Parametric sensitivity analysis of avian pancreatic polypeptide (APP)

Hong Zhang, Chung F. Wong, Tom Thacher, Herschel Albert Rabitz

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Computer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters. © 1995 Wiley‐Liss, Inc.

Original languageEnglish (US)
Pages (from-to)218-232
Number of pages15
JournalProteins: Structure, Function, and Bioinformatics
Volume23
Issue number2
DOIs
StatePublished - Jan 1 1995

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Keywords

  • OPLS/Amber force field
  • avian pancreatic polypeptide (APP)
  • continuum solvation model
  • molecular dynamics simulation
  • protein conformation
  • protein stability
  • sensitivity analysis

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