cationic interaction centers of the latter might account for the larger binding constants of PGK1 for like-ligands but the modeling suggests that PGK4 might be kinetically faster in binding bulkier ligands. The binding site region of PAK2, which also binds Lys, resembles those of PGK1 and PGK4. Since PAK2 lacks both cationic center Arg residues, ligand carboxylate binding appears to be accomplished though an imidazolium ion of His64, which is located just below the outer surface of the kringle.
    Additional Material: 6 Ill.
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  • 74
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    Site-directed mutations altering methyl-accepting residues of a sensory transducer protein (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 102-112 
    Details
    ISSN: 0887-3585
    Keywords: bacterial chemotaxis ; sensory adaptation ; protein modification ; membrane protein ; receptor protein ; transmembrane signalling ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Trg protein is one of a family of transducer proteins that mediate chemotactic response in Escherichia coli. Transducers are methylaccepting proteins that gain or lose methyl esters on specific glutamyl residues during sensory adaptation. In this study, the significance of multiple sites of methylation on transducer proteins was addressed by using oligonucleotide-directed, site-specific mutagenesis to substitute an alanyl residue at each of the five methyl-accepting sites in Trg. The resulting collection of five mutations, each inactivating a single site, was analyzed for effects on covalent modification at the remaining sites on Trg and for the ability of the altered proteins to mediate sensory adaptation. Most of the alanyl substitutions had substantial biochemical effects, enhancing or reducing methyl-accepting activity of other sites, including one case of activation of a site not methylated in wild-type protein. Analysis of the altered proteins provided explanations for many features of the complex pattern of electrophoretic forms exhibited by Trg. The mutant proteins were less efficient than normal Trg in mediating adaptation. Correlation of biochemical and behavioral data indicated that reduction in the number of methyl-accepting sites on the transducer lengthened the time required to reach an adapted state.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030205
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    Human myeloperoxidase and thyroid peroxidase, two enzymes with separate and distinct physiological functions, are evolutionarily related members of the same gene family (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 113-120 
    Details
    ISSN: 0887-3585
    Keywords: evolution ; proximal histidine ; distal histidine ; heme enzyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human myeloperoxidase and human thyroid peroxidase nucleotide and amino acid sequences were compared. The global similarities of the nucleotide and amino acid sequences are 46% and 44%, respectively. These similarities are most evident within the coding sequence, especially that encoding the myeloperoxidase functional subunits. These results clearly indicate that myeloperoxidase and thyroid peroxidase are members of the same gene family and diverged from a common ancestral gene. The residues at 416 in myeloperoxidase and 407 in thyroid peroxidase were estimated as possible candidates for the proximal histidine residues that link to the iron centers of the enzymes. The primary structures around these histidine residues were compared with those of other known peroxidases. The similarity in this region between the two animal peroxidases (amino acid 396-418 in thyroid peroxidase and 405-427 in myeloperoxidase) is 74%; however, those between the animal peroxidases and other yeast and plant peroxidases are not significantly high, although several conserved features have been observed. The possible location of the distal histidine residues in myeloperoxidase and thyroid peroxidase amino acid sequences are also discussed.
    Additional Material: 4 Ill.
