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Dutta M, Jana B. Computational modeling of dynein motor proteins at work. Chem Commun (Camb) 2021; 57:272-283. [PMID: 33332489 DOI: 10.1039/d0cc05857b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.
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Affiliation(s)
- Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata - 700032, India.
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2
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Cho U, Chen JK. Lanthanide-Based Optical Probes of Biological Systems. Cell Chem Biol 2020; 27:921-936. [PMID: 32735780 DOI: 10.1016/j.chembiol.2020.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/28/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
The unique photophysical properties of lanthanides, such as europium, terbium, and ytterbium, make them versatile molecular probes of biological systems. In particular, their long-lived photoluminescence, narrow bandwidth emissions, and large Stokes shifts enable experiments that are infeasible with organic fluorophores and fluorescent proteins. The ability of these metal ions to undergo luminescence resonance energy transfer, and photon upconversion further expands the capabilities of lanthanide probes. In this review, we describe recent advances in the design of lanthanide luminophores and their application in biological research. We also summarize the latest detection systems that have been developed to fully exploit the optical properties of lanthanide luminophores. We conclude with a discussion of remaining challenges and new frontiers in lanthanide technologies. The unprecedented levels of sensitivity and multiplexing afforded by rare-earth elements illustrate how chemistry can enable new approaches in biology.
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Affiliation(s)
- Ukrae Cho
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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3
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Zhou Y, Srinivasan P, Razavi S, Seymour S, Meraner P, Gudlur A, Stathopulos PB, Ikura M, Rao A, Hogan PG. Initial activation of STIM1, the regulator of store-operated calcium entry. Nat Struct Mol Biol 2013; 20:973-81. [PMID: 23851458 PMCID: PMC3784406 DOI: 10.1038/nsmb.2625] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/21/2013] [Indexed: 12/11/2022]
Abstract
Physiological Ca2+ signalling in T lymphocytes and other cells depends on the STIM-ORAI pathway of store-operated Ca2+ entry. STIM1 and STIM2 are Ca2+ sensors located in the endoplasmic reticulum (ER) membrane, with ER-luminal domains that monitor cellular Ca2+ stores and cytoplasmic domains that gate ORAI channels in the plasma membrane. The STIM ER-luminal domain dimerizes or oligomerizes upon dissociation of Ca2+, but the mechanism transmitting activation to the STIM cytoplasmic domain has not been defined. Here we demonstrate, using Tb3+–acceptor energy transfer, that dimerization of STIM1 ER-luminal domains can initiate an extensive conformational change in murine STIM1 cytoplasmic domains. The conformational change, triggered by apposition of the predicted coiled-coil 1 (CC1) regions, releases the ORAI-activating domains from their interaction with the CC1 regions and allows physical extension of the STIM1 cytoplasmic domain across the gap between ER and plasma membrane to communicate with ORAI channels.
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Affiliation(s)
- Yubin Zhou
- La Jolla Institute for Allergy & Immunology, La Jolla, California, USA
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4
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Laporte D, Coffman VC, Lee IJ, Wu JQ. Assembly and architecture of precursor nodes during fission yeast cytokinesis. ACTA ACUST UNITED AC 2011; 192:1005-21. [PMID: 21422229 PMCID: PMC3063137 DOI: 10.1083/jcb.201008171] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mapping of fission yeast precursor node interaction modules and assembly reveals important steps in contractile ring assembly. The contractile ring is essential for cytokinesis in most fungal and animal cells. In fission yeast, cytokinesis nodes are precursors of the contractile ring and mark the future cleavage site. However, their assembly and architecture have not been well described. We found that nodes are assembled stoichiometrically in a hierarchical order with two modules linked by the positional marker anillin Mid1. Mid1 first recruits Cdc4 and IQGAP Rng2 to form module I. Rng2 subsequently recruits the myosin-II subunits Myo2 and Rlc1. Mid1 then independently recruits the F-BAR protein Cdc15 to form module II. Mid1, Rng2, Cdc4, and Cdc15 are stable node components that accumulate close to the plasma membrane. Both modules recruit the formin Cdc12 to nucleate actin filaments. Myo2 heads point into the cell interior, where they efficiently capture actin filaments to condense nodes into the contractile ring. Collectively, our work characterizing the assembly and architecture of precursor nodes defines important steps and molecular players for contractile ring assembly.
