Sampling small-scale and large-scale conformational changes in proteins and molecular complexes.
Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.
Yun
Mi-Ran
MR
Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique et Université Paris 7, 13 Rue Pierre et Marie Curie, 75005 Paris, France.
Mousseau
N
N
Derreumaux
P
P
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D002147:Calmodulin / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D017854:Diphosphotransferases / Q000737:chemistry / Q000378:metabolism; D005095:Exoribonucleases / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D002147:Calmodulin; D010446:Peptide Fragments; D011506:Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; D017854:Diphosphotransferases; C019684:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; D005095:Exoribonucleases; C022535:exoribonuclease II