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Catalytic Strategy Used by the Myosin Motor to Hydrolyze Catalytic strategy used by the myosin motor to PNAS PLUS hydrolyze ATP Farooq Ahmad Kiani and Stefan Fischer1 Computational Biochemistry, Interdisciplinary Center for Scientific Computing, University of Heidelberg, D-69120 Heidelberg, Germany Edited by Donald G. Truhlar, University of Minnesota, Minneapolis, MN, and approved June 6, 2014 (received for review January 30, 2014) − + Myosin is a molecular motor responsible for biological motions triphosphate4 /Mg2 moiety of ATP. A structure of myosin such as muscle contraction and intracellular cargo transport, for bound to the dissociated product (ADP/Pi) has not been which it hydrolyzes adenosine 5’-triphosphate (ATP). Early steps of available so far. This product state is important, because the the mechanism by which myosin catalyzes ATP hydrolysis have inorganic phosphate (Pi) and ADP products are only released been investigated, but still missing are the structure of the final later by myosin, upon rebinding to the actin filament during the ADP·inorganic phosphate (Pi) product and the complete pathway power stroke. This rebinding can only take place when the nu- leading to it. Here, a comprehensive description of the catalytic cleotide is in the ADP/Pi product state. Some residues thought strategy of myosin is formulated, based on combined quantum– to be catalytically relevant are Glu459 (22), Ser181 (23), Ser236 classical molecular mechanics calculations. A full exploration of (24–25), and Gly457 (26) (using the residue numbering of Dic- catalytic pathways was performed and a final product structure tyostelium discoideum), which are all strictly conserved. Whereas was found that is consistent with all experiments. Molecular movies Glu459 has been proposed to act as a general base in the catalysis, of the relevant pathways show the different reorganizations of the exact role played by the other residues remained unclear. Both the H-bond network that lead to the final product, whose associative (9, 17, 21) and dissociative (18, 19) pathways in myosin 2− γ-phosphate is not in the previously reported HPγO4 state, but − have been investigated by combined quantum-classical (QM/MM) in the H2PγO4 state. The simulations reveal that the catalytic strat- simulations. In an associative mechanism, the breaking of the i egy of myosin employs a three-pronged tactic: ( ) Stabilization of Pβ–Oβγ bond is concerted with the attack of water onto the γ − the -phosphate of ATP in a dissociated metaphosphate (PγO3 ) γ-phosphate (Fig. 2A), whereas in a dissociative mechanism state. (ii) Polarization of the attacking water molecule, to abstract they are sequential (Fig. 2B). The simulations have shown that a proton from that water. (iii) Formation of multiple proton wires only dissociative pathways have transition barriers that are low in the active site, for efficient transfer of the abstracted proton to enough to be consistent with the experimental rates (9, 18, 19). various product precursors. The specific role played in this strategy Recently, we have explained how myosin achieves the stabiliza- by each of the three loops enclosing ATP is identified unambigu- − tion of the metaphosphate (PγO3 ) that is generated by the ously. It explains how the precise timing of the ATPase activation dissociative mechanism (20). Furthermore, Nemukhin and co- during the force generating cycle is achieved in myosin. The cata- workers have shown that Glu459 can promote the abstraction of lytic strategy described here for myosin is likely to be very similar a proton from a close-by water (Wa in Fig. 1A) to produce the BIOPHYSICS AND in most nucleotide hydrolyzing enzymes. − attacking OH hydroxyl (Fig. 2B) (18, 19). However, the fate of COMPUTATIONAL BIOLOGY the abstracted proton in the final myosin-bound ADP/Pi product he molecular motor myosin cyclically interacts with the actin has not been elucidated. Without this knowledge the catalytic Tfilament to generate the mechanical force that is used in pathway remains incomplete. living cells to achieve muscle contraction (1), cytokinesis (2, 3), Here we address the open questions about the catalytic and intracellular cargo transport (4). Hydrolysis of one ATP mechanism and present a comprehensive view of the strategy molecule per cycle provides the free energy that drives the acto– used by myosin to catalyze ATP hydrolysis. In particular: (i) myosin interaction cycle, as originally described by Lymn and Taylor (5). ATP is the common energy currency in biology, and is Significance extremely stable in aqueous solution (6, 7). ATPases, the – – enzymes that catalyze the hydrolysis of the Pβ O Pγ anhydride Biomolecular motor proteins like myosin generate mechanical linkage in ATP, are ubiquitous in biology because they are force from the chemical energy of ATP. Like gas engines, they needed to accelerate the release of free energy stored in ATP. 7 have different parts (protein