All-Atom Structure Prediction and Folding Simulations of a Stable Protein
- 28 August 2002
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 124 (38), 11258-11259
- https://doi.org/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 Å Cα root-mean-square-deviation (rmsd) and 1.4 Å 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.Keywords
This publication has 8 references indexed in Scilit:
- Mini-proteins Trp the light fantasticNature Structural & Molecular Biology, 2002
- Designing a 20-residue proteinNature Structural & Molecular Biology, 2002
- β-hairpin folding simulations in atomistic detail using an implicit solvent model 1 1Edited by F. CohenJournal of Molecular Biology, 2001
- Critical assessment of methods of protein structure prediction (CASP): Round IVProteins-Structure Function and Bioinformatics, 2001
- Theory and applications of the generalized born solvation model in macromolecular simulationsBiopolymers, 2000
- Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force FieldsJournal of the American Chemical Society, 1997
- A new analysis of proton chemical shifts in proteinsJournal of the American Chemical Society, 1991
- Semianalytical treatment of solvation for molecular mechanics and dynamicsJournal of the American Chemical Society, 1990