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PreprintCited by 12Cardiomyopathy and Myosin StudiesProtein Structure and DynamicsMicrotubule and mitosis dynamics

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High resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory

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Chavali, Sai Shashank, Carman, Peter J., Shuman, Henry, Ostap, E. Michael, Sindelar, Charles V.·2025·Proceedings of the National Academy of Sciences
DOI 10.1101/2025.01.10.632429PMC PMC11892617

Preprint — published as 10.1073/pnas.2415457122 · Paper page

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Abstract

Myosin-IC (myo1c) is a class-I myosin that supports transport and remodeling of the plasma membrane and membrane-bound vesicles. Like other members of the myosin family, its biochemical kinetics are altered in response to changes in mechanical loads that resist the power stroke. However, myo1c is unique in that the primary force-sensitive kinetic transition is the isomerization that follows ATP binding, not ADP release as in other slow myosins. Myo1c also powers actin gliding along curved paths, propelling actin filaments in leftward circles. To understand the origins of this unique force-sensing and motile behavior, we solved actin-bound myo1c cryo-EM structures in the presence and absence of ADP. Our structures reveal that in contrast with other myosins, the myo1c lever arm swing is skewed, partly due to a different actin interface that reorients the motor domain on actin. The structures also reveal unique nucleotide-dependent behavior of both the nucleotide pocket as well as an element called the N-terminal extension. We incorporate these observations into a model that explains why force primarily regulates ATP binding in myo1c, rather than ADP release as in other myosins. Integrating our cryo-EM data with available crystallography structures allows the modeling of full-length myo1c during force generation, supplying insights into its role in membrane remodeling. These results highlight how relatively minor sequence differences in members of the myosin superfamily can significantly alter power stroke geometry and force-sensing properties, with important implications for biological function. Significance Statement: Myosin-IC (myo1c) uses an ATP-driven ‘power-stroke’ to support slow intracellular membrane and vesicle transport. We used cryo-electron microscopy to understand adaptations of myo1c to perform its unique roles. We discovered an altered interface between myo1c and actin compared with the closely related myo1b, which repositions the motor domain and alters the trajectory of its lever arm swing compared to other myosins. This explains why myo1c propels actin filaments in a leftward circular path. We also discovered a unique role in force sensing for a structural element called the N-terminal extension and built a full-length atomic model for the myo1c power-stroke. Our findings highlight how myosins can tune their power-stroke geometries and force-sensing properties to adapt to diverse cellular functions.

