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  • 1
    Electronic Resource
    Electronic Resource
    Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein (1997)
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 745-757 
    Details
    ISSN: 0006-3525
    Keywords: protein folding ; simplified folding models ; off-lattice ; Langevin dynamics ; WHAM ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamic properties of a 46-mer β-barrel protein model are investigated using Langevin dynamics and the histogram analysis method. By obtaining the density of states distribution and using the methods of statistical mechanics, we are able to identify the thermodynamic transitions for this model protein and characterize the nature of these transitions. Consistent with an earlier study of this model, we find that the transition from a random coil state to a manifold of collapsed but nonnative states is a continuous transition, and the transition from the manifold of collapsed states to the native state is first order-like. However, our calculations indicate that the folding transition is only weakly first order. Most importantly, we are able to characterize the free energy surface of the protein model, as well as the processes of compaction and native structure formation, from a statistical point of view. We also examined the thermodynamic transition state. By combining the earlier kinetic analysis for the same protein model, we provide a more complete description of this model protein and propose possible further modifications of the model to improve its stability and foldability. © 1997 John Wiley & Sons, Inc. Biopoly 42: 745-757, 1997
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 2
    Electronic Resource
    Electronic Resource
    Protein-drug interactions: Characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 52-61 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulations ; dihydrofolate reductase ; trimethoprim ; drug binding ; solvation ; binding free energies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of diphydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodyanmic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall bindings, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070106
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Curious structure in “canonical” alanine-based peptides (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 59-71 
    Details
    ISSN: 0887-3585
    Keywords: π helix ; i,i+5 hydrogen bonding ; molecular dynamics simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have performed all atom simulations of blocked peptides of the form (AAXAA)3, where X = Gln, Asn, Glu, Asp, Arg, and Lys with explicit water molecules to examine the interactions between side chains spaced i,i-5 in the sequence. Although side chains in this i,i-5 arrangement are commonly believed to be noninteracting, we have observed the formation of unusual i,i-5 main chain hydrogen bonding in such sequences with positively charged residues (Lys) as well as polar uncharged groups (Gln). Our results are consistent with the unusual percentage of hydrogen bonding curves produced by amide exchange measurements on the well-studied sequence acetyl-(AAQAA)3-amide in water (Shalongo, W., Dugad, L., Stellwagen, E. J. Am. Chem. Soc. 116:8288-8293, 1994). Analysis of our simulations indicated that the glutamine side chain showed the greatest propensity to support π helix formation and that the i,i-5 intramolecular hydrogen bonds were stabilized by water-bridging side chain interactions. This intermittent formation of the unusual π helix structure was observed for up to 23% of the total simulation time in some residues in (AAQAA)3. Control studies on peptides with glutamine side chains spaced i,i-3, i,i-4, and i,i-6 did not reveal similar unique structures, providing stronger evidence for the unique role side chain interactions with i,i-5 spacing. © 1997 Wiley-Liss Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    A molecular dynamics simulation study of segment B1 of protein G (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 193-202 
    Details
    ISSN: 0887-3585
    Keywords: protein G ; molecular dynamics ; protein folding ; NMR spectroscopy and x-ray crystallography ; bound water ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The immunoglobulin binding protein, segment B1 of protein G, has been studied experimentally as a paradigm for protein folding. This protein consists of 56 residues, includes both β sheet and α helix and contains neither disulfide bonds nor proline residues. We report an all-atom molecular dynamics study of the native manifold of the protein in explicit solvent. A 2-ns simulation starting from the nuclear magnetic resonance (NMR) structure and a 1-ns control simulation starting from the x-ray structure were performed. The difference between average structures calculated over the equilibrium portion of trajectories is smaller than the difference between their starting conformations. These simulation averages are structurally similar to the x-ray structure and differ in systematic ways from the NMR-determined structure. Partitioning of the fluctuations into fast (〈20 ps) and slow (〈20 ps) components indicates that the β sheet displays greater long-time mobility than does the α helix. Clore and Gronenborn [J. Mol. Biol. 223:853-856, 1992] detected two