Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 23 November 1990:
Vol. 250. no. 4984, pp. 1121 - 1125
DOI: 10.1126/science.250.4984.1121
Prev | Table of Contents | Next

Articles

Simulations of the Folding of a Globular Protein

Jeffrey Skolnick 1 and Andrzej Kolinski 2

1 Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037
2 Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland

Dynamic Monte Carlo simulations of the folding of a globular protein, apoplastocyanin, have been undertaken in the context of a new lattice model of proteins that includes both side chains and a-carbon backbone atoms and that can approximate native conformations at the level of 2 angstroms (root mean square) or better. Starting from random-coil unfolded states, the model apoplastocyanin was folded to a native conformation that is topologically similar to the real protein. The present simulations used a marginal propensity for local secondary structure consistent with but by no means enforcing the native conformation and a full hydrophobicity scale in which any nonbonded pair of side chains could interact. These molecules folded through a punctuated on-site mechanism of assembly where folding initiated at or near one of the turns ultimately found in the native conformation. Thus these simulations represent a partial solution to the globular-protein folding problem.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Comparing Folding Codes in Simple Heteropolymer Models of Protein Evolutionary Landscape: Robustness of the Superfunnel Paradigm.
R. Wroe, E. Bornberg-Bauer, and H. S. Chan (2005)
Biophys. J. 88, 118-131
   Abstract »    Full Text »    PDF »
A statistical mechanical method to optimize energy functions for protein folding.
U. Bastolla, M. Vendruscolo, and E.-W. Knapp (2000)
PNAS 97, 3977-3981
   Abstract »    Full Text »    PDF »
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.
J. Lee, A. Liwo, and H. A. Scheraga (1999)
PNAS 96, 2025-2030
   Abstract »    Full Text »    PDF »
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution.
Y. Duan and P. A. Kollman (1998)
Science 282, 740-744
   Abstract »    Full Text »
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation.
Y. Duan, L. Wang, and P. A. Kollman (1998)
PNAS 95, 9897-9902
   Abstract »    Full Text »    PDF »
Characteristic temperatures of folding of a small peptide.
U. H. E. Hansmann, M. Masuya, and Y. Okamoto (1997)
PNAS 94, 10652-10656
   Abstract »    Full Text »    PDF »
The combination of symbolic and numerical computation for three-dimensional modeling of RNA.
F Major, M Turcotte, D Gautheret, G Lapalme, E Fillion, and R Cedergren (1991)
Science 253, 1255-1260
   Abstract »    PDF »


ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)