All-atom structure prediction and folding simulations of a stable protein

Carlos Simmerling; Bentley Strockbine; Adrian E Roitberg

doi:10.1021/ja0273851

All-atom structure prediction and folding simulations of a stable protein

J Am Chem Soc. 2002 Sep 25;124(38):11258-9. doi: 10.1021/ja0273851.

Authors

Carlos Simmerling¹, Bentley Strockbine, Adrian E Roitberg

Affiliation

¹ Center for Structural Biology and Department of Chemistry, State University of New York - Stony Brook, Stony Brook, New York 11794, USA. carlos.simmerling@sunysb.edu

PMID: 12236726
DOI: 10.1021/ja0273851

Abstract

We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Amino Acid Sequence
Computer Simulation
Models, Chemical
Models, Molecular
Molecular Sequence Data
Nuclear Magnetic Resonance, Biomolecular
Oligopeptides / chemistry*
Protein Folding*
Thermodynamics

Substances

Oligopeptides

Grants and funding

GM6167803/GM/NIGMS NIH HHS/United States