Eur. Phys. J. E (2007) 24: 311-316
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

Abstract

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.