Optimized folding simulations of protein A.
We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3 A to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only approximately 10 % frequency in our simulations. Possible shortcomings in our energy function are discussed.
Trebst
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Microsoft Research, Station Q, University of California, Santa Barbara, CA 93106, USA.
Hansmann
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UH
D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012399:Rotation; D013205:Staphylococcal Protein A / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
D013205:Staphylococcal Protein A