single-molecule dynamics reveals cooperative binding-folding in protein recognition单分子动力学显示合作binding-folding蛋白质识别.pdfVIP

Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition 1,2* 2 3* Jin Wang , Qiang Lu , H. Peter Lu 1 State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, People’s Republic of China, 2 Department of Chemistry and Department of Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America, 3 Pacific Northwest National Laboratory, Fundamental Science Division, MSIN K8-88, Richland, Washington, United States of America The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape–inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure (the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state. The single-molecule experimental finding of dynamic fluctuations among the loosely and closely bound conformational