Collective Motions and Dynamical Couplings in the Kinesin Motor Domain

Abstract

Kinesin motor proteins transport cargo along microtubule tracks to support essential cellular functions including cell growth, axonal signaling and the separation of chromosomes during cell division. All kinesins contain one or more conserved motor domains that modulate binding and movement along microtubules via cycles of ATP hydrolysis. Important conformational transitions occurring during this cycle have been characterized with extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in conformational change and microtubule interaction modulation remain unclear. Here we describe a comprehensive principal component analysis of 114 available motor domain crystallographic structures supplemented with extensive unbiased conventional and accelerated molecular dynamics simulations. This combined approach quantitatively assess the structural and dynamical features of distinct motor domain conformations, characterizes the response to nucleotide hydrolysis and microtubule binding, and probes the apparent allosteric link between functional sites. Simulations of unprecedented length for this system reveal the atomic details of large scale conformational transitions (most notably of the microtubule binding α4-α5, loop8 subdomain, α2b-β4-β6-β7 motor domain tip and loop5 regions), as well as novel dynamical couplings, of distal nucleotide and microtubule binding sites (mediated by loop7 and loop13). Our results also indicate that the crystallographically reported ATP and ADP-like conformations of kinesin in isolation are intrinsically accessible regardless of nucleotide state. Comparison with kinesin-tubulin simulations support a model where complex formation and neck-linker docking leads to a tighter coupling of the microtubule and nucleotide binding regions. Furthermore, mutational simulations highlight sites potentially critical for conformational transitions and allosteric coupling that are prime targets for experimental study.