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  • 1
    Digitale Medien
    Digitale Medien
    An analysis of protein folding pathways (1991)
    s.l. : American Chemical Society
    Biochemistry 30 (1991), S. 3816-3824 
    Details
    ISSN: 1520-4995
    Quelle: ACS Legacy Archives
    Thema: Biologie , Chemie und Pharmazie
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/bi00230a003
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  • 2
    Digitale Medien
    Digitale Medien
    Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications (1993)
    Springer
    Bulletin of mathematical biology 55 (1993), S. 1183-1198 
    Details
    ISSN: 1522-9602
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie , Mathematik
    Notizen: Abstract The protein folding problem and the notion of NP-completeness and NP-hardness are discussed. A lattice model is suggested to capture the essece of protein folding. For this model we present a proof that finding the lowest free energy conformation belongs to the class of NP-hard problems. The implications of the proof are discussed and we suggest that the natural folding process cannot be considered as a search for the global free energy minimum. However, we suggest an explanation as to why, for many proteins, the native functional conformation maycoincide with the lowest free energy conformation.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/BF02460703
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  • 3
    Digitale Medien
    Digitale Medien
    The importance of short structural motifs in protein structure analysis (1993)
    Springer
    Journal of computer aided molecular design 7 (1993), S. 457-472 
    Details
    ISSN: 1573-4951
    Schlagwort(e): Protein structure ; Structural motifs ; Secondary structure ; Building blocks ; Clustering ; Structure verification ; Structure prediction
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Summary Proteins tend to use recurrent structural motifs on all levels of organization. In this paper we first survey the topics of recurrent motifs on the local secondary structure level and on the global fold level. Then, we focus on the intermediate level which we call the short structural motifs. We were able to identify a set of structural building blocks that are very common in protein structure. We suggest that these building blocks can be used as an important link between the primary sequence and the tertiary structure. In this framework, we present our latest results on the structural variability of the extended strand motifs. We show that extended strands can be divided into three distinct structural classes, each with its own sequence specificity. Other approaches to the study of short structural motifs are reviewed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/BF02337561
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  • 4
    Digitale Medien
    Digitale Medien
    Chaos in protein dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 417-425 
    Details
    ISSN: 0887-3585
    Schlagwort(e): nonlinear dynamics ; chaotic motion in complex systems ; protein folding pathways ; molecular dynamics ; Lyapunov exponent ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: MD simulations, currently the most detailed description of the dynamic evolution of proteins, are based on the repeated solution of a set of differential equations implementing Newton's second law. Many such systems are known to exhibit chaotic behavior, i.e., very small changes in initial conditions are amplified exponentially and lead to vastly different, inherently unpredictable behavior. We have investigated the response of a protein fragment in an explicit solvent environment to very small perturbations of the atomic positions (10-3-10-9 Å). Independent of the starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading to conformations that differ by approximately 1 Å RMSD within 1-2 ps. Furthermore, introducing the perturbation more than 1-2 ps before a significant conformational transition leads to a loss of the transition in the perturbed trajectories. We present evidence that the observed chaotic behavior reflects physical properties of the system rather than numerical instabilities of the calculation and discuss the implications for models of protein folding and the use of MD as a tool to analyze protein folding pathways. Proteins 29:417-425, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 5
    Digitale Medien
    Digitale Medien
    A 3D building blocks approach to analyzing and predicting structure of proteins (1989)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 355-373 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein ; structure ; prediction ; primary ; secondary ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well-refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/prot.340050410
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  • 6
    Digitale Medien
    Digitale Medien
    Analysis of dihedral angles distribution: The doublets distribution determines polypeptides conformations (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 499-508 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: It is possible to construct fragments of protein structures by using the known values for the fixed bond lengths, bond angles, and torsion angles, and “dialing” in the dihedral angles φ and ψ. By choosing these angles in different ways, it is possible to create different populations of fragments and to investigate their properties. We analyzed the following populations: Real fragments taken randomly from known structures. Reconstructed fragments, which are constructed, using the “fixed geometry” assumption, from a set of consecutive pairs of dihedral angles drawn from known structures. Random fragments that are constructed from a random set of dihedral angles from known structures, and doublet-preserving fragments, which are constructed from a set of dihedral angles drawn at random from known structures in a way such that the distribution of two consecutive pairs of dihedral angles in this population is similar to that distribution in the known structures. We examine the fixed geometry assumption and demonstrate that even reconstructed fragments contain many atomic collisions. We show that random fragments have only slightly more interatomic collisions than the reconstructed fragments. Nevertheless, the population of random fragments is structurally different from the population of reconstructed fragments. On the other hand, we show that the doublet-preserving fragments exhibit properties that are similar to the real population. Thus the doublet preserving random population can be used to simulate the structure of short polypeptides.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360300503
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