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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc Natl Acad Sci U S A 2019; 116:19777-19785. [PMID: 31506355 DOI: 10.1073/pnas.1818589116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5'-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F1-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.
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Hong L, Vani BP, Thiede EH, Rust MJ, Dinner AR. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Proc Natl Acad Sci U S A 2018; 115:E11475-E11484. [PMID: 30442665 PMCID: PMC6298084 DOI: 10.1073/pnas.1812555115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.
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Affiliation(s)
- Lu Hong
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637
| | - Bodhi P Vani
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Erik H Thiede
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
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Cordova JC, Olivares AO, Lang MJ. Mechanically Watching the ClpXP Proteolytic Machinery. Methods Mol Biol 2018; 1486:317-341. [PMID: 27844434 DOI: 10.1007/978-1-4939-6421-5_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Energy-dependent protein degradation is studied through the dual bead ClpXP motility assay. Processing of folded proteins involves recognition, unfolding, translocation, and degradation stages. A dual optical trap, in a passive force-clamp geometry, exhibits bead-to-bead displacements that directly follow subprocesses underlying protein degradation. Discrete nanometer-scale displacements of the bead position reveal steps, dwells and pauses during the unfolding and translocation substeps. With a few structural modifications to the protease machinery and an engineered substrate, the assay represents a "chassis" for the measurement of a wide range of substrates and related machinery. The methods described faithfully record our assay as implemented, including substrate design, wet assay preparation, and the motility assay experiment protocol. The strategies herein permit adaptation of the ClpXP mechanical assay to a wide range of protein degradation systems.
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Affiliation(s)
- Juan Carlos Cordova
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA
| | - Adrian O Olivares
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA.
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Winardhi RS, Tang Q, Chen J, Yao M, Yan J. Probing Small Molecule Binding to Unfolded Polyprotein Based on its Elasticity and Refolding. Biophys J 2017; 111:2349-2357. [PMID: 27926836 DOI: 10.1016/j.bpj.2016.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/21/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022] Open
Abstract
Unfolded protein, a disordered structure found before folding of newly synthesized protein or after protein denaturation, is a substrate for binding by many cellular factors such as heat-stable proteins, chaperones, and many small molecules. However, it is challenging to directly probe such interactions in physiological solution conditions because proteins are largely in their folded state. In this work we probed small molecule binding to mechanically unfolded polyprotein using sodium dodecyl sulfate (SDS) as an example. The effect of binding is quantified based on changes in the elasticity and refolding of the unfolded polyprotein in the presence of SDS. We show that this single-molecule mechanical detection of binding to unfolded polyprotein can serve, to our knowledge, as a novel label-free assay with a great potential to study many factors that interact with unfolded protein domains, which underlie many important biological processes.
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Affiliation(s)
- Ricksen S Winardhi
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jin Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Mingxi Yao
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.
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Nyquist K, Martin A. Marching to the beat of the ring: polypeptide translocation by AAA+ proteases. Trends Biochem Sci 2013; 39:53-60. [PMID: 24316303 DOI: 10.1016/j.tibs.2013.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/07/2013] [Accepted: 11/12/2013] [Indexed: 11/28/2022]
Abstract
ATP-dependent proteases exist in all cells and are crucial regulators of the proteome. These machines consist of a hexameric, ring-shaped motor responsible for engaging, unfolding, and translocating protein substrates into an associated peptidase for degradation. Here, we discuss recent work that has established how the six motor subunits coordinate their ATP-hydrolysis and translocation activities. The closed topology of the ring and the rigidity of subunit/subunit interfaces cause conformational changes within a single subunit to drive motions in other subunits of the hexamer. This structural effect generates allostery between the ATP-binding sites, leading to a preferred order of binding and hydrolysis events among the motor subunits as well as a unique biphasic mechanism of translocation.
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Affiliation(s)
- Kristofor Nyquist
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Andreas Martin
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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Sen M, Maillard RA, Nyquist K, Rodriguez-Aliaga P, Pressé S, Martin A, Bustamante C. The ClpXP protease unfolds substrates using a constant rate of pulling but different gears. Cell 2013; 155:636-646. [PMID: 24243020 DOI: 10.1016/j.cell.2013.09.022] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 08/09/2013] [Accepted: 09/11/2013] [Indexed: 11/25/2022]
Abstract
ATP-dependent proteases are vital to maintain cellular protein homeostasis. Here, we study the mechanisms of force generation and intersubunit coordination in the ClpXP protease from E. coli to understand how these machines couple ATP hydrolysis to mechanical protein unfolding. Single-molecule analyses reveal that phosphate release is the force-generating step in the ATP-hydrolysis cycle and that ClpXP translocates substrate polypeptides in bursts resulting from highly coordinated conformational changes in two to four ATPase subunits. ClpXP must use its maximum successive firing capacity of four subunits to unfold stable substrates like GFP. The average dwell duration between individual bursts of translocation is constant, regardless of the number of translocating subunits, implying that ClpXP operates with constant "rpm" but uses different "gears."
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Affiliation(s)
- Maya Sen
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Rodrigo A Maillard
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720, USA.,QB3 Institute, University of California, Berkeley, CA 94720, USA
| | - Kristofor Nyquist
- QB3 Institute, University of California, Berkeley, CA 94720, USA.,Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Piere Rodriguez-Aliaga
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720, USA.,QB3 Institute, University of California, Berkeley, CA 94720, USA.,Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Steve Pressé
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720, USA
| | - Andreas Martin
- QB3 Institute, University of California, Berkeley, CA 94720, USA.,Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720, USA.,QB3 Institute, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Department of Physics, University of California, Berkeley, CA 94720, USA.,Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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Roberts AJ, Kon T, Knight PJ, Sutoh K, Burgess SA. Functions and mechanics of dynein motor proteins. Nat Rev Mol Cell Biol 2013; 14:713-26. [PMID: 24064538 DOI: 10.1038/nrm3667] [Citation(s) in RCA: 346] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fuelled by ATP hydrolysis, dyneins generate force and movement on microtubules in a wealth of biological processes, including ciliary beating, cell division and intracellular transport. The large mass and complexity of dynein motors have made elucidating their mechanisms a sizable task. Yet, through a combination of approaches, including X-ray crystallography, cryo-electron microscopy, single-molecule assays and biochemical experiments, important progress has been made towards understanding how these giant motor proteins work. From these studies, a model for the mechanochemical cycle of dynein is emerging, in which nucleotide-driven flexing motions within the AAA+ ring of dynein alter the affinity of its microtubule-binding stalk and reshape its mechanical element to generate movement.
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Affiliation(s)
- Anthony J Roberts
- 1] Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. [2] Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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