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  • 76
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    Peptide synthesis catalyzed by polyethylene glycol-modified chymotrypsin in organic solvents (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 130-137 
    Details
    ISSN: 0887-3585
    Keywords: peptide synthesis ; chymotrypsin specificity ; polyethylene glycol ; nonaqueous solvents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Chymotrypsin modified with polyethylene glycol was successfully used for peptide synthesis in organic solvents. The benzene-soluble modified enzyme readily catalyzed both aminolysis of N-benzoyl-L-tyrosine p-nitroanilide and synthesis of N-benzoyl-L-tyrosine butylamide in the presence of trace amounts of water. A quantitative reaction was obtained when either hydrophobic or bulky amides of L- as well as D-amino acids were used as acceptor nucleophiles, while almost no reaction occurred with free amino acids or ester derivativesThe acceptor nucleophile specificity of modified chymotrypsin as a catalyst in the formation of both amide and peptide bonds in organic solvents was quite comparable to that in aqueous solution as well as to that of the leaving group in hydrolysis reactions. By contrast, the substrate specificity of modified chymotrypsin in organic solvents was different from that in water since arginine and lysine esters were found to be as effective as aromatic amino acids to form the acyl-enzyme with subsequent synthesis of a peptide bond.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030208
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  • 77
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    Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonantes during the photocycle (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 219-229 
    Details
    ISSN: 0887-3585
    Keywords: proton transport ; energy transduction ; purple membrane ; proton wire ; Schiff base counter-ion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The techniques of FTIR difference spectroscopy and site-directed mutagenesis have been combined to investigate the role of individual tyrosine side chains in the proton-pumping mechanism of bacteriorhodopsin (bR). For each of the 11 possible bR mutants containing a single Tyr→Phe substitution, difference spectra have been obtained for the bR→K and bR→M photoreactions. Only the Tyr-185→Phe mutation results in the disappearance of a set of bands that were previously shown to be due to protonation of a tryosinate during the br→K photoreaction [Rothschild et al.: Proceedings of the National Academy of Sciences of the United states of America 83:347, (1986)]. The Tyr-185→Phe mutation also eliminates a set of bands in the bR→M difference spectrum associated with deprotonation of a Tyr; most of these bands (e.g., positive 1272-cm-1 peak) are completely unaffected by the other ten Tyr→Phe mutations. Thus, tyrosinate-185 gains a proton during the bR→K reaction and loses it again when M is formed. Our FTIR spectra also provide evidence that Tyr-185 interacts with the protonated Schiff base linkage of the retinal chromophore, since the negative C=NH+ stretch band shifts from 1640 cm-1 in the wild type to 1636 cm-1 in the Tyr-185→Phe mutant. A model that is consistent with these results is that Tyr-185 is normally ionized and serves as a counter-ion to the protonated Schiff base. The primary photoisomerization of the chromophore translocates the Schiff base away from Tyr-185, which raises the pKa of the latter group and results in its protonation.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030403
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    Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30 (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 243-251 
    Details
    ISSN: 0887-3585
    Keywords: protein evolution ; structural homology ; ribosome structure ; x-ray crystallography ; common motif ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of two prokaryotic ribosomal proteins, the carboxyterminal half of L7/L12 from Escherichia coli (L12CTF) and 1.30 from Bacilus Stearothermophilus display a remarkably similar fold in which alpaha-helices pack onto one side of an antiparallel, three-stranded, beta-pleated sheet. A detailed comparison of the structures by least-squares methods reveals that more than two-thirds of the alpha carbons can be superimposed with a root mean square distance of 2.33 Å. The principal difference is an extra alpha-helix in L12 CTF. The sequences of the proteins display a distinct conservation in regions which are crucial to the common fold, in particular the hydrophobic core. It is proposed that the similarity is a result of divergent evolution.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030405
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    Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 77-88 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; diffraction ; anomalous scattering ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The molecular structure of lamprey hemoglobin was previously determined and refined by conventional crystallographic analysis. In this study, the structural analysis has been repeated in the course of developing the method of multiwavelength anomalous diffraction (MAD) for phase determination. New experimental and analytical procedures that were devised to perform this determination should have general applicability. These include an experimental design to optimize signal strength and reduce systematic errors, experimental evaluation of anomalous scattering factors, and a least-squares procedure for analyzing the MAD data. MAD phases for the structure at 3Å resolution are as accurate overall as the multiple isomorphous replacement (MIR) phases determined previously.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040202
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  • 80
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    Conformation of alamethicin in phospholipid vesicles: Implications for insertion models (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 89-98 
    Details
    ISSN: 0887-3585
    Keywords: membrane proteins ; channels ; circular dichroism spectroscopy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The secondary structure of alamethicin, a membrane channel-forming polypeptide, has been examined by circular dichroism spectroscopy to determine the relationship of its conformation in organic solution to its conformation in a membrane-bound state. The spectrum of alamethicin in small unilamellar dimyristoyl phosphatidylcholine vesicles is significantly different from its spectrum in 10% methanol/acetonitrile, the solvent from which it was crystallized (Fox and Richards: Nature 300:325-330, 1982), as well as its spectrum in methanol, the solvent in which NMR studies have been done (Banerjee and Chan: Biochemistry 22:3709-3713, 1983). This suggests that structural models based on studies of the molecule in organic solvents may not be entirely appropriate for the membrane-bound state. To distinguish between different models for channel formation and insertion, two different methods were used to associate the alamethicin with vesicles; in addition, the effect of oligomerization on the conformation of the membrane-bound state was investigated. These studies are consistent with a modified insertion model in which alamethicin monomers, dimers, or trimers associate with the bilayer and then spontaneously oligomerize to form a prechannel with a higher helix content. This aggregate could then “open” upon application of an appropriate gating transmembrane potential.