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Affiliation(s)
- Damien Laporte
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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Chiu YL, Chen SA, Chen JH, Chen KJ, Chen HL, Sung HW. A dual-emission Förster resonance energy transfer nanoprobe for sensing/imaging pH changes in the biological environment. ACS NANO 2010; 4:7467-74. [PMID: 21082810 DOI: 10.1021/nn102644u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A dual-emission nanoprobe that can sense changes in the environmental pH is designed based on the concept of pH-responsive Förster resonance energy transfer induced by the conformational transition of an associating polyelectrolyte, N-palmitoyl chitosan, bearing a donor (Cy3) or an acceptor (Cy5) moiety. We demonstrate that the developed pH-responsive nanoprobe can be used to ratiometrically image and thus discriminate the pH changes in the biological environment at different length scales.
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Affiliation(s)
- Ya-Ling Chiu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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6
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Thomas DD, Kast D, Korman VL. Site-directed spectroscopic probes of actomyosin structural dynamics. Annu Rev Biophys 2009; 38:347-69. [PMID: 19416073 DOI: 10.1146/annurev.biophys.35.040405.102118] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Spectroscopy of myosin and actin has entered a golden age. High-resolution crystal structures of isolated actin and myosin have been used to construct detailed models for the dynamic actomyosin interactions that move muscle. Improved protein mutagenesis and expression technologies have facilitated site-directed labeling with fluorescent and spin probes. Spectroscopic instrumentation has achieved impressive advances in sensitivity and resolution. Here we highlight the contributions of site-directed spectroscopic probes to understanding the structural dynamics of myosin II and its actin complexes in solution and muscle fibers. We emphasize studies that probe directly the movements of structural elements within the myosin catalytic and light-chain domains, and changes in the dynamics of both actin and myosin due to their alternating strong and weak interactions in the ATPase cycle. A moving picture emerges in which single biochemical states produce multiple structural states, and transitions between states of order and dynamic disorder power the actomyosin engine.
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Affiliation(s)
- David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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Ghysels A, Van Speybroeck V, Pauwels E, Van Neck D, Brooks BR, Waroquier M. Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules. J Chem Theory Comput 2009; 5:1203-15. [DOI: 10.1021/ct800489r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Ghysels
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - V. Van Speybroeck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - E. Pauwels
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - D. Van Neck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - B. R. Brooks
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - M. Waroquier
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium, and Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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8
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Affiliation(s)
- Pinghua Ge
- Department of Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Paul R. Selvin
- Department of Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
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Lepesheva GI, Seliskar M, Knutson CG, Stourman NV, Rozman D, Waterman MR. Conformational dynamics in the F/G segment of CYP51 from Mycobacterium tuberculosis monitored by FRET. Arch Biochem Biophys 2007; 464:221-7. [PMID: 17585868 PMCID: PMC3042880 DOI: 10.1016/j.abb.2007.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 05/21/2007] [Accepted: 05/22/2007] [Indexed: 11/28/2022]
Abstract
A cysteine was introduced into the FG-loop (P187C) of CYP51 from Mycobacterium tuberculosis (MT) for selective labeling with BODIPY and fluorescence energy transfer (FRET) analysis. Förster radius for the BODIPY-heme pair was calculated assuming that the distance between the heme and Cys187 in solution corresponds to that in the crystal structure of ligand free MTCYP51. Interaction of MTCYP51 with azole inhibitors ketoconazole and fluconazole or the substrate analog estriol did not influence the fluorescence, but titration with the substrate lanosterol quenched BODIPY emission, the effect being proportional to the portion of substrate bound MTCYP51. The detected changes correspond to approximately 10A decrease in the calculated distance between BODIPY-Cys187 and the heme. The results confirm (1) functional importance of conformational motions in the MTCYP51 F/G segment and (2) applicability of FRET to monitor them in solution.
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Affiliation(s)
- Galina I. Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, USA
| | - Matej Seliskar
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Charles G. Knutson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, USA
| | - Nina V. Stourman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, USA
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Michael R. Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, USA
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Abstract
Fluorescence resonance energy transfer (FRET) is a spectroscopic phenomenon that consists of long-range dipole-dipole interaction between two chromophores. This method can be employed to gain quantitative distance information on macromolecules. FRET is particularly useful to characterize structural states of motor proteins, because the spatial relationship between various mechanical elements of the motor undergoing its mechanical cycle is essential to understand how force and movement are generated. In this chapter, we describe the technique, including the equations, methods of introducing fluorescence probes in specific loci of the protein, and data analysis. Practical guidelines and hints are also provided for protein preparation, labeling, and measuring FRET efficiency. The protocol is presented for interhead distance measurements in the dimeric kinesin-like motor, Ncd. However, it can easily be adapted to many other motor proteins.