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Figures

Fig. 1. ADP-dependent lever swing of myo1c revealed by near-atomic cryo-EM structures. (A) View of the 2.8 Å resolution structure of actin-bound ADP myo1c, in the AM.ADPA state. The actin barbed-end points out of the page, slightly obliquely, toward the reader. Myosin subdomains are color coded as follows: (yellow) upper-50 kDa domain; (caramel) lower 50-kDa domain; (light blue) N-terminal subdomain; (light green) HF and HH helices; (light pink) lever arm plus converter; (red) ADP; (magenta) N-terminal extension (NTE). Only a few C-terminal residues of the NTE are ordered (dashed box). (B) Cryo-EM structure of the myo1c AM.ADPB state with identical coloring and view as AM.ADPA. The lever arm swings 24° relative to AM.ADPA, and density for docked NTE bridges between the lever and the N-terminal subdomain. (C) AM state of myo1c cryo-EM structure, showing a lever position very similar to AM.ADPB. (D) AM myo1cΔN cryo-EM structure, showing a lever that reorients ~7° back toward the AM.ADPA position compared with wild-type. Density maps are shown as colored isosurfaces superposed on the molecular models, which are rendered with ribbon cartoons. To improve visibility of lever features, the isosurface contour threshold level is locally decreased in all four panels (SI Appendix, Fig. S1). The actomyosin ATPase scheme is shown with correlated structural states identified by figure panel.
Fig. 1. ADP-dependent lever swing of myo1c revealed by near-atomic cryo-EM structures. (A) View of the 2.8 Å resolution structure of actin-bound ADP myo1c, in the AM.ADPA state. The actin barbed-end points out of the page, slightly obliquely, toward the reader. Myosin subdomains are color coded as follows: (yellow) upper-50 kDa domain; (caramel) lower 50-kDa domain; (light blue) N-terminal subdomain; (light green) HF and HH helices; (light pink) lever arm plus converter; (red) ADP; (magenta) N-terminal extension (NTE). Only a few C-terminal residues of the NTE are ordered (dashed box). (B) Cryo-EM structure of the myo1c AM.ADPB state with identical coloring and view as AM.ADPA. The lever arm swings 24° relative to AM.ADPA, and density for docked NTE bridges between the lever and the N-terminal subdomain. (C) AM state of myo1c cryo-EM structure, showing a lever position very similar to AM.ADPB. (D) AM myo1cΔN cryo-EM structure, showing a lever that reorients ~7° back toward the AM.ADPA position compared with wild-type. Density maps are shown as colored isosurfaces superposed on the molecular models, which are rendered with ribbon cartoons. To improve visibility of lever features, the isosurface contour threshold level is locally decreased in all four panels (SI Appendix, Fig. S1). The actomyosin ATPase scheme is shown with correlated structural states identified by figure panel.CC BY-NC-ND · PubMed Central
Fig. 2. Structural origin of a skewed lever swing in myo1c. See also SI Appendix, Figs. S6 and S7 and Movies S0 and S1. (A) Side view of acto-myo1c (actin axis is horizontal) showing eight-degree rotation of the myo1c motor domain on actin compared with myo1b. Myo1b (14) (transparent ribbons) and myo1c cryo-EM structures (colored ribbons) are aligned by their central three actin subunits. Starting from this alignment, a thick red cylinder depicts the binding reorientation axis required for least-squares superposition of rigor myo1b upper and lower 50-kDa domains onto myo1c; the axes for ADP-state superpositions are similar. The reorientation tilts the lever arm helix (pink ribbons with cylinders running through them, and white ribbons and cylinders for myo1c and myo1b, respectively) toward the actin pointed-end. Three myosin loops whose actin contacts are linked to the binding orientation change are depicted as green van der Waals spheres. Full details of the binding reorientation axis calculation are given in the Movie S1 caption. (B), Orthogonal view of (A) revealing that the ADP lever arm swing of myo1c is more skewed (larger off-axis component) than myo1b. Lever rotation axes defining the hinge points of the myo1b and myo1c ADP lever swings are depicted as thin cylinders, colored white and pink, respectively. Full details of lever arm rotation axis estimation are given in SI Appendix, Fig. S7. For reference, the black vertical dashed line denotes a lever rotation axis with no off-axis component (C) Restructuring of myo1c loop-3 that accommodates its repositioning on the actin surface compared with myo1b (SI Appendix, Fig. S6A). In this and the following panels, structure alignments are the same as (A) and (B) and the viewing angles are close to (A), but individually adjusted for best viewing of selected elements. (D) Side chain substitutions in the myo1c activation loop that accommodate its repositioning on the actin surface compared with myo1b (SI Appendix, Fig. S6B). (E) Restructuring of myo1c loop-2 accommodates the orientation change (SI Appendix, Fig. S6 C and D and Movie S2). Conserved side chains that serve as anchor pivots for the myo1b to myo1c reorientation are represented using van der Waals spheres. Note that, different to Fig. 2 A and B, the binding reorientation axis is rendered in this panel as a thin rather than thick cylinder.