    Additional Material: 4 Ill.
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  • 81
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    Internal motion of a tryptophan residue in Streptomyces subtilisin inhibitor: Deuterium nuclear magnetic resonance in solution (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 131-136 
    Details
    ISSN: 0887-3585
    Keywords: 2H NMR ; selective deuteration ; tryptophan internal motion ; SSI-subtilisin complex ; protein conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Deuterium NMR spectroscopy was used to study internal motions of a deuterium-labeled single tryptophan (Trp) residue (per subunit) of Streptomyces subtilisin inhibitor (SSI) in solution. The free inhibitor with the five ring protons of the Trp replaced with deuterons showed a narrow resonance component (56 Hz) of about one-quarter of the total intensity, in addition to the broad resonance component (about 600 Hz) at 25°C, showing that it exits in an equilibrium mixture of two conformers, in one of which the typtophan side chain is highly mobile. In analogy to the two structures of SSI found in the crystal, these two conformers were attributed to the one in which the contact between the α-lobe and the beta;-lobe of the subunit is tight and the other in which the same contact is loose. When SSI forms a complex with subtilisin BPN′, the broad component becomes invisibly broad, but the narrow component increases with even further narrowing, suggesting that the binding to the enzyme favors the “loose” conformer over the “tight” conformer.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040206
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    Surface interactions of γ-crystallins in the crystal medium in relation to their association in the eye lens (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 137-147 
    Details
    ISSN: 0887-3585
    Keywords: eye lens proteins ; protein association ; crystal packing ; surface area ; homologous proteins ; point mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparative study of intermolecular interactions in crystals of two homologous low molecular weight proteins, γ-II and γ-IIIb crystallins, from calf eye lens was carried out. Crystal packings for these proteins are very different: intermolecular contact areas compose about 33% of the total accessible surface area of γ-II as compared with 13% in γ-III. Two key residues seem to be mainly responsible for the differences in protein association in the crystal medium. These are Ser 103 and Leu 155 in γ-II, which are replaced by Met 103 and His 155 in γ-IIIb. A similar substitution of these residues is observed in different gene products of γ-crystallins from a number of vertebrates. This is consistent with the existence of a genetically controlled mechanism for determining intermolecular association of γ-crystallins in the native medium of the lens.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040207
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  • 83
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    Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 148-156 
    Details
    ISSN: 0887-3585
    Keywords: Protein structure ; empirical energy ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.
    Additional Material: 3 Ill.
