1
|
Chou YC. Mechanical mechanism for the translocation of hexameric and nonstructural helicases: Dependence on physical parameters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:21. [PMID: 32303848 DOI: 10.1140/epje/i2020-11944-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
Three recently observed facts of the translocation of actual hexameric and nonstructural (NS) helicases are related to the various physical quantities and are in accordance with the recently proposed mechanical mechanism: a) the translocation of hexameric helicases might be led by either the N-terminal domain (NTD) or C-terminal domain (CTD) depending on which domain has a smaller central pore, b) the translocation speed (vt) of the ring-shaped helicases and NS helicases decreased with decreasing applied tension, and c) a large difference in the vt of the NS helicase was observed for the helicase translocating on DNA and RNA. These findings are the effects of the physical quantities of the helicase/nuclei acid strands on the translocation of helicases and are difficult to explain with biochemical models. We predict that a similar behavior as described in b) and c) is also shown by hexameric helicases. The validity of the mechanical mechanism is demonstrated in simulation experiments.
Collapse
Affiliation(s)
- Y C Chou
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
2
|
Xie P. Non-tight and tight chemomechanical couplings of biomolecular motors under hindering loads. J Theor Biol 2020; 490:110173. [PMID: 31982418 DOI: 10.1016/j.jtbi.2020.110173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 10/25/2022]
Abstract
Biomolecular motors make use of free energy released from chemical reaction (typically ATP hydrolysis) to perform mechanical motion or work. An important issue is whether a molecular motor exhibits tight or non-tight chemomechanical (CM) coupling. The tight CM coupling refers to that each ATPase activity is coupled with a mechanical step, while the non-tight CM coupling refers to that an ATPase activity is not necessarily coupled with a mechanical step. Here, we take kinesin, monomeric DNA helicase, ring-shaped hexameric DNA helicase and ribosome as examples to study this issue. Our studies indicate that some motors such as kinesin, monomeric helicase and ribosome exhibit non-tight CM coupling under hindering forces, while others such as the ring-shaped hexameric helicase exhibit tight or nearly tight CM coupling under any force. For the former, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the CM coupling efficiency, while the ATPase rate is independent or nearly independent of the force. For the latter, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the ATPase rate, while the CM coupling efficiency is independent or nearly independent of the force.
Collapse
Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| |
Collapse
|
3
|
Chakrabarti S, Jarzynski C, Thirumalai D. Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases. Biophys J 2019; 117:867-879. [PMID: 31400912 PMCID: PMC6731385 DOI: 10.1016/j.bpj.2019.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/20/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Helicases are components of the cellular replisome that are essential for unwinding double-strand nucleic acids during the process of replication. Intriguingly, most helicases are inefficient and require either oligomerization or assistance from other partner proteins to increase the processivity of unwinding in the presence of the replication fork, which acts as a barrier to progress. Single-molecule force spectroscopy has emerged as a promising experimental technique to probe how relieving this barrier on the helicase can allow for increased efficiency of unwinding. However, there exists no comprehensive theoretical framework to provide unique interpretations of the underlying helicase kinetics from the force spectroscopy data. This remains a major confounding issue in the field. Here, we develop a mathematical framework and derive analytic expressions for the velocity and run length of a general model of finitely processive helicases, the two most commonly measured experimental quantities. We show that in contrast to the unwinding velocity, the processivity exhibits a universal increase in response to external force, irrespective of the underlying architecture and unwinding kinetics of the helicase. Our work provides the first, to our knowledge, explanation to a wide array of experiments and suggests that helicases may have evolved to maximize processivity rather than speed. To demonstrate the use of our theory on experimental data, we analyze velocity and processivity data on the T7 helicase and provide unique inferences on the kinetics of the helicase. Our results show that T7 is a weakly active helicase that destabilizes the fork ahead by less than 1 kBT and back steps very frequently while unwinding DNA. Our work generates fundamental insights into the force response of helicases and provides a widely applicable method for inferring the underlying helicase kinetics from force spectroscopy data.
Collapse
Affiliation(s)
- Shaon Chakrabarti
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.
