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  • 1
    Electronic Resource
    Electronic Resource
    Correlated chemisorption: The effect of coalescence and diffusion on chemisorption islands (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 5488-5496 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The theory of island formation in chemisorption [Becker and Ben-Shaul, Phys. Rev. Lett. 61, 2859 (1988)], which treats chemisorption as a combination of direct adsorption and cluster formation, is generalized to account for the effects of cluster–cluster coalescence and of surface diffusion. The effect of cluster–cluster coalescence is approximated by series expansion in increasing "overlaps.'' Exact calculation of the second order term, which describes the two-cluster overlaps, yields a good agreement with Monte Carlo simulation results. By incorporating the surface diffusion process it is shown that upon increasing the diffusion rate (i.e., raising the surface temperature) the system changes its behavior from correlated chemisorption (cluster formation) to random chemisorption. The extended formalism includes, as specific realizations, both the case of immobile particles and the cases of rapid diffusing particles (Langmuir's and Kisliuk's models).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.462704
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  • 2
    Electronic Resource
    Electronic Resource
    Temperature quench echoes in proteins (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 3112-3123 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Temperature quench echoes are analyzed in terms of the temperature–temperature correlation function in the harmonic approximation, and the resulting expressions are compared with molecular dynamics simulations. The relationship between the time dependence of the echo depth and the density of states is demonstrated for harmonic systems. For a protein, which has significant anharmonicity, the time dependence is dominated by relaxation effects that originate from dephasing of the periodic motions. A simple relaxation model is shown to provide a good description of the results observed in the simulations. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470270
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  • 3
    Electronic Resource
    Electronic Resource
    The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 1495-1517 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent "attraction basins'' and generates a "disconnectivity'' graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)3-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete list of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall "funnel'' shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its "folding'' behavior. Even in this very simple system, the kinetics exhibit a "trapping'' state which appears as a "kinetic intermediate,'' as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surfaces and the time development of complex systems. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473299
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  • 4
    Electronic Resource
    Electronic Resource
    Melittin at a membrane/water interface: Effects on water orientation and water penetration (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8672-8685 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Melittin, a small peptide found in bee venom, is known to induce membrane lysis. A molecular dynamics simulation of melittin embedded in a hydrated dipalmitoylphosphatidylcholine bilayer is analyzed in order to study the peptide's effect on water molecules at the membrane/water interface. The peptide, with a protonated N-terminus, was embedded in a trans-bilayer orientation. The simulation highlights the microscopic mechanism by which melittin induces the formation of transmembrane water "pores," leading to membrane lysis. It was found that melittin has a profound effect on the behavior of the water molecules at the membrane/water interface. It modifies the orientation of the water dipoles and induces water penetration into the bilayer. In fact, melittin's residue Lys-7 and its protonated N-terminus facilitate the formation of transmembrane water pores by steering water penetration from both sides of the bilayer. The initial step towards pore formation takes about 200 ps, and the process relays on melittin's bent conformation and tilted orientation. A large body of experimental observations supports the simulation results and the suggested microscopic mechanism. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480207
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  • 5
    Electronic Resource
    Electronic Resource
    Dynamics of hierarchical folding on energy landscapes of hexapeptides (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 10533-10547 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we apply the master equation approach to study the effects of the energy landscape topology and topography on the kinetics of folding, and on kinetic transitions of three alanine-hexapeptides analogs which involve polypeptides with neutral and charged groups and a cyclized polypeptide. We rely on the potential-energy landscapes of these molecular systems, which have been constructed using both a topological mapping analysis and a principal component analysis. It was found that the different topology and topography of the energy landscapes result in different "folding" time scales and that the systems with geometrical constraints (cyclization and opposite charges at the termini) "fold" more slowly than the unconstrained peptide. In addition, for each of the three polypeptide systems, the kinetics is nonexponential at the temperature range 400–600 K. The relaxation kinetics is characterized by logarithmic oscillations, which indicate hierarchical dynamics characterized by multiple time scales of fast (few ps) and slow (few μs) events. At higher temperatures, successive relaxation channels with similar characteristic time scales collapse into a single relaxation channel. While the kinetics of the unconstrained peptide at 600 K can be reasonably well described by a single exponential time scale, the kinetics of the constrained hexapeptides are inherently hierarchical and featured by multiple time scales even at high temperatures. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1415444
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  • 6
    Electronic Resource
    Electronic Resource
    Energy landscapes of conformationally constrained peptides (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 993-1009 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Conformation constraints are known to affect the flexibility and bioactivity of peptides. In this study we analyzed the effect of conformation constraints on the topography of the energy landscapes of three analogous hexapeptides. The three analogs vary in the degree of constraint imposed on their conformational motion: linear alanine hexapeptide with neutral terminals (Ala6), linear alanine hexapeptide with charged terminals (chrg-Ala6), and cyclic alanine hexapeptide (cyc-Ala6). It was found that significantly different energy landscapes characterize each of the three peptides, leading to different folding behaviors. Since all three analogs would be encoded by the same gene, these results suggest that nongenomic post-translational modifications may play an important role in determining the properties of proteins as well as of their folding pathways. In addition, the present study indicates that the complexity of those energy landscapes that are dominated by funnel topography can be captured by one or two reaction coordinates, such as conformational similarity to the native state. However, for more complex landscapes characterized by multiple basins such a description is insufficient. This study also shows that similar views of the landscape topography were obtained by principal component analysis (based only on local minima) and by topological mapping analysis (based on minima and barrier information). Both methods were able to resolve the complex landscape topographies for all three peptides. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1329646
