Figure 1.
The Lymn–Taylor Functional Cycle of Myosin-II–Actin [13–17]
Only a myosin monomer is shown for simplicity. The binding of ATP to the actin–myosin complex (the “rigor state”) leads to rapid dissociation of myosin from actin without immediate hydrolysis of ATP. Coupled with a major structural change in the orientation of the lever arm (recovery stroke), ATP hydrolysis proceeds, after which the motor domain rebinds to actin weakly. Following the release of Pi, the motor domain undergoes “powerstroke” during which the orientation of the lever arm changes back to that in the “rigor state” and the motor domain becomes strongly bound to actin. Dissociation of ADP leads the system back to the “rigor state.” Note that the sum of free-energy drops in an entire cycle is equal to the hydrolysis free energy of ATP in solution, which is the ultimate thermodynamic driving force of the system.
Figure 2.
Structural Differences between Conformations of the D. discoideum Myosin Motor Domain
(A) The difference between the post-rigor (1FMW [18]) and pre-powerstroke (1VOM [19]) states. The structures are aligned based on backbone atoms in the first 650 residues; red and blue correspond to 1FMW, green and yellow correspond to 1VOM. Trp501 is shown in the van der Waals form.
(B) Superposition of the active-site region in 1FMW and 1VOM (same color coding as in (A); the nucleotide is shown in the van der Waals form).
(C) Superposition of the relay helix and relay loop in 1FMW and 1VOM with the same color coding as in (A).
Table 1.
Structural Characteristics for the Three Conformations of the Myosin Motor Domain Characterized with X-ray Crystallographya
Figure 3.
PMF Calculations for the Open/Close of the Active Site with Different Converter Orientations
The reaction coordinate for 1-D PMFs is ΔRMSD relative to the open and closed active-site configurations; those for 2-D PMFs are RMSDs relative to the open and closed active-site configurations.
(A,B) PMFs (in kcal/mol) for the 1FMW:ATP state.
(C,D) PMFs (in kcal/mol) for the 1VOM:ATP state.
(E,F) PMFs (in kcal/mol) for the 1VOM:ADP·Pi state.
(G) Superimposition of the final structure from the 1FMW:ATP simulation at ΔDmin = 2.2 Å (opaque) and the closed reference structure (transparent).
(H) Superimposition of the final structure from the 1VOM:ATP simulation at ΔDmin = 2.2Å (opaque) and the open reference structure (transparent).
Figure 4.
Free-Energy Map (in kcal/mol) for the Conformations of Arg238 Sidechain (χ2, χ3) and Main Chains (ϕ, ψ) in the Switch II Region (454–459), Calculated Using Equations 5 and 6
For each residue, map on the left is for the 1FMW:ATP state and map on the right is for the 1VOM:ATP state.
Table 2.
Dihedral Angles (in Degrees) for Arg238 and Switch II Residues in X-Ray Structures 1FMW [18] and 1VOM [19]
Figure 5.
Displacements of the Cα Atoms in the PMF Simulations of the 1FMW:ATP and 1VOM:ATP States, Relative to the Corresponding X-ray Structure
The structures are taken as the last snapshot from PMF simulations at ΔDmin = 2.2 Å, or at ΔDmin = −2.2 Å. Region A, the C-terminal of the second central ß sheet; Region B, the loop between the N-terminal of the relay helix and Switch II; Regions C and D, the actin-binding clefts.
Figure 6.
Same as Figure 4, but for Residues within the Loop between Switch II and the N-Terminal of the Relay Helix
For each residue, the map on the left is for the 1FMW:ATP state and the map on the right is for the 1VOM:ATP state.
Figure 7.
Structural Properties of the Closed Myosin Active Site During Equilibrium MD Simulations with Different Nucleotide Chemical States (ATP or ADP·Pi)
(A–D) Instantaneous distances between Mg2+ and oxygen atoms in its four nonwater ligands. (A) MM ATP state. (B) MM ADP·Pi state. (C) QM/MM ATP state. (D) QM/MM ADP·Pi state. O1ß refers to O1ß in ATP or ADP; O1γ refers to O1γ in ATP or the closest oxygen atom in Pi; OSer237 refers to Oγ in Ser237; OThr186 refers to Oγ2 in Thr186.
(E) Overlay of the active site in two snapshots from MM simulations with ATP and ADP·Pi, respectively. The one with color coding is for the ATP state while the one in grey is for the ADP·Pi state. The Mg2+-OSer237 distance is much longer in the ADP·Pi-state snapshot, due to displacements in both the Ser237 sidechain and the hydrolyzed nucleotide.
(F) Root mean square fluctuation (RMSF) for Cα atoms in the three critical active-site motifs based on equilibrium MM simulations. Ser237 has notably larger fluctuations in the ADP·Pi state, although the rest residues do not show distinct differences.
Figure 8.
A Schematic Illustration of Thermodynamic Coupling between Processes Involved in the Myosin Detached States (Characterized by the PDB codes 1FMW, 1VOM; see Table 1)
The open(O)/close(C) transition of the active site, the hydrolysis of ATP (TP versus DP·Pi), and the rotation of the converter domain (Down versus Up); different converter orientation is presumed to be correlated with different relay helix conformations as implied in the X-ray structures. The schematic free-energy maps (red indicates high-energy region, blue low-energy region, and green intermediate-energy region) are sketched based on results from the previous QM/MM simulations [29], current PMF simulations, and thermodynamic cycle considerations. The dashed and solid arrows indicate a likely sequence of events during the 1FMW → 1VOM transition.