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Affiliation(s)
- Andrzej A Kasprzak
- Motor Proteins Laboratory, Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
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11
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Guo B, Guilford WH. Mechanics of actomyosin bonds in different nucleotide states are tuned to muscle contraction. Proc Natl Acad Sci U S A 2006; 103:9844-9. [PMID: 16785439 PMCID: PMC1502541 DOI: 10.1073/pnas.0601255103] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Muscle contraction and many other cell movements are driven by cyclic interactions between actin filaments and the motor enzyme myosin. Conformational changes in the actin-myosin binding interface occur in concert with the binding of ATP, binding to actin, and loss of hydrolytic by-products, but the effects of these conformational changes on the strength of the actomyosin bond are unknown. The force-dependent kinetics of the actomyosin bond may be particularly important at high loads, where myosin may detach from actin before achieving its full power stroke. Here we show that over a physiological range of rapidly applied loads, actomyosin behaves as a "catch" bond, characterized by increasing lifetimes with increasing loads up to a maximum at approximately 6 pN. Surprisingly, we found that the myosin-ADP bond is possessed of longer lifetimes under load than rigor bonds, although the load at which bond lifetime is maximal remains unchanged. We also found that actomyosin bond lifetime is ultimately dependent not only on load, but loading history as well. These data suggest a complex relationship between the rate of actomyosin dissociation and muscle force and shortening velocity. The 6-pN load for maximum bond lifetime is near the force generated by a single myosin molecule during isometric contraction. This raises the possibility that all catch bonds between load-bearing molecules are "mechanokinetically" tuned to their physiological environment.
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Affiliation(s)
- Bin Guo
- Department of Biomedical Engineering, University of Virginia, Box 800759, Charlottesville, VA 22908
| | - William H. Guilford
- Department of Biomedical Engineering, University of Virginia, Box 800759, Charlottesville, VA 22908
- To whom correspondence should be addressed. E-mail:
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12
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Abstract
We suggest a simple method to assess how many normal modes are needed to map a conformational change. By projecting the conformational change onto a subspace of the normal-mode vectors and using root mean square deviation as a test of accuracy, we find that the first 20 modes only contribute 50% or less of the total conformational change in four test cases (myosin, calmodulin, NtrC, and hemoglobin). In some allosteric systems, like the molecular switch NtrC, the conformational change is localized to a limited number of residues. We find that many more modes are necessary to accurately map this collective displacement. In addition, the normal-mode "spectra" can provide useful information about the details of the conformational change, especially when comparing structures with different bound ligands, in this case, calmodulin. Indeed, this approach presents normal-mode analysis as a useful basis in which to capture the mechanism of conformational change, and shows that the number of normal modes needed to capture the essential collective motions of atoms should be chosen according to the required accuracy.
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Affiliation(s)
- Paula Petrone
- Department of Biophysics, Stanford University, Stanford, California 94305-5080, USA
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13
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Miller BM, Zhang S, Suggs JA, Swank DM, Littlefield KP, Knowles AF, Bernstein SI. An alternative domain near the nucleotide-binding site of Drosophila muscle myosin affects ATPase kinetics. J Mol Biol 2005; 353:14-25. [PMID: 16154586 DOI: 10.1016/j.jmb.2005.08.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 08/05/2005] [Accepted: 08/10/2005] [Indexed: 11/29/2022]
Abstract
In Drosophila melanogaster expression of muscle myosin heavy chain isoforms occurs by alternative splicing of transcripts from a single gene. The exon 7 domain is one of four variable regions in the catalytic head and is located near the nucleotide-binding site. To ascribe a functional role to this domain, we created two chimeric myosin isoforms (indirect flight isoform-exon 7a and embryonic-exon 7d) that differ from the native indirect flight muscle and embryonic body-wall muscle isoforms only in the exon 7 region. Germline transformation and subsequent expression of the chimeric myosins in the indirect flight muscle of myosin-null Drosophila allowed us to purify the myosin for in vitro studies and to assess in vivo structure and function of transgenic muscles. Intriguingly, in vitro experiments show the exon 7 domain modulates myosin ATPase activity but has no effect on actin filament velocity, a novel result compared to similar studies with other Drosophila variable exons. Transgenic flies expressing the indirect flight isoform-exon 7a have normal indirect flight muscle structure, and flight and jump ability. However, expression of the embryonic-exon 7d chimeric isoform yields flightless flies that show improvements in both the structural stability of the indirect flight muscle and in locomotor abilities as compared to flies expressing the embryonic isoform. Overall, our results suggest the exon 7 domain participates in the regulation of the attachment of myosin to actin in order to fine-tune the physiological properties of Drosophila myosin isoforms.
