title: Simulating Protein Fold Switching by Replica Exchange with Tunneling.
abstract: Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms that are essential for its function or are important during folding or association. These various forms populate a multifunnel folding and association landscape where mutations, changes in environment, or interaction with other molecules switch between the encoded folds. We introduce replica exchange with tunneling as a way to efficiently simulate switching between distinct folds of proteins and protein aggregates. The correctness and efficiency of our approach are demonstrated in a series of simulations covering a wide range of proteins, from a small 11-residue large designed peptide to two 56-residue large mutants of the A and B domains of protein G.
authors: Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors: Nathan A
authors: NA
authors: Bernhardt
authors: Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors: Wenhui
authors: W
authors: Xi
authors: Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors: Wei
authors: W
authors: Wang
authors: Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors: Ulrich H E
authors: UH
authors: Hansmann
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D000685:Serum Amyloid A Protein / Q000737:chemistry / Q000378:metabolism; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins; D000685:Serum Amyloid A Protein