Maintaining solvent accessible surface area under rotamer substitution for protein design

Andrew Leaver-Fay, Glenn Butterfoss, Jack Snoeyink, Brian Kuhlman

Research output: Contribution to journalArticle

Abstract

Although quantities derived from solvent accessible surface areas (SASA) are useful in many applications in protein design and structural biology, the computational cost of accurate SASA calculation makes SASA-based scores difficult to integrate into commonly used protein design methodologies. We demonstrate a method for maintaining accurate SASA during a Monte Carlo search of sequence and rotamer space for a fixed protein back-bone. We extend the fast Le Grand and Merz algorithm (Le Grand and Merz, J Comput Chem, 14, 349), which discretizes the solvent accessible surface for each atom by placing dots on a sphere and combines Boolean masks to determine which dots are exposed. By replacing semigroup operations with group operations (from Boolean logic to counting dot coverage) we support SASA updates. Our algorithm takes time proportional to the number of atoms affected by rotamer substitution, rather than the number of atoms in the protein. For design simulations with a one hundred residue protein our approach is ∼ 145 times faster than performing a Le Grand and Merz SASA calculation from scratch following each rotamer substitution. To demonstrate practical effectiveness, we optimize a SASA-based measure of protein packing in the complete redesign of a large set of proteins and protein-protein interfaces.

Original languageEnglish (US)
Pages (from-to)1336-1341
Number of pages6
JournalJournal of Computational Chemistry
Volume28
Issue number8
DOIs
StatePublished - Jun 1 2007

Fingerprint

Surface area
Substitution
Substitution reactions
Proteins
Protein
Atoms
Design
Backbone
Large Set
Demonstrate
Packing
Biology
Mask
Design Methodology
Computational Cost
Masks
Counting
Bone
Coverage
Semigroup

Keywords

  • Computational protein design
  • Protein stability
  • Solvent accessible
  • Surface area

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

Maintaining solvent accessible surface area under rotamer substitution for protein design. / Leaver-Fay, Andrew; Butterfoss, Glenn; Snoeyink, Jack; Kuhlman, Brian.

In: Journal of Computational Chemistry, Vol. 28, No. 8, 01.06.2007, p. 1336-1341.

Research output: Contribution to journalArticle

Leaver-Fay, Andrew ; Butterfoss, Glenn ; Snoeyink, Jack ; Kuhlman, Brian. / Maintaining solvent accessible surface area under rotamer substitution for protein design. In: Journal of Computational Chemistry. 2007 ; Vol. 28, No. 8. pp. 1336-1341.
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