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Published online on November 24, 2003, 10.1073/pnas.2436463100
PNAS | December 9, 2003 | vol. 100 | no. 25 | 14812-14816


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BIOPHYSICS
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

Jorge A. Vila * {dagger}, Daniel R. Ripoll {ddagger}, and Harold A. Scheraga * §

*Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; {dagger}Facultad de Ciencias Físico Matemáticas y Naturales, Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Universidad Nacional de San Luis, Ejército de Los Andes 950-5700 San Luis, Argentina; and {ddagger}Computational Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, NY 14853-3801

Contributed by Harold A. Scheraga, October 6, 2003

The conformational space of the 10–55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 Å and 4.54 Å were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information.

Abbreviations: ECEPP/3, empirical conformational energy program for peptides; EDMC, electrostatically driven Monte Carlo; RMSD, rms deviation; SRFOPT, solvent radii fixed with atomic solvation parameters OPTimized; OONS, Ooi, Oobatake, Némethy, and Scheraga solvation model.

Residue numbers correspond to those used for the NMR form in the Protein Data Bank: file 1BDD.

|| Residue numbers correspond to those used for the crystalline form in the Protein Data Bank: file 1FC2.

§ To whom correspondence should be addressed. E-mail: has5{at}cornell.edu.


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