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  • 7
    Electronic Resource
    Electronic Resource
    Geometric versus topological clustering: An insight into conformation mapping (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 213-226 
    Details
    ISSN: 0887-3585
    Keywords: conformation space ; potential energy surface ; connectivity ; topological mapping ; family clustering ; principal coordinate projections ; visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Clustering molecular conformations into “families” is a common procedure in conformational analysis of molecular systems. An implicit assumption which often underlies this clustering approach is that the resulting geometric families reflect the energetic structure of the system's potential energy surface. In a broader context we address the question whether structural similarity is correlated with energy basins, i.e., whether conformations that belong to the same energy basin are also geometrically similar. “Topological mapping” and principal coordinate projections are used here to address this question and to assess the quality of the “family clustering” procedure. Applying the analysis to a small tetrapeptide it was found that the general correlation that exists between energy basins and structural similarity is not absolute. Clusters generated by the geometric “family clustering” procedure do not always reflect the underlying energy basins. In particular it was found that the “family tree” that is generated by the “family clustering” procedure is completely inconsistent with its real topological counterpart, the “disconnectivity” graph of this system. It is also demonstrated that principal coordinate analysis is a powerful visualization technique which, at least for this system, works better when distances are measured in dihedral angle space rather than in cartesian space. © 1997 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Representing protein and peptide structures with parallel-coordinates (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1893-1902 
    Details
    ISSN: 0192-8651
    Keywords: parallel coordinates ; visualization ; peptides ; proteins ; conformational analysis ; secondary structure ; disulfide bonds ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Graphical representation of molecular conformations is an important tool used by chemists to gain molecular insight. In spite of today's enhanced computer graphics there are still situations, such as in multiple conformation displays, in which standard visualization techniques are limited. Parallel-coordinate (‖-coords) representation, which was originally developed for visualizing multivariant datasets in fields other than chemistry, offers an alternative basis for graphical representation of molecular structures. In parallel-coordinates, the axes are drawn parallel rather than perpendicular to each other, allowing many axes to be placed and seen. This mapping procedure has unique geometric properties and useful relationships to the original space. In this article, we apply the parallel-coordinate representation for presenting peptide and protein structural conformations. In particular, we demonstrate the usefulness of parallel-coordinates in the context of conformational analysis where this representation, combined with multiple filters, allows nontrivial clustering of data points, leading to new observations. The ‖-coords representation is also demonstrated as a tool for two-dimensional (2D) representation of protein secondary structure and for identification of disulfide-bonded pairs in protein structures. Regardless of the application, an advantage of the ‖-coords approach is that it retains its inherent simplicity and ease of use, and requires little or no software development.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1893-1902, 1997
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Principal coordinate maps of molecular potential energy surfaces (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1255-1267 
    Details
    ISSN: 0192-8651
    Keywords: conformation space ; potential energy surface ; energy landscape ; principal component analysis ; principal coordinate analysis ; peptide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Obtaining useful representations of molecular conformation spaces and visualizing the associated potential energy surfaces is a complex task, mainly due to the high dimensionality of these spaces. Principal component analysis (PCA), which projects multidimensional data on low-dimensional subspaces, is thus becoming a common technique for studying such spaces. Three issues, relating to the use of principal component techniques for mapping molecular potential energy surfaces, are discussed in this study: the effectiveness of the projection; its accuracy; and the mapping procedure. The effectiveness of PCA is demonstrated through detailed analyses of principal component projections of several peptides. In these cases PCA projected conformation space into a subspace smaller even than that defined by the peptide's backbone dihedral angles. The average accuracy as well as the distribution of errors in the projection (i.e., the errors in reproducing individual distances) are studied as a function of the dimensionality of the projection. The wide variation in accuracy between different systems suggests that it is imperative to indicate the accuracy of the projection whenever PCA projections are used. Furthermore, when projecting potential energy surfaces on the principal two-dimensional (2D) plane, the projection errors result in artificial roughening of the surface. A new mapping procedure, the “minimal energy envelope” procedure, is introduced to overcome this problem. This procedure yields relatively smooth “energy landscapes,” which highlight the basin structure of the real multidimensional energy surface. It is demonstrated that the projected potential energy maps can be used for charting conformational transitions or dynamic trajectories in the system.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1255-1267, 1998
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Book
    Book
    Guide to biomolecular simulations /; 4 (2006)
    Dordrecht [u.a.] :Springer Kluwer,
    Details
    Title: Guide to biomolecular simulations /; 4
    Author: Becker, Oren M.
    Contributer: Karplus, Martin
    Publisher: Dordrecht [u.a.] :Springer Kluwer,
    Year of publication: 2006
    Pages: IX, 231 S. : , graph. Darst. +
    Series Statement: Focus on structural biology 4
    ISBN: 1-4020-3586-1 , 978-1-4020-3586-9
    Type of Medium: Book
    Language: English
    URL: Inhaltsverzeichnis
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