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040301
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  • 85
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    X-ray and model-building studies on the specificity of the active site of proteinase K (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 157-164 
    Details
    ISSN: 0887-3585
    Keywords: synthetic inhibitors ; serine proteinase crystallography ; active site geometry ; computer graphics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteinase K, the extracellular serine endopeptidase (E.C. 3.4.21.14) from the fungus Tritirachium album limber, is homologous to the bacterial subtilisin proteases. The binding geometry of the synthetic inhibitor carbobenzoxy-Ala-Phechloromethyl Ketone to the active site of proteinase K was the first determined from a Fourier synthesis based on synchrotron X-ray diffraction data between 1.8 Å and 5.0 Å resolution. The protein inhibitor complexes was refined by restrained least-squares minimization with the data between 10.0 and 1.8 Å. The final R factor was 19.1% and the model contained 2,018 protein atoms, 28 inhibitors atoms, 125 water molecules, and two Ca2+ ions. The peptides portion of the inhibitor is bound to the active center of proteinase K by means of a three-stranded antiparallel pleated sheet, with the side chain of the phenylalanine located in the P1 site. Model building studies, with lysine replacing phenylalanine in the inhibitor, explain the relatively unspecific catalytic activity of the enzyme.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040302
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    Structural analysis of the 2.8 Å model of xylose isomerase from Actinoplanes missouriensis (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 165-172 
    Details
    ISSN: 0887-3585
    Keywords: α/β barrels ; crystal structure ; glucose isomerase ; xylose isomerase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of Xylose isomerase (X.I.) from Actinoplanes missouriensis has been solved to 2.8 Angstroms resolution. Phases were determined from a single Eu3+ derivative and from the noncrystallographic 22 symmetry of the tetrameric molecule. An atomic model was built and subjected to restrained crystallographic refinement. The resulting model is shown to be closely similar to the recently reported X.I.'s structures from three other bacterial sources. Each monomer is found to be composed of an eight-stranded α/β “T.I.M.” barrel forming an N-terminal domain of 328 residues followed by a large loop of 66 residues embracing an adjacent subunit. Analysis of intersubunit packing shows that the X.I. tetramer is an assembly of two tight dimers. The β barrel fits a simple hyperboloid model as other T.I.M. barrels do. The active site, identified as the binding site for the inhibitor xylitol, is located at the carboxyl end of the beta strands in the barrel next to a pair binding site for Eu3+ ions, which are assumed to the sites for the divalent ions involved in catalysis. Active sites in the tetramer are oriented towards the interface between dimmers. It is suggested that subunit interfaces might stabilize the active site region and this might explain the oligomeric nature of the other α/β barrel enzymes.
    Additional Material: 5 Ill.
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    Formation of heterodimers between wild type and mutant trp aporepressor polypeptides of Escherichia coli (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 173-181 
    Details
    ISSN: 0887-3585
    Keywords: DNA binding protein ; ligand binding ; equilibrium dialysis ; dimer ; stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Availability of the three-dimensional structure of the trp repressor of Escherichia coli and a large group of repressor mutants has permitted the identification and analysis of mutants with substitutions of the amino acid residues that from the tryptophan binding pocket. Mutant aporepressors selected for study were overproduced using a multicopy expression plasmid. Equilibrium dialysis with 14C-tryptophan and purified mutant and wild type aporepressors was employed to determine tryptophan binding constants. The results obtained indicate that replacement of theronine 44 by methionine (TM44) or arginine 84 by histidine (RH84) lowers the affinity for tryptophan approximately two-and four-fold, respectively. Replacement of ariginine 54 by histidine (RH84) or glycine 85 by ariginine (GR85) results in complete loss of tryptophan binding activity. Purified mutant and wild type aporepressors were used in vitro heterodimer studies. The trp repressor of E. coli functions as a stable dimer. A large number of trp repressor mutants prduces defective repressors that are transdominant to the wild type repressor in vivo. The transdominance presumably results from the formation of inactive or slightly active heterodimers between the mutant and wild type polypeptide subunits. An in vitro assay was developed to detect and measure heterodimer formation. Heterodimer formation was thermally induced, and heterodimers were separated on nondenaturing polyacrylamide gels. Aporepressors readily formed heterodimer formation upon treatment at 65°C for 3 minutes. Heterodimer formation was significantly retarded by the presence of the corepressor, L-tryptophan. Indole-3-propionic acid, 5-methyl tryptophan, and other analogs of tryptophan, as well as indole, also inhibited heterodimer formation. These results indicate that the presence of the indole moiety in the corepressor binding pocket increases the stability of the dimer.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040304
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  • 88
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    Interaction of peptide boronic acids with elastase: Circular dichroism studies (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 205-210 
