https://doi.org/10.1140/epje/i2007-10241-1
Regular Article
Optimized folding simulations of protein A
1
Microsoft Research, Station Q, University of California, 93106, Santa Barbara, CA, USA
2
Department of Physics, Michigan Technological University, 49931, Houghton, MI, USA
3
John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425, Jülich, Germany
* e-mail: hansmann@mtu.edu
Received:
9
August
2007
Accepted:
9
November
2007
Published online:
11
December
2007
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 ≈ 3 Å to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only ≈ 10 % frequency in our simulations. Possible shortcomings in our energy function are discussed.
PACS: 87.14.Ee Proteins – / 87.15.Aa Theory and modeling; computer simulation – / 87.15.He Dynamics and conformational changes – / 87.15.Cc Folding and sequence analysis –
© EDP Sciences, Società Italiana di Fisica and Springer-Verlag, 2007