Fig. 2. Structural origin of a skewed lever swing in myo1c. See also SI Appendix, Figs. S6 and S7 and Movies S0 and S1. (A) Side view of acto-myo1c (actin axis is horizontal) showing eight-degree rotation of the myo1c motor domain on actin compared with myo1b. Myo1b (14) (transparent ribbons) and myo1c cryo-EM structures (colored ribbons) are aligned by their central three actin subunits. Starting from this alignment, a thick red cylinder depicts the binding reorientation axis required for least-squares superposition of rigor myo1b upper and lower 50-kDa domains onto myo1c; the axes for ADP-state superpositions are similar. The reorientation tilts the lever arm helix (pink ribbons with cylinders running through them, and white ribbons and cylinders for myo1c and myo1b, respectively) toward the actin pointed-end. Three myosin loops whose actin contacts are linked to the binding orientation change are depicted as green van der Waals spheres. Full details of the binding reorientation axis calculation are given in the Movie S1 caption. (B), Orthogonal view of (A) revealing that the ADP lever arm swing of myo1c is more skewed (larger off-axis component) than myo1b. Lever rotation axes defining the hinge points of the myo1b and myo1c ADP lever swings are depicted as thin cylinders, colored white and pink, respectively. Full details of lever arm rotation axis estimation are given in SI Appendix, Fig. S7. For reference, the black vertical dashed line denotes a lever rotation axis with no off-axis component (C) Restructuring of myo1c loop-3 that accommodates its repositioning on the actin surface compared with myo1b (SI Appendix, Fig. S6A). In this and the following panels, structure alignments are the same as (A) and (B) and the viewing angles are close to (A), but individually adjusted for best viewing of selected elements. (D) Side chain substitutions in the myo1c activation loop that accommodate its repositioning on the actin surface compared with myo1b (SI Appendix, Fig. S6B). (E) Restructuring of myo1c loop-2 accommodates the orientation change (SI Appendix, Fig. S6 C and D and Movie S2). Conserved side chains that serve as anchor pivots for the myo1b to myo1c reorientation are represented using van der Waals spheres. Note that, different to Fig. 2 A and B, the binding reorientation axis is rendered in this panel as a thin rather than thick cylinder.CC BY-NC-ND · PubMed Central
Fig. 3. Nucleotide-dependent domain movements related to ADP release from actin-bound myo1c. (A) Subdomain rotations comparing our AM.ADPA and AM.ADPB structures, from a reference alignment where lower 50 kDa subdomains are superimposed. The myo1c lever/converter and other domains are represented as isosurfaces of 16 Å resolution synthetic density maps generated from our atomic models of AM.ADPA and AM myo1c; domains are colored as in Fig. 1. Colored cylinders depict the rotation axis required to superimpose respective myo1b and myo1c subdomains with respect to the reference alignment. Colored arrows denote the rotation direction. Subdomains rotate very little except for the (pink) lever/converter where a significant lever swing is evident. The lever rotation axis (pink colored cylinder) is positioned at the structural hinge location as in Fig. 2 A and B. The remaining rotation axes are positioned at the respective subunit centers of mass. (B and C) Analysis as in (A) showing that nucleotide-binding subdomain rotations going from AM.ADPB to AM are subtle and are partially reversed in the AM myo1cΔN structure. (D–G) Details of the nucleotide pocket for the four myo1c structures. Atomic models are rendered as ribbon cartoons with stick models for selected residues; reference ribbon structures corresponding to the comparisons in (A–C) are overlaid as transparent silhouettes. Strained H-bond between the P-loop and A-loop is colored red in (F). Subdomain rotations and shifts were estimated using published python scripts (25) within UCSF ChimeraX (26).
Fig. 3. Nucleotide-dependent domain movements related to ADP release from actin-bound myo1c. (A) Subdomain rotations comparing our AM.ADPA and AM.ADPB structures, from a reference alignment where lower 50 kDa subdomains are superimposed. The myo1c lever/converter and other domains are represented as isosurfaces of 16 Å resolution synthetic density maps generated from our atomic models of AM.ADPA and AM myo1c; domains are colored as in Fig. 1. Colored cylinders depict the rotation axis required to superimpose respective myo1b and myo1c subdomains with respect to the reference alignment. Colored arrows denote the rotation direction. Subdomains rotate very little except for the (pink) lever/converter where a significant lever swing is evident. The lever rotation axis (pink colored cylinder) is positioned at the structural hinge location as in Fig. 2 A and B. The remaining rotation axes are positioned at the respective subunit centers of mass. (B and C) Analysis as in (A) showing that nucleotide-binding subdomain rotations going from AM.ADPB to AM are subtle and are partially reversed in the AM myo1cΔN structure. (D–G) Details of the nucleotide pocket for the four myo1c structures. Atomic models are rendered as ribbon cartoons with stick models for selected residues; reference ribbon structures corresponding to the comparisons in (A–C) are overlaid as transparent silhouettes. Strained H-bond between the P-loop and A-loop is colored red in (F). Subdomain rotations and shifts were estimated using published python scripts (25) within UCSF ChimeraX (26).CC BY-NC-ND · PubMed Central