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Affiliation(s)
- Becky M Miller
- Department of Biology and Molecular Biology Institute, San Diego State University, San Diego, CA 92182-4614, USA
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14
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Sweeney HL, Houdusse A. The motor mechanism of myosin V: insights for muscle contraction. Philos Trans R Soc Lond B Biol Sci 2005; 359:1829-41. [PMID: 15647159 PMCID: PMC1693472 DOI: 10.1098/rstb.2004.1576] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is 50 years since the sliding of actin and myosin filaments was proposed as the basis of force generation and shortening in striated muscle. Although this is now generally accepted, the detailed molecular mechanism of how myosin uses adenosine triphosphate to generate force during its cyclic interaction with actin is only now being unravelled. New insights have come from the unconventional myosins, especially myosin V. Myosin V is kinetically tuned to allow movement on actin filaments as a single molecule, which has led to new kinetic, mechanical and structural data that have filled in missing pieces of the actomyosin-chemo-mechanical transduction puzzle.
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Affiliation(s)
- H Lee Sweeney
- Department of Physiology, University of Pennsylvania School of Medicine, A700 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104-6085, USA.
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15
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Zeng W, Conibear PB, Dickens JL, Cowie RA, Wakelin S, Málnási-Csizmadia A, Bagshaw CR. Dynamics of actomyosin interactions in relation to the cross-bridge cycle. Philos Trans R Soc Lond B Biol Sci 2005; 359:1843-55. [PMID: 15647160 PMCID: PMC1693466 DOI: 10.1098/rstb.2004.1527] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transient kinetic measurements of the actomyosin ATPase provided the basis of the Lymn-Taylor model for the cross-bridge cycle, which underpins current models of contraction. Following the determination of the structure of the myosin motor domain, it has been possible to introduce probes at defined sites and resolve the steps in more detail. Probes have been introduced in the Dicytostelium myosin II motor domain via three routes: (i) single tryptophan residues at strategic locations throughout the motor domain; (ii) green fluorescent protein fusions at the N and C termini; and (iii) labelled cysteine residues engineered across the actin-binding cleft. These studies are interpreted with reference to motor domain crystal structures and suggest that the tryptophan (W501) in the relay loop senses the lever arm position, which is controlled by the switch 2 open-to-closed transition at the active site. Actin has little effect on this process per se. A mechanism of product release is proposed in which actin has an indirect effect on the switch 2 and lever arm position to achieve mechanochemical coupling. Switch 1 closing appears to be a key step in the nucleotide-induced actin dissociation, while its opening is required for the subsequent activation of product release. This process has been probed with F239W and F242W substitutions in the switch 1 loop. The E706K mutation in skeletal myosin IIa is associated with a human myopathy. To simulate this disease we investigated the homologous mutation, E683K, in the Dictyostelium myosin motor domain.
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Affiliation(s)
- Wei Zeng
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK
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16
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Holmes KC, Schröder RR, Sweeney HL, Houdusse A. The structure of the rigor complex and its implications for the power stroke. Philos Trans R Soc Lond B Biol Sci 2005; 359:1819-28. [PMID: 15647158 PMCID: PMC1693467 DOI: 10.1098/rstb.2004.1566] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Decorated actin provides a model system for studying the strong interaction between actin and myosin. Cryo-energy-filter electron microscopy has recently yielded a 14 A resolution map of rabbit skeletal actin decorated with chicken skeletal S1. The crystal structure of the cross-bridge from skeletal chicken myosin could not be fitted into the three-dimensional electron microscope map without some deformation. However, a newly published structure of the nucleotide-free myosin V cross-bridge, which is apparently already in the strong binding form, can be fitted into the three-dimensional reconstruction without distortion. This supports the notion that nucleotide-free myosin V is an excellent model for strongly bound myosin and allows us to describe the actin-myosin interface. In myosin V the switch 2 element is closed although the lever arm is down (post-power stroke). Therefore, it appears likely that switch 2 does not open very much during the power stroke. The myosin V structure also differs from the chicken skeletal myosin structure in the nucleotide-binding site and the degree of bending of the backbone beta-sheet. These suggest a mechanism for the control of the power stroke by strong actin binding.
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Affiliation(s)
- K C Holmes
- Max Planck Institute for Medical Research, 69120 Heidelberg, Germany.
