Steered molecular dynamics simulations of force-induced protein domain unfolding

Hui Lu, Klaus Schulten

Research output: Contribution to journalArticle

Abstract

Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiments, but proceed on much shorter time scales. The simulations on different domains for 0.6 nanosecond each reveal two types of protein responses: the first type, arising in certain β-sandwich domains, exhibits nanosecond unfolding only after a force above 1,500 pN is applied; the second type, arising in a wider class of protein domain structures, requires significantly weaker forces for nanosecond unfolding. In the first case, strong forces are needed to concertedly break a set of interstrand hydrogen bonds which protect the domains against unfolding through stretching; in the second case, stretching breaks backbone hydrogen bonds one by one, and does not require strong forces for this purpose. Stretching of β-sandwich (immunoglobulin) domains has been investigated further revealing a specific relationship between response to mechanical strain and the architecture of β-sandwich domains.

Original languageEnglish (US)
Pages (from-to)453-463
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume35
Issue number4
DOIs
StatePublished - Jun 1 1999

Keywords

  • Domain classification
  • Fibronectin type III domain
  • Immunoglobulin domain
  • Protein folding
  • Steered molecular dynamics

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

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