Protein structural change upon ligand binding: linear response theory.
A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. By regarding ligand binding as an external perturbation, the structural change as a response is described by atomic fluctuations in the ligand-free form and the protein-ligand interactions. The results for three protein systems of various sizes are consistent with the observations in the crystal structures, confirming the validity of the linear relationship between the equilibrium fluctuations and the structural change upon ligand binding.
Ikeguchi
Mitsunori
M
Graduate School of Integrated Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan.
Ueno
Jiro
J
Sato
Miwa
M
Kidera
Akinori
A
D000105:Acetyl Coenzyme A / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002950:Citrate (si)-Synthase / Q000737:chemistry*; D005290:Ferric Compounds / Q000737:chemistry / Q000378:metabolism; D033862:Iron-Binding Proteins / Q000737:chemistry*; D008024:Ligands; D016014:Linear Models; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D006180:Proton-Translocating ATPases / Q000737:chemistry*
D005290:Ferric Compounds; D033862:Iron-Binding Proteins; D008024:Ligands; D000105:Acetyl Coenzyme A; D000255:Adenosine Triphosphate; D002950:Citrate (si)-Synthase; D006180:Proton-Translocating ATPases