| | - Christopher Jarzynski
- Department of Chemistry and Biochemistry, Institute for Physical Sciences and Technology, Department of Physics, University of Maryland, College Park, Maryland
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| |
Collapse
|
4
|
Xie P. Modeling DNA Unwinding by AddAB Helicase-Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD. Cell Mol Bioeng 2018; 12:179-191. [PMID: 31719908 DOI: 10.1007/s12195-018-00563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/29/2018] [Indexed: 01/28/2023] Open
Abstract
Introduction AddAB enzyme is a helicase-nuclease complex that initiates recombinational repair of double-stranded DNA breaks. It catalyzes processive DNA unwinding and concomitant resection of the unwound strands, which are modulated by the recognition of a recombination hotspot called Chi in the 3'-terminated strand. Despite extensive structural, biochemical and single molecule studies, the detailed molecular mechanism of DNA unwinding by the complex and modulation by Chi sequence remains unclear. Methods A model of DNA unwinding by the AddAB complex and modulation by Chi recognition was presented, based on which the dynamics of AddAB complex was studied analytically. Results The theoretical results explain well the available experimental data on effect of DNA sequence on velocity, effect of Chi recognition on velocity, static disorder peculiar to the AddAB complex, and dynamics of pausing of wild-type and mutant AddAB complexes occurring at Chi or Chi-like sequence. Predictions were provided. Comparisons of AddAB complex with other helicase-nuclease complexes such as RecBCD and AdnAB were made. Conclusions The study has strong implications for the molecular mechanism of DNA unwinding by the AddAB complex. The intriguing issues are addressed of why Chi recognition is an inefficient process, how AddAB complex pauses upon recognizing Chi sequence, how the paused state transits to the translocating state, why the mutant AddAB with a stronger affinity to Chi sequence has a shorter pausing lifetime, why the pausing lifetime is sensitive to the solution temperature, and so on.
Collapse
Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190 China
| |
Collapse
|
7
|
Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand J, Bensimon D, Croquette V. A mechanistic study of helicases with magnetic traps. Protein Sci 2017; 26:1314-1336. [PMID: 28474797 PMCID: PMC5477542 DOI: 10.1002/pro.3187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023]
Abstract
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
Collapse
Affiliation(s)
- Samar Hodeib
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Saurabh Raj
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Maria Manosas
- Departament de Física FonamentalFacultat de Física, Universitat de BarcelonaBarcelona08028Spain
- CIBER‐BBN de BioingenieriaBiomateriales y Nanomedicina, Instituto de Sanidad Carlos IIIMadridSpain
| | - Weiting Zhang
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Debjani Bagchi
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Present address: Physics DepartmentFaculty of Science, The M.S. University of BarodaVadodaraGujarat390002India
| | - Bertrand Ducos
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Francesca Fiorini
- Univ Lyon, Molecular Microbiology and Structural Biochemistry, MMSB‐IBCP UMR5086 CNRS/Lyon1Lyon Cedex 769367France
| | - Joanne Kanaan
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Jean‐François Allemand
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - David Bensimon
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia90095
| | - Vincent Croquette
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| |
Collapse
|
8
|
Xie P, Chen H. Mechanism of ribosome translation through mRNA secondary structures. Int J Biol Sci 2017; 13:712-722. [PMID: 28655997 PMCID: PMC5485627 DOI: 10.7150/ijbs.19508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/07/2017] [Indexed: 02/03/2023] Open
Abstract
A ribosome is a macromolecular machine that is responsible for translating the genetic codes in messenger RNA (mRNA) into polypeptide chains. It has been determined that besides translating through the single-stranded region, the ribosome can also translate through the duplex region of mRNA by unwinding the duplex. To understand the mechanism of ribosome translation through the duplex, several models have been proposed to study the dynamics of mRNA unwinding. Here, we present a comprehensive review of these models and also discuss other possible models. We evaluate each model and discuss the consistency and/or inconsistency between the theoretical results that are obtained based on each model and the available experimental data, thus determining which model is the most reasonable one to describe the mRNA unwinding mechanism and dynamics of the ribosome. Moreover, a framework for future studies in this subject is provided.
Collapse
Affiliation(s)
- Ping Xie
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China.,Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China
| |
Collapse
|
10
|
Xie P. Processivity of nucleic acid unwinding and translocation by helicases. Proteins 2016; 84:1590-1605. [PMID: 27410462 DOI: 10.1002/prot.25102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 11/05/2022]
Abstract
Helicases are a class of enzymes that use the chemical energy of NTP hydrolysis to drive mechanical processes such as translocation and nucleic acid (NA) strand separation. Besides the NA unwinding speed, another important factor for the helicase activity is the NA unwinding processivity. Here, we study the NA unwinding processivity with an analytical model that captures the phenomenology of the NA unwinding process. First, we study the processivity of the non-hexameric helicase that can unwind NA efficiently in the form of a monomer and the processivity of the hexameric helicase that can unwind DNA effectively, providing quantitative explanations of the available single-molecule experimental data. Then, we study the processivity of the non-hexameric helicases, in particular UvrD, in the form of a dimer and compare with that in the form of a monomer. The available single-molecule and some biochemical data showing that while UvrD monomer is a highly processive single-stranded DNA translocase it is inactive in DNA unwinding, whereas other biochemical data showing that UvrD is active in both single-stranded DNA translocation and DNA unwinding in the form of a monomer can be explained quantitatively and consistently. In addition, the recent single-molecule data are also explained quantitatively showing that constraining the 2B subdomain in closed conformation by intramolecular cross-linking can convert Rep monomer with a very poor DNA unwinding activity into a superhelicase that can unwind more than thousands of DNA base pairs processively, even against a large opposing force. Proteins 2016; 84:1590-1605. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|