    Details
    ISSN: 0887-3585
    Keywords: slow-binding inhibition ; transition-state analog ; conformational change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Boronic acid derivatives of good peptide substrate of the serine proteases cause slow-binding inhibition, manifested as biphasic binding (Kettner and Shenvi: J. Biol. Chem. 259:15106-15114, 1984). These inhibitors are thought to act as reaction-intermediate analogs. Three peptides Boronic acids - Ac-Pro-boro-Val-OH, DNS-Ala-Pro-boro-Val-OH, and Ac-Ala-Ala-Pro-boro-Val-OH - were chosen for farultraviolet circular dichroism (CD) studies in order to determine whether the second phase involves a conformational change of pancreatic elastase. The dipeptide is a simple competitive inhibitors (Ki = 0.27 μM) and the latter are slow-binding inhibitors (Ki = 16.4 and 0.25 nM, respectively). Spectral deconvolution and correction for the formation of antiparallel β-sheet by the peptide inhibitors itself indicate that there is no significant change in the secondary structure of the enzyme in the either the initial or final inhibitors complex. A kinetic experiment confirmed that the slow-binding step was not associated with a CD spectral change, and that therefore a protein conformational change was not responsible for the sow binding.
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    URL: http://dx.doi.org/10.1002/prot.340040307
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  • 89
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040401
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  • 90
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    Diffusion-collision model for the folding kinetics of myoglobin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 211-227 
    Details
    ISSN: 0887-3585
    Keywords: protein-folding ; multiple pathways ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The diffusion-collision model has been used to analyze the folding kinetics of myoglobins. The microdomains, which are the basic units that coalesce during the folding, are identified with the helices and the stabilizing contacts between helices are determined form the native structure. Both association and disassociation reactions are included and a range of stabilization parameters is investigated to determine the variations in overall rate and the relative contributions made by the different intermediates during the folding process. In a comparison of folding to the native state and to the midpoint of the folding transitions. (i.e., 50% native protein at the completion of the reaction) significant differences in the contributing intermediates are found.
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    URL: http://dx.doi.org/10.1002/prot.340040308
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  • 91
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    Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 262-273 
    Details
    ISSN: 0887-3585
    Keywords: hierarchical assignment ; cereal grain ; mistletoe ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin.The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945 Å resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S. W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W. C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (α1- and β-purothionin, phoratoxin A and B, an viscotoxin A3 and B).The new program SEQ (pronounced “seek”) was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location.Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of Purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040405
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    Refined structure of human carbonic anhydrase II at 2.0 Å resolution (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 274-282 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure-factor least-squares refinement at 2.0 Å resolution. The conventional crystallographic R value is 17.3%. Of 167 solvent molecules associated with the protein, four are buried and stabilize secondary structure elements. The zinc ion is ligated to three histidyl residues and one water molecule in a nearly tetrahedral geometry. In addition to the zinc-bound water, seven more water molecules are identified in the active site. Assuming that Glu-106 is deprotonated at pH 8.5, some of the hydrogen bond donor-acceptor relations in the active site can be assigned and are described here in detail. The Oγ1 atom of Thr-199 donates its proton to the Oε1 atom of Glu-106 and can function as a hydrogen bond acceptor only in additional hydrogen bonds.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040406
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  • 93
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    Stereochemistry of salt-bridge formation in α-helices and β-strands (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 294-295 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040408
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  • 94
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030101
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  • 95
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    Two trifluoperazine-binding sites on calmodulin predicted from comparative molecular modeling with troponin-C (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 1-17 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; trifluoperazine ; conformational change ; calcium binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Among the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin-C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X-ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin-C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non-bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+-binding loops, the amino- and carboxy-terminal hydrophobic patches of the Ca2+-bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin in missing the N-terminal helix characteristic of troponin-C. The deletion of three residues from the central helical linker (denoted D/E in troponin-D) shortens the molecule and changes the orientation of the two domains of calmodulin by 60° relative to those in troponin-C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibitor of calmodulin activity.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030102
