Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics.
Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.
Lu
Qiang
Q
State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.
Lu
H Peter
HP
Wang
Jin
J
D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013050:Spectrometry, Fluorescence; D020764:cdc42 GTP-Binding Protein / Q000737:chemistry
D011506:Proteins; D012997:Solvents; D020764:cdc42 GTP-Binding Protein