title: Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis.
abstract: Kinesin-microtubule (MT) binding plays a critical role in facilitating and regulating the motor function of kinesins. To obtain a detailed structural and energetic picture of kinesin-MT binding, we performed large-scale computational alanine-scanning mutagenesis based on long-time molecular dynamics (MD) simulations of the kinesin-MT complex in both ADP and ATP states. First, we built three all-atom kinesin-MT models: human conventional kinesin bound to ADP and mouse KIF1A bound to ADP and ATP. Then, we performed 30 ns MD simulations followed by kinesin-MT binding free energy calculations for both the wild type and mutants obtained after substitution of each charged residue of kinesin with alanine. We found that the kinesin-MT binding free energy is dominated by van der Waals interactions and further enhanced by electrostatic interactions. The calculated mutational changes in kinesin-MT binding free energy are in excellent agreement with results of an experimental alanine-scanning study with a root-mean-square error of ~0.32 kcal/mol [Woehlke, G., et al. (1997) Cell 90, 207-216]. We identified a set of important charged residues involved in the tuning of kinesin-MT binding, which are clustered on several secondary structural elements of kinesin (including well-studied loops L7, L8, L11, and L12, helices α4, α5, and α6, and less-explored loop L2). In particular, we found several key residues that make different contributions to kinesin-MT binding in ADP and ATP states. The mutations of these residues are predicted to fine-tune the motility of kinesin by modulating the conformational transition between the ADP state and the ATP state of kinesin.
authors.affiliation: Physics Department, University at Buffalo, Buffalo, New York 14260, United States.
authors.forename: Minghui
authors.initials: M
authors.lastname: Li
authors.forename: Wenjun
authors.initials: W
authors.lastname: Zheng
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000409:Alanine / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D016547:Kinesins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D007700:Kinetics; D051379:Mice; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D014404:Tubulin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: C490576:Kif1a protein, mouse; D014404:Tubulin; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D016547:Kinesins; D000409:Alanine