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Computational Simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation

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Protein Supersecondary Structures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 932))

Abstract

The dynamics of protein folding are complicated because of the various types of amino acid interactions that create secondary, supersecondary, and tertiary interactions. Computational modeling can be used to simulate the biophysical and biochemical interactions that determine protein folding. Effective folding to a desired protein configuration requires a compromise between speed, stability, and specificity. If the primary sequence of amino acids emphasizes one of these characteristics, the others might suffer and the folding process may not be optimized. We provide an example of a model peptide whose primary sequence produces a highly stable supersecondary two-helix bundle structure, but at the expense of lower speed and specificity of the folding process. We show how computational simulations can be used to discover the configuration of the kinetic trap that causes the degradation in the speed and specificity of folding. We also show how amino acid sequences can be engineered by specific substitutions to optimize the folding to the desired supersecondary structure.

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Authors and Affiliations

  1. Department of Physics, Florida International University, Miami, FL, USA

    Bernard S. Gerstman & Prem P. Chapagain

Authors
  1. Bernard S. Gerstman
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  2. Prem P. Chapagain
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Corresponding author

Correspondence to Bernard S. Gerstman .

Editor information

Editors and Affiliations

  1. , Department of Mathematics, Rutgers University, Frelinghuysen Road 110, Piscataway, 08854-8019, USA

    Alexander E. Kister

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Gerstman, B.S., Chapagain, P.P. (2012). Computational Simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 932. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-065-6_12

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  • DOI: https://doi.org/10.1007/978-1-62703-065-6_12

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-064-9

  • Online ISBN: 978-1-62703-065-6

  • eBook Packages: Springer Protocols

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