Anisotropy of fluctuation dynamics of proteins with an elastic network model.
Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein.
Atilgan
A R
AR
School of Engineering and Polymer Research Center, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Bebek 80815, Istanbul, Turkey.
Durell
S R
SR
Jernigan
R L
RL
Demirel
M C
MC
Keskin
O
O
Bahar
I
I
D016880:Anisotropy; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D004548:Elasticity; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012177:Retinol-Binding Proteins / Q000737:chemistry; D013816:Thermodynamics
D011506:Proteins; D012177:Retinol-Binding Proteins