domains) that run through a well- Myosin manages to speed up the hydrolysis by a factor of 10 over defined cycle of motions, consuming one ATP per cycle. Be- the uncatalyzed rate in solution. The experimental uncatalyzed − cause ATP is very stable, motor proteins catalyze its breakdown energy barrier is 29 kcal mol 1 (7, 8), and the catalyzed barrier has − (hydrolysis). The catalytic mechanism is at the core of un- been determined experimentally between 14.4 kcal mol 1 (9) and −1 derstanding how these motors work, because the activation of 14.8 kcal mol (10). Understanding how myosin achieves its the catalytic ATPase-function coordinates the motion of the ATPase function is necessary to understand how myosin works as different domains. Identifying which protein groups are es- a motor, but also helps one to understand the functioning of the sential for catalysis allows one to understand how the precise multitude of other nucleotide hydrolyzing enzymes. The cat- coupling between ATPase activation and mechanical motion is alytic mechanism of ATP hydrolysis in myosin has been stud- achieved. Moreover, ATPases are involved in most biochemical ied extensively with methods such as protein crystallography processes and are expected to have a catalytic strategy very – (11 14), mutagenesis (15, 16), photochemical kinetics (10), and similar to the one reported here. quantum-mechanical simulations of the active site (9, 17–21). This has yielded structures of analogs of the reactant and Author contributions: S.F. designed research; F.A.K. performed research; F.A.K. and S.F. transition states, a list of residues affecting the catalytic pro- analyzed data; and F.A.K. and S.F. wrote the paper. cess, and a number of proposed catalytic pathways. A reactant The authors declare no conflict of interest. (ATP-bound) structure of the catalytically competent state This article is a PNAS Direct Submission. of the Lymn–Taylor cycle, such as the one shown in Fig. 1A, 1To whom correspondence should be addressed. Email: [email protected]. can be derived from the crystals. In that state, three loops (called This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. the Switch 1, the Switch 2, and the P loop) are closed over the 1073/pnas.1401862111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1401862111 PNAS | Published online July 8, 2014 | E2947–E2956 Downloaded by guest on October 1, 2021 catalytic strategy of myosin combines three tactics, and the role of the protein residues that are specifically involved in each tactic can now be identified: The initial metaphosphate intermediate is stabilized by interactions with the P-loop backbone and the + Lys185 side chain (Fig. 1A), which pull negative charge from the γ-phosphate to the α- and β-phosphate groups, thereby fa- voring the dissociation (compare the charge distribution in Fig. 2 A and B). The backbone carbonyl of Ser237 activates the attacking water Wa by polarizing it with a H-bond (Fig. 1A). We find that the role of the Glu459 carboxylic side chain is to po- larize a “helping” water molecule (Wh in Fig. 1A), rather than serving as a general base itself and accepting a proton as pre- viously proposed (18, 19). Water Wh accepts the proton ab- stracted from the attacking water and transiently becomes a + H3O hydronium. The precise positioning of this helping water is achieved by Gly457. The abstracted proton is then transferred from the helping water to the inorganic γ-phosphate group via a proton wire through the side chain of Ser181. Thus, the specific role of the residues involved in the catalytic strategy is now identified for myosin. Significantly, residues that are central to the strategy are located on each of the three active-site loops, so that a primary role can be assigned to each loop: The P loop, the Switch 1, and the Switch 2 are, respectively, responsible for metaphosphate stabilization, polarization of water Wa, and po- larization of water Wh. An overlap of the crystal structures of different myosins in the ATPase competent conformation (listed − in Table 1) shows that they all have identical configurations of Fig. 1. End states of ATP hydrolysis in myosin. (A) ATP4 reactant state R.(B) 3− − the active site, indicating that probably all myosins use the same Final ADP /H2PγO4 product state P. The phosphorus atoms of ATP are colored gold. The adenosine and the two waters coordinating the Mg2+ are catalytic strategy. Analogous active sites are found in other not displayed. Interatomic distances are in Å. All hydrogen bonds of less than motors and ATPases (20), and a similar catalytic strategy is seen 2.8 Å length (between the heavy atoms) are shown as dotted lines. in enzymes catalyzing the hydrolysis of other types of P–O bonds, such as DNA restriction endonucleases (31). Where are the protons positioned in the final ADP/Pi product Results (before F-actin binding)? (ii) How is the abstracted proton The Reactant and Product Structures.
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