The blind search for the closed states of hinge-bending proteins.
The hinge-bending proteins provide the most pronounced example of the large-amplitude slow motions in a number of proteins, which are critical for their functioning. They are often used as the test ground for developing novel approaches to the simulation of slow protein dynamics. In the present study, we present the algorithm, which allows physically-consistent simulations of slow protein dynamics in globular proteins. Our algorithm is based on the hierarchical clustering of the correlation patterns (HCCP) technique of domain identification, which allows subdividing the protein into the hierarchy of the rigid-body-like clusters. The clusters are allowed to rotate relative to one another on the automatically identified hinges. The clusters are found in the course of automated, objective and well-tested procedure. In the present communication, our technique is applied to 10 hinge-bending proteins. For each of the proteins, we performed the blind search for the closed conformation, staring from the open one. Resulting closed conformations are compared with the closed states observed in crystallographic structures. It is shown that our technique produces realistic closed conformations for 8 out of 10 studied proteins. This demonstrates that HCCP technique can be used for finding alternative protein conformations and for sampling the slow motions in proteins.
Yesylevskyy
Semen O
SO
Department of Physics of Biological Systems, Institute of Physics, National Academy of Science of Ukraine, Prospect Nauki, Kiev-03039, Ukraine. yesint3@yahoo.com
Kharkyanen
Valery N
VN
Demchenko
Alexander P
AP
D000465:Algorithms; D000818:Animals; D002147:Calmodulin / Q000737:chemistry; D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000737:chemistry; D006801:Humans; D007781:Lactoferrin / Q000737:chemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D002147:Calmodulin; D011506:Proteins; D019951:DNA Polymerase beta; D007781:Lactoferrin