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Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints.

Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Research Abstract Details 

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  • Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Abstract Text:

    s r mcallisterS R McAllister,b e mickusB E Mickus,j l klepeisJ L Klepeis,c a floudasC A Floudas,

    The protein folding problem represents one of the most challenging problems in computational biology. Distance constraints and topology predictions can be highly useful for the folding problem in reducing the conformational space that must be searched by deterministic algorithms to find a protein structure of minimum conformational energy. We present a novel optimization framework for predicting topological contacts and generating interhelical distance restraints between hydrophobic residues in alpha-helical globular proteins. It should be emphasized that since the model does not make assumptions about the form of the helices, it is applicable to all alpha-helical proteins, including helices with kinks and irregular helices. This model aims at enhancing the ASTRO-FOLD protein folding approach of Klepeis and Floudas (Journal of Computational Chemistry 2003;24:191-208), which finds the structure of global minimum conformational energy via a constrained nonlinear optimization problem. The proposed topology prediction model was evaluated on 26 alpha-helical proteins ranging from 2 to 8 helices and 35 to 159 residues, and the best identified average interhelical distances corresponding to the predicted contacts fell below 11 A in all 26 of these systems. Given the positive results of applying the model to several protein systems, the importance of interhelical hydrophobic-to-hydrophobic contacts in determining the folding of alpha-helical globular proteins is highlighted.

    Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Publishing Authors By Initials

    sr mcallisterSR McAllister,be mickusBE Mickus,jl klepeisJL Klepeis,ca floudasCA Floudas,

    For similar proteins research abstracts see: proteins research

    PUBMED ID PMID:

    MEDLINE DATE:

    Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Journal Published:

    PUBLICATION TYPE: Research Support, U.S. Gov't,

    Journal: Proteins

    VOLUME: 65

    Page Numbers: 930-52

    Journal Abbreviation: Proteins

    ISSN: 1097-0134

    DAY: 1

    MONTH: Dec

    YEAR: 2006

    Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Information

    Number of References:

    LANGUAGE: eng

    NlmUniqueID: 8700181

    Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Keywords Mesh Terms:

    KEYWORDS: Proteins

    MESH TERMS: chemistry

    Chemical & Substance for Abstract: Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Information

    Substance Name: Proteins

    Registry Number: 0

    Grant and Affiliation Information for Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints.

    AFFILIATION: Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, USA.

    Country: United States

    United States Research PublicationUnited States Research Publication

    AGENCY: United States NIGMS

    GRANT: R01 GM52032

    ACRONYM: GM

    MEDLINETA: Proteins

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