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  • 96
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    Flexibility of the DNA-binding domains of trp repressor (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 18-31 
    Details
    ISSN: 0887-3585
    Keywords: flexibility ; trp repressor ; DNA-binding domains ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An orthorhombic crystal form of trp repressor (aporepressor plus L-tryptophan ligand) was solved by molecular replacement, refined to 1.65 Å resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crystal forms of repressor were grown under identical conditions, the refined structures have distinctly different conformations of the DNA-binding domains. Unlike the repressor/aporepressor structural transition, the conformational shift is not caused by the binding or loss of the L-tryptophan ligand. We conclude that while L-tryptophan binding is essential for forming a specific complex with trp operator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator. This flexibility may be required by the various binding modes proposed for trp repressor in its search for and adherence to its three different operator sites.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030103
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  • 97
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    Ribosome-inhibiting proteins, retroviral reverse transcriptases, and RNase H share common structural elements (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 53-59 
    Details
    ISSN: 0887-3585
    Keywords: ricin ; retroviral integrase ; conserved residues ; homologous sequences ; active site ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Plant ribosome-inhibiting proteins are shown to be homologous at the domain level to RNase H form Escherichia coli and to two regions of the pol gene product of retroviral reverse transcriptases. One of these regions carries the viral integrase or int function, while the other has previously been suggested to contain the viral RNase H exo activity. Several residues conserved among the ribosome inhibitors, E. coli RNase H, and the integrase proteins are seen to occupy a prominent cleft in the tertiary structure of the ribosome inhibitor ricin, suggesting roles in binding or catalysis. It is likely that these homologous sequences represent modern derivatives of an ancient protein-folding unit capable of nucleic acid binding and modification which has been incorporated into a variety of enzyme functions.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030105
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  • 98
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    Energetics of charge-charge interactions in proteins (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 32-52 
    Details
    ISSN: 0887-3585
    Keywords: alpha-helix ; distance-dependent ; finite-difference method ; Poisson-Boltzmann equation ; protein electrostatics ; rhodanese ; solvent effects ; subtilisin ; Tanford-Kirkwood theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson-Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate or rhodanese is analyzed, with attention to the influence of α-helices. Finally, relationships between electrostatic potential and charge-charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance-dependent dielectric constant (∊ = R) and a fixed dielectric constant (∊ = 2), and Tanford-Kirkwood theory. The primary conclusions are as follows: (1) The Poisson-Boltzmann model agrees with the subtilisin data over a range of ionic strengths; (2) two α-helices generate a large potential in the active site of rhodanese; (3) ∊ = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; (4) Tanford-Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson-Boltzmann equation in globular proteins; and (5) the modified Tanford-Kirkwood theory overscreens the measured electrostatic interactions in subtilisin.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030104
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    Mechanism of protein folding: I. General considerations and refolding of myoglobin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 199-207 
    Details
    ISSN: 0887-3585
    Keywords: folding pathway ; hydrophobic interaction ; long-range and long-distance interactions ; secondary structure ; tertiary structure ; module structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To explain the rapidity of the process of protein folding, we cite two aspects of hydrophobic interaction: its long-range nature and the specificity of pairing after the formation of secondary structures. These two factors, when incorporated with the growth-type mechanism, can determine the folding pathway of proteins. This mechanism is applied to myoglobin. Appropriate introduction of side chins of amino acid residues and the heme group attached to His 93 yield a refolded tertiary structure that is in good agreement with the native structure.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030308
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  • 100
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030401
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