long-residence water molecules by NMR in a solution structure of segment B1 of protein G. Both molecules were found in the fully exposed regions and were proposed to be stabilized by bifurcated hydrogen bonds to the protein backbone. One of these long-residence water molecules, found near an exposed loop region, is identified in both of our simulations, and is seen to be involved in the formation of a stable water-mediated hydrogen bond bridge. The second water molecule, located near the middle of the α helix, is not seen with an exceptional residence time in either as a result of the conformation being closer to the x-ray structure in this region of the protein. Proteins 29:193-202, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Virtual rigid body dynamics (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 77-100 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An important direction in biological simulations is the development of methods that permit the study of larger systems and/or longer simulation time scales than is currently feasible by molecular dynamics. One such method designed with this objective in mind is stochastic boundary molecular dynamics (SBMD). SBMD was developed for the characterization of spatially localized processes in proteins, and has been shown to successfully reproduce structural and dynamical properties of these macromolecules, as compared to a molecular dynamics control simulation, when concerted or global motions are not present. The virtual rigid body dynamics method presented in this work extends the range of applicability of the SBMD method, by providing a framework to include these important long time scale conformational transitions. In this paper we describe the two-step implementation of the virtual rigid body model: first, the reduction of the full atomic representation to a reduced particle (virtual bond) model, and second, the propagation of the dynamics of flexibly connected rigid bodies containing virtual atom sites.
    Additional Material: 27 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360310108
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  • 6
    Electronic Resource
    Electronic Resource
    Assessing search strategies for flexible docking (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1623-1631 
    Details
    ISSN: 0192-8651
    Keywords: docking ; genetic algorithms (GA) ; simulated annealing (SA) ; Monte Carlo (MC) ; molecular dynamics (MD) ; scoring functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We assess the efficiency of molecular dynamics (MD), Monte Carlo (MC), and genetic algorithms (GA) for docking five representative ligand-receptor complexes. All three algorithms employ a modified CHARMM-based energy function. The algorithms are also compared with an established docking algorithm, AutoDock. The receptors are kept rigid while flexibility of ligands is permitted. To test the efficiency of the algorithms, two search spaces are used: an 11-Å-radius sphere and a 2.5-Å-radius sphere, both centered on the active site. We find MD is most efficient in the case of the large search space, and GA outperforms the other methods in the small search space. We also find that MD provides structures that are, on average, lower in energy and closer to the crystallographic conformation. The GA obtains good solutions over the course of the fewest energy evaluations. However, due to the nature of the nonbonded interaction calculations, the GA requires the longest time for a single energy evaluation, which results in a decreased efficiency. The GA and MC search algorithms are implemented in the CHARMM macromolecular package.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1623-1631, 1998
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Assessing energy functions for flexible docking (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1612-1622 
    Details
    ISSN: 0192-8651
    Keywords: docking ; energy functions ; simulated annealing ; molecular dynamics ; scoring functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that a correctly docked structure can be identified quickly. We assess the selectivity and efficiency of a broad spectrum of energy functions, derived from systematic modifications of the CHARMM param19/toph19 energy function. In particular, we examine the effects of the dielectric constant, the solvation model, the scaling of surface charges, reduction of van der Waals repulsion, and nonbonded cutoffs. Based on an assessment of the energy functions for the docking of five different ligand-receptor complexes, we find that selective energy functions include a variety of distance-dependent dielectric models together with truncation of the nonbonded interactions at 8 Å. We evaluate the docking efficiency, the mean number of docked structures per unit of time, of the more selective energy functions, using a simulated annealing molecular dynamics protocol. The largest improvements in efficiency come from a reduction of van der Waals repulsion and a reduction of surface charges. We note that the most selective potential is quite inefficient, although a hierarchical approach can be employed to take advantage of both selective and efficient energy functions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1612-1622, 1998
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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