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17
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Gourinath S, Himmel DM, Brown JH, Reshetnikova L, Szent-Györgyi AG, Cohen C. Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head. Structure 2004; 11:1621-7. [PMID: 14656445 DOI: 10.1016/j.str.2003.10.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have extended the X-ray structure determination of the complete scallop myosin head in the pre-power stroke state to 2.6 A resolution, allowing an atomic comparison of the three major (weak actin binding) states of various myosins. We can now account for conformational differences observed in crystal structures in the so-called "pliant region" at the motor domain-lever arm junction between scallop and vertebrate smooth muscle myosins. A hinge, which may contribute to the compliance of the myosin crossbridge, has also been identified for the first time within the regulatory light-chain domain of the lever arm. Analysis of temperature factors of key joints of the motor domain, especially the SH1 helix, provides crystallographic evidence for the existence of the "internally uncoupled" state in diverse isoforms. The agreement between structural and solution studies reinforces the view that the unwinding of the SH1 helix is a part of the cross-bridge cycle in many myosins.
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Affiliation(s)
- S Gourinath
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
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18
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Robblee JP, Olivares AO, de la Cruz EM. Mechanism of nucleotide binding to actomyosin VI: evidence for allosteric head-head communication. J Biol Chem 2004; 279:38608-17. [PMID: 15247304 DOI: 10.1074/jbc.m403504200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined the kinetics of nucleotide binding to actomyosin VI by monitoring the fluorescence of pyrene-labeled actin filaments. ATP binds single-headed myosin VI following a two-step reaction mechanism with formation of a low affinity collision complex (1/K(1)' = 5.6 mm) followed by isomerization (k(+2)' = 176 s-1) to a state with weak actin affinity. The rates and affinity for ADP binding were measured by kinetic competition with ATP. This approach allows a broader range of ADP concentrations to be examined than with fluorescent nucleotide analogs, permitting the identification and characterization of transiently populated intermediates in the pathway. ADP binding to actomyosin VI, as with ATP binding, occurs via a two-step mechanism. The association rate constant for ADP binding is approximately five times greater than for ATP binding because of a higher affinity in the collision complex (1/K(5b)' = 2.2 mm) and faster isomerization rate constant (k(+5a)' = 366 s(-1)). By equilibrium titration, both heads of a myosin VI dimer bind actin strongly in rigor and with bound ADP. In the presence of ATP, conditions that favor processive stepping, myosin VI does not dwell with both heads strongly bound to actin, indicating that the second head inhibits strong binding of the lead head to actin. With both heads bound strongly, ATP binding is accelerated 2.5-fold, and ADP binding is accelerated >10-fold without affecting the rate of ADP release. We conclude that the heads of myosin VI communicate allosterically and accelerate nucleotide binding, but not dissociation, when both are bound strongly to actin.
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Affiliation(s)
- James P Robblee
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Baumann BAJ, Liang H, Sale K, Hambly BD, Fajer PG. Myosin regulatory domain orientation in skeletal muscle fibers: application of novel electron paramagnetic resonance spectral decomposition and molecular modeling methods. Biophys J 2004; 86:3030-41. [PMID: 15111417 PMCID: PMC1304169 DOI: 10.1016/s0006-3495(04)74352-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Accepted: 01/20/2004] [Indexed: 10/21/2022] Open
Abstract
Reorientation of the regulatory domain of the myosin head is a feature of all current models of force generation in muscle. We have determined the orientation of the myosin regulatory light chain (RLC) using a spin-label bound rigidly and stereospecifically to the single Cys-154 of a mutant skeletal isoform. Labeled RLC was reconstituted into skeletal muscle fibers using a modified method that results in near-stoichiometric levels of RLC and fully functional muscle. Complex electron paramagnetic resonance spectra obtained in rigor necessitated the development of a novel decomposition technique. The strength of this method is that no specific model for a complex orientational distribution was presumed. The global analysis of a series of spectra, from fibers tilted with respect to the magnetic field, revealed two populations: one well-ordered (+/-15 degrees ) with the spin-label z axis parallel to actin, and a second population with a large distribution (+/-60 degrees ). A lack of order in relaxed or nonoverlap fibers demonstrated that regulatory domain ordering was defined by interaction with actin rather than the thick filament surface. No order was observed in the regulatory domain during isometric contraction, consistent with the substantial reorientation that occurs during force generation. For the first time, spin-label orientation has been interpreted in terms of the orientation of a labeled domain. A Monte Carlo conformational search technique was used to determine the orientation of the spin-label with respect to the protein. This in turn allows determination of the absolute orientation of the regulatory domain with respect to the actin axis. The comparison with the electron microscopy reconstructions verified the accuracy of the method; the electron paramagnetic resonance determined that axial orientation was within 10 degrees of the electron microscopy model.
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Affiliation(s)
- Bruce A J Baumann
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
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