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. 2013;9(11):e1003329.
doi: 10.1371/journal.pcbi.1003329. Epub 2013 Nov 7.

Mapping the Structural and Dynamical Features of Kinesin Motor Domains

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Free PMC article

Mapping the Structural and Dynamical Features of Kinesin Motor Domains

Guido Scarabelli et al. PLoS Comput Biol. .
Free PMC article

Abstract

Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound). These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck-linker docking leads to a tighter coupling of the microtubule and nucleotide binding regions. Furthermore, simulations highlight sites critical for large-scale conformational changes and the allosteric coupling between distal functional sites.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Structure and catalytic cycle of the kinesin motor domain.
(A) The motor domain is composed of an eight-stranded antiparallel β-sheet surrounded by three major helices on either side. The ATPase catalytic site sits at the top of the β-sheet and is flanked by highly conserved loops, the P-loop (red), SI (blue) and SII (orange), which connect to helices on either side of the central sheet (α2, α3 and α4 respectively). The microtubule-binding interface has been mapped by Alanine scanning mutagenesis and limited proteolysis to the opposite side of the motor domain (green, encompassing the loop11, α4, loop12 and loop8 regions). Adjacent to the motor domain is the neck linker (purple), a flexible region that has been shown to undergo a nucleotide-dependent transition from a disordered to an ordered structure. Loop7 (yellow) and the motor domain tip are also indicated. (B) Motor domain secondary structure topology. β-strands are depicted as triangles and α-helices as circles. Regions are colored as in panel A. (C) Kinesin catalytic cycle. Kinesin (K) has a weak affinity for the microtubule (MT) in the ADP-state. ADP release, which is promoted by MT binding, is followed by strong binding to the MT. Subsequently, ATP binding may occur followed by hydrolysis and product release to regenerate the weakly bound ADP state.
Figure 2
Figure 2. Results of PCA on the kinesin motor domain.
(A) Conformer plot: projection of all kinesin X-ray structures onto the principal planes defined by the two most significant PCs (PC1 and PC2). Structures are colored by ligand bound, triphosphate (red), diphosphate (green), and Eg5 inhibitor (pink). Structures are also labeled with their RCSB PDB code where space permits (see Table S1 for full details). Colored dashed ovals represent the major groupings obtained from hierarchical clustering of the projected structures in the PC1 to PC5 planes (see cluster dendrogram in Figure S1B). Insert: eigenvalue spectrum detailing results obtained from diagonalization of the atomic displacement correlation matrix of Ca atom coordinates. The magnitude of each eigenvalue is expressed as the percentage of the total variance (mean-square fluctuation) captured by the corresponding eigenvector. Labels beside each point indicate the cumulative sum of the total variance accounted for in all preceding eigenvectors. (B) Kinesin motor domain structures colored according to their clustering in PC-space (i.e ovals in panel A). Red = ATP-like, Pink = Eg5 inhibitor-bound, green = ADP-like.
Figure 3
Figure 3. Analysis of structures from aMD simulations of Eg5.
Projection of simulation snapshots sampled every 20ps from (A) nucleotide free, (B) ADP, and (C) ATP simulations onto the first two PCs defined by the X-ray structures (black circles, see Figure 2 and main text).
Figure 4
Figure 4. Time evolution of local and global structural changes.
(A) The protrusion angle of α4 relative to β3. Dashed lines depict the average angle for ATP-like (red) and ADP-like (green) crystallographic structures. (B) The secondary structure content of SI and (C) SII-α4. Yellow represents beta strand, blue alpha helix, and white coil secondary structure types (see text for details). (D) Contact formation and breaking activity during nucleotide free simulations. The plot reports the contact formation events (green), the contact breaking events (red) and total events (gray, formation + breaking) as a function of simulation time.
Figure 5
Figure 5. Residue-residue plot of correlated motions.
The extent of correlation of atomic displacements for all residue pairs during ATP-like (upper triangle) and ADP-like (lower triangle) trajectory segments. The color scale runs from pink (for values ranging between −1 to −0.5), through white (−0.5 to 0.5) to cyan (0.5 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are labeled and indicated schematically with helices in black and strands in gray.
Figure 6
Figure 6. Dynamically coupled networks for ATP-like and ADP-like conformations.
Molecular figures (A and B) highlighting communities (composed of clustered edges – representing residues) for ATP and ADP states respectively. Red spheres indicate residues that occur in a majority of shortest paths connecting nodes in different communities (i.e. residues important for the connection between communities). (C and D) Community network representation (colored as in A and B). Each node (circle) represents a community with its grouped protein regions labeled. The width of connecting lines is proportional to the number of shortest paths passing through corresponding junctions (i.e. their betweenness values). The pathway connecting nucleotide binding switch regions to the neck-linker in the ATP-like conformation graph is highlighted in red. Abbreviations: L = loop, cm = conserved motif, nt = n-terminal, ct = c-terminal.
Figure 7
Figure 7. Results of loop13 G325A/G326A simulations.
(A) Correlation of atomic displacement for all residue pairs for Eg5 mutant G325A/G326A. The color scale runs from pink (for values ranging between −1 to −0.5), through white (−0.5 to 0.5) to cyan (0.5 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are labeled and indicated schematically with helices in black and strands in gray. (B) Molecular representation of dynamic community partitioning for G325A/G326A mutant.

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Grant support

We gratefully acknowledge support from the University of Michigan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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