Fig. 4. Conformational changes in the myo1c and myo1b lever arm and NTE associated with ADP release and force-sensitivity. (A) Overview of the myo1c structure, shown in the AM state with a docked N-terminal extension; viewing angle and coloring are the same as in Figs. 1 and 3. (B) Close-up of the docked NTE in (A), highlighting electrostatic interactions (ball-and-stick-rendered side chains) unique to myo1c that lock the lever orientation with respect to the N-terminal subdomain, including a cation–pi stacking interaction between R8 in the NTE and F689 in the lever. A hydrophobically interacting side chain pair is depicted using VDW spheres. (C–E) Angle-dependent changes in lever–motor domain interactions for different myo1c conformational substates. View is of the same region as in (B), but from the opposite side (180° rotation around y). Residues depicted as VDW spheres are involved in a hydrophobic contact bridge (“L5–lever bridge”) between the lever and loop-5, which severs upon lever rotation from the (C) AM.ADPA to (D) AM states. Curved arrows indicate interaction changes of residue pair F74-Y75 in loop-5. Cryo-EM density in this region of the AM structure is essentially indistinguishable from the AM.ADPB structure (SI Appendix, Fig. S10). (E) Myo1cΔN AM state. (F and G), Corresponding region in myo1b AM.ADPA and AM structures (14), showing that the L5–lever bridge distorts but does not break during ADP release.
Fig. 4. Conformational changes in the myo1c and myo1b lever arm and NTE associated with ADP release and force-sensitivity. (A) Overview of the myo1c structure, shown in the AM state with a docked N-terminal extension; viewing angle and coloring are the same as in Figs. 1 and 3. (B) Close-up of the docked NTE in (A), highlighting electrostatic interactions (ball-and-stick-rendered side chains) unique to myo1c that lock the lever orientation with respect to the N-terminal subdomain, including a cation–pi stacking interaction between R8 in the NTE and F689 in the lever. A hydrophobically interacting side chain pair is depicted using VDW spheres. (C–E) Angle-dependent changes in lever–motor domain interactions for different myo1c conformational substates. View is of the same region as in (B), but from the opposite side (180° rotation around y). Residues depicted as VDW spheres are involved in a hydrophobic contact bridge (“L5–lever bridge”) between the lever and loop-5, which severs upon lever rotation from the (C) AM.ADPA to (D) AM states. Curved arrows indicate interaction changes of residue pair F74-Y75 in loop-5. Cryo-EM density in this region of the AM structure is essentially indistinguishable from the AM.ADPB structure (SI Appendix, Fig. S10). (E) Myo1cΔN AM state. (F and G), Corresponding region in myo1b AM.ADPA and AM structures (14), showing that the L5–lever bridge distorts but does not break during ADP release.CC BY-NC-ND · PubMed Central
Fig. 5. Full-length myo1c model complexed with actin suggests roles in membrane remodeling. (A) VDW sphere representation depicting the two-step lever swing associated with Pi release and ADP release. The myo1c ADP·Pi state is represented by the crystal structure of a myo1c vanadate cocomplex [PDB: 4BYF; (30)]; this structure is docked to actin by aligning the lower 50 kDa subdomain with our AM structure. (B and C) Putative motion of myo1c and actin during the power stroke when the myo1c tail is anchored to a membrane, as inferred from the structures in (A). (B) If the actin filament orientation is held fixed with respect to the membrane, the power stroke increases the distance between the actin filament and the membrane. (C) If the myo1c tail orientation is held fixed with respect to the membrane, the power stroke rotates the filament, swiveling the barbed end toward the membrane.
Fig. 5. Full-length myo1c model complexed with actin suggests roles in membrane remodeling. (A) VDW sphere representation depicting the two-step lever swing associated with Pi release and ADP release. The myo1c ADP·Pi state is represented by the crystal structure of a myo1c vanadate cocomplex [PDB: 4BYF; (30)]; this structure is docked to actin by aligning the lower 50 kDa subdomain with our AM structure. (B and C) Putative motion of myo1c and actin during the power stroke when the myo1c tail is anchored to a membrane, as inferred from the structures in (A). (B) If the actin filament orientation is held fixed with respect to the membrane, the power stroke increases the distance between the actin filament and the membrane. (C) If the myo1c tail orientation is held fixed with respect to the membrane, the power stroke rotates the filament, swiveling the barbed end toward the membrane.CC BY-NC-ND · PubMed Central
