Allostery Wiring Map for Kinesin Energy Transduction and its Evolution

Abstract

How signals between the kinesin active and cytoskeletal binding sites are transmitted is an open question and an allosteric question. By extracting correlated evolutionary changes within 700؉ sequences, we built a model of residues that are energetically coupled and that define molecular routes for signal transmission. Typically, these coupled residues are located at multiple distal sites and thus are predicted to form a complex, non-linear network that wires together different functional sites in the protein. Of note, our model connected the site for ATP hydrolysis with sites that ultimately utilize its free energy, such as the microtubule-binding site, drug-binding loop 5, and necklinker. To confirm the calculated energetic connectivity between non-adjacent residues, double-mutant cycle analysis was conducted with 22 kinesin mutants. There was a direct correlation between thermodynamic coupling in experiment and evolutionarily derived energetic coupling. We conclude that energy transduction is coordinated by multiple distal sites in the protein rather than only being relayed through adjacent residues. Moreover, this allosteric map forecasts how energetic orchestration gives rise to different nanomotor behaviors within the superfamily.Biological motors function by converting the chemical energy of ATP hydrolysis into mechanical work in the cell. Thus, molecular motors are free energy transducers, i.e. free energy from the active site is redistributed through the motor protein and ultimately produces a new protein conformational state. Diverse microtubule (MT)-based 2 functions arise in part from differences in their mechanotransduction cycle. For example, members of certain kinesin families are capable of transporting cargo, whereas others modify the MT track (reviewed in Ref. 1).Our goal here is identification of key residues that choreograph transduction between the active site and the microtubule-binding site (see Fig. 1A). It is anticipated that this set of residues couples components that catalyze the free energy-donating reaction with the free energy-accepting ones that result in directed motion. Furthermore, this wiring network should be shared among kinesins and predict adjustment of mechanotransduction between motor families. Such knowledge would reveal mutations that can be used to systematically tune motor protein function.By definition, mechanotransduction is one form of allostery, given that its quintessential property is long range communication. Long range effects in kinesin have been reported. In the first type of study, allosteric mechanisms are inferred from comparisons of well populated conformational states (2, 3) and are primarily descriptive. In the second, molecular dynamics calculations describe dynamic properties of motor proteins as thermally stochastic and yet asymmetric (see Fig. 1B; reviewed in Refs. 4 -6). Theoretical treatments of allostery in other systems also show promise in uncovering fundamental principles of energy conversion, such as the idea that energy storage and transmi...

Pathogenic Mutations in the Kinesin-3 Motor KIF1A Diminish Force Generation and Movement Through Allosteric Mechanisms

“…The V8M mutation is located in b1, immediately following the CS, and may therefore prevent CNB formation. Notably, a valine in this position is highly conserved across the kinesin superfamily [ Fig S1, (45)]. The Y89D mutation is located at the a1-b3 intersection and an aromatic residue (tyrosine or phenylalanine) at this position is highly conserved across the kinesin superfamily [ Fig S1, (36,45)].…”

“…Notably, a valine in this position is highly conserved across the kinesin superfamily [ Fig S1, (45)]. The Y89D mutation is located at the a1-b3 intersection and an aromatic residue (tyrosine or phenylalanine) at this position is highly conserved across the kinesin superfamily [ Fig S1, (36,45)]. To provide insights into the molecular effects of these mutations, we performed molecular dynamics (MD) simulations, which predicted attenuating effects of both mutations on the motility and force generation of KIF1A.…”