ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes.
We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.
Yun
Mi-Ran
MR
Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Université Paris, France.
Lavery
R
R
Mousseau
N
N
Zakrzewska
K
K
Derreumaux
P
P
D000409:Alanine / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013816:Thermodynamics
D010455:Peptides; D016914:Ribonuclease H; C078856:ribonuclease HI; D000409:Alanine