Fig. 6. Schematic model of force-mediated nucleotide exchange in actin-bound myo1c and myo1b. (A) Force-insensitive ADP release and force-sensitive ATP binding in myo1c. The ADP lever swing is proposed to consist of several force-insensitive substeps: 1) slow detachment of the lever from loop-5 with little lever movement, possibly initiated by isomerization of F77-Y78 in loop-5 (Fig. 4); 2) ADP lever swing, uncoupled from the nucleotide pocket conformation due to plasticity in the loop that connects the converter to SH2 in the motor domain (see SI Appendix, Fig. S11); 3) docking of the NTE, which bridges between the lever and the motor domain and opens the nucleotide pocket slightly to accelerate ADP release (Fig. 3). The undocked or docked NTE is depicted as a dashed red line (labeled “Nu”) or red-colored wedge (“Nd”), respectively. In the absence of the NTE (Myo1cΔN; Bottom cartoon in panel A), opening of the nucleotide pocket is destabilized, introducing a subpopulation that releases ADP slowly. Following ADP release, the docked NTE tightly couples lever position to nucleotide pocket conformation in the wild-type motor. This confers force-sensitivity to subsequent motor isomerizations that accompany ATP binding, likely involving further movement of the lever that has not been visualized (15). Lacking a docked NTE, ATP binding is uncoupled from lever movement in Myo1cΔN, eliminating force sensitivity. (B) Model for force-sensitive ADP release and ATP binding in myo1b. Unlike myo1c, the lever maintains continuous contact with loop-5 in the motor domain during the ADP lever swing, which is proposed to impart force-sensitivity to this step. The myo1b NTE also has a different role than in myo1c, maintaining interactions with the hydrophobic bridge throughout ADP release and “catalyzing” this step by preferentially stabilizing the transition state (presumed similar to AM.ADPB) and final state (AM) over the AM.ADPA state. The red X’s between motor domain and lever (panel A, Top row, Middle two states) denote severing of the Φ-bridge. The partially docked myo1b NTE in the ADPA state is depicted as a small red-colored wedge and a dashed red line (labeled “Np”), while the fully docked myo1b NTE is depicted as a larger red-colored wedge (“Nd”). Note that AM.ADPB and AM structures are combined as a single depicted image in (A) and (B); this transition is unlikely to contribute to force sensitivity due to minimal motion of the lever in either myo1b or myo1c.
Fig. 6. Schematic model of force-mediated nucleotide exchange in actin-bound myo1c and myo1b. (A) Force-insensitive ADP release and force-sensitive ATP binding in myo1c. The ADP lever swing is proposed to consist of several force-insensitive substeps: 1) slow detachment of the lever from loop-5 with little lever movement, possibly initiated by isomerization of F77-Y78 in loop-5 (Fig. 4); 2) ADP lever swing, uncoupled from the nucleotide pocket conformation due to plasticity in the loop that connects the converter to SH2 in the motor domain (see SI Appendix, Fig. S11); 3) docking of the NTE, which bridges between the lever and the motor domain and opens the nucleotide pocket slightly to accelerate ADP release (Fig. 3). The undocked or docked NTE is depicted as a dashed red line (labeled “Nu”) or red-colored wedge (“Nd”), respectively. In the absence of the NTE (Myo1cΔN; Bottom cartoon in panel A), opening of the nucleotide pocket is destabilized, introducing a subpopulation that releases ADP slowly. Following ADP release, the docked NTE tightly couples lever position to nucleotide pocket conformation in the wild-type motor. This confers force-sensitivity to subsequent motor isomerizations that accompany ATP binding, likely involving further movement of the lever that has not been visualized (15). Lacking a docked NTE, ATP binding is uncoupled from lever movement in Myo1cΔN, eliminating force sensitivity. (B) Model for force-sensitive ADP release and ATP binding in myo1b. Unlike myo1c, the lever maintains continuous contact with loop-5 in the motor domain during the ADP lever swing, which is proposed to impart force-sensitivity to this step. The myo1b NTE also has a different role than in myo1c, maintaining interactions with the hydrophobic bridge throughout ADP release and “catalyzing” this step by preferentially stabilizing the transition state (presumed similar to AM.ADPB) and final state (AM) over the AM.ADPA state. The red X’s between motor domain and lever (panel A, Top row, Middle two states) denote severing of the Φ-bridge. The partially docked myo1b NTE in the ADPA state is depicted as a small red-colored wedge and a dashed red line (labeled “Np”), while the fully docked myo1b NTE is depicted as a larger red-colored wedge (“Nd”). Note that AM.ADPB and AM structures are combined as a single depicted image in (A) and (B); this transition is unlikely to contribute to force sensitivity due to minimal motion of the lever in either myo1b or myo1c.CC BY-NC-ND · PubMed Central

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Metadata

Authors
Chavali, S. S., Carman, P. J., Shuman, H., Ostap, E. M., & Sindelar, C. V.
Affiliations
  • Yale University (US)
  • University of Pennsylvania (US)
Corresponding author
  • Ostap, E. Michael
  • Sindelar, Charles V.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
openRxiv
Published
2025-01-12
Volume
122
Issue
9
Pages
e2415457122-e2415457122
ISSN
0027-8424 (ISSN-L)
DOI
10.1101/2025.01.10.632429
PMC
PMC11892617
OpenAlex
W4408019650
Cited by
12
References
1
Citations by year
2026: 9 · 2025: 3
FWCI
8.38
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
Funders
  • National Science Foundation (CMMI Grant 15-48571, 1548571)
  • Yale University
  • University of Pennsylvania
  • National Institutes of Health
  • National Institute of General Medical Sciences (R01GM110530, R37GM057247)
  • Division of Civil, Mechanical and Manufacturing Innovation (15–48571)
Topics
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiomyopathy and Myosin Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
Keywords
Myo1c, class I myosin, force sensing, ATP binding, N-terminal extension, membrane remodeling, cryo-EM structure

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