1
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Winokan M, Slocombe L, Al-Khalili J, Sacchi M. Multiscale simulations reveal the role of PcrA helicase in protecting against spontaneous point mutations in DNA. Sci Rep 2023; 13:21749. [PMID: 38065963 PMCID: PMC10709646 DOI: 10.1038/s41598-023-48119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G[Formula: see text]C[Formula: see text]) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.
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Affiliation(s)
- Max Winokan
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford, GU2 7XH, UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, GU2 7XH, UK
| | - Jim Al-Khalili
- School of Mathematics and Physics, University of Surrey, Guildford, GU2 7XH, UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, GU2 7XH, UK.
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2
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Ghasemi F, Tirandaz A. Environment assisted quantum model for studying RNA-DNA-error correlation created due to the base tautomery. Sci Rep 2023; 13:10788. [PMID: 37402822 PMCID: PMC10319750 DOI: 10.1038/s41598-023-38019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
The adaptive mutation phenomenon has been drawing the attention of biologists for several decades in evolutionist community. In this study, we propose a quantum mechanical model of adaptive mutation based on the implications of the theory of open quantum systems. We survey a new framework that explain how random point mutations can be stabilized and directed to be adapted with the stresses introduced by the environments according to the microscopic rules dictated by constraints of quantum mechanics. We consider a pair of entangled qubits consist of DNA and mRNA pair, each coupled to a distinct reservoir for analyzing the spreed of entanglement using time-dependent perturbation theory. The reservoirs are physical demonstrations of the cytoplasm and nucleoplasm and surrounding environments of mRNA and DNA, respectively. Our predictions confirm the role of the environmental-assisted quantum progression of adaptive mutations. Computing the concurrence as a measure that determines to what extent the bipartite DNA-mRNA can be correlated through entanglement, is given. Preventing the entanglement loss is crucial for controlling unfavorable point mutations under environmental influences. We explore which physical parameters may affect the preservation of entanglement between DNA and mRNA pair systems, despite the destructive role of interaction with the environments.
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Affiliation(s)
- Fatemeh Ghasemi
- Department of Energy Engineering, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran.
| | - Arash Tirandaz
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran.
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3
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King B, Winokan M, Stevenson P, Al-Khalili J, Slocombe L, Sacchi M. Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair during DNA Strand Separation. J Phys Chem B 2023; 127:4220-4228. [PMID: 36939840 DOI: 10.1021/acs.jpcb.2c08631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the time scales and dynamics of DNA strand separation and the statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerization reaction. We propose that DNA strand separation allows the stable tautomerization of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.
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Affiliation(s)
- Benjamin King
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Max Winokan
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 7XH, U.K
| | - Paul Stevenson
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Jim Al-Khalili
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, U.K
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, U.K
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4
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Slocombe L, Winokan M, Al-Khalili J, Sacchi M. Proton transfer during DNA strand separation as a source of mutagenic guanine-cytosine tautomers. Commun Chem 2022; 5:144. [PMID: 36697962 PMCID: PMC9814255 DOI: 10.1038/s42004-022-00760-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Proton transfer between the DNA bases can lead to mutagenic Guanine-Cytosine tautomers. Over the past several decades, a heated debate has emerged over the biological impact of tautomeric forms. Here, we determine that the energy required for generating tautomers radically changes during the separation of double-stranded DNA. Density Functional Theory calculations indicate that the double proton transfer in Guanine-Cytosine follows a sequential, step-like mechanism where the reaction barrier increases quasi-linearly with strand separation. These results point to increased stability of the tautomer when the DNA strands unzip as they enter the helicase, effectively trapping the tautomer population. In addition, molecular dynamics simulations indicate that the relevant strand separation time is two orders of magnitude quicker than previously thought. Our results demonstrate that the unwinding of DNA by the helicase could simultaneously slow the formation but significantly enhance the stability of tautomeric base pairs and provide a feasible pathway for spontaneous DNA mutations.
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Affiliation(s)
- Louie Slocombe
- grid.5475.30000 0004 0407 4824Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford, GU2 7XH UK ,grid.5475.30000 0004 0407 4824Department of Chemistry, University of Surrey, Guildford, GU2 7XH UK
| | - Max Winokan
- grid.5475.30000 0004 0407 4824Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford, GU2 7XH UK
| | - Jim Al-Khalili
- grid.5475.30000 0004 0407 4824Department of Physics, University of Surrey, Guildford, GU2 7XH UK
| | - Marco Sacchi
- grid.5475.30000 0004 0407 4824Department of Chemistry, University of Surrey, Guildford, GU2 7XH UK
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5
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Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution. Proc Natl Acad Sci U S A 2022; 119:e2202489119. [PMID: 36037333 PMCID: PMC9457475 DOI: 10.1073/pnas.2202489119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule picometer-resolution nanopore tweezers (SPRNT) to resolve the millisecond single-nucleotide steps of superfamily 1 helicase PcrA as it translocates on, or unwinds, several kilobase-long DNA molecules. We recorded more than two million enzyme steps under various assisting and opposing forces in diverse adenosine tri- and diphosphate conditions to comprehensively explore the mechanochemistry of PcrA motion. Forces applied in SPRNT mimic forces and physical barriers PcrA experiences in vivo, such as when the helicase encounters bound proteins or duplex DNA. We show how PcrA's kinetics change with such stimuli. SPRNT allows for direct association of the underlying DNA sequence with observed enzyme kinetics. Our data reveal that the underlying DNA sequence passing through the helicase strongly influences the kinetics during translocation and unwinding. Surprisingly, unwinding kinetics are not solely dominated by the base pairs being unwound. Instead, the sequence of the single-stranded DNA on which the PcrA walks determines much of the kinetics of unwinding.
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6
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Belan S, Kardar M. Active motion of passive asymmetric dumbbells in a non-equilibrium bath. J Chem Phys 2021; 154:024109. [PMID: 33445886 DOI: 10.1063/5.0030623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Persistent motion of passive asymmetric bodies in non-equilibrium media has been experimentally observed in a variety of settings. However, fundamental constraints on the efficiency of such motion are not fully explored. Understanding such limits, and ways to circumvent them, is important for efficient utilization of energy stored in agitated surroundings for purposes of taxis and transport. Here, we examine such issues in the context of erratic movements of a passive asymmetric dumbbell driven by non-equilibrium noise. For uncorrelated (white) noise, we find a (non-Boltzmann) joint probability distribution for the velocity and orientation, which indicates that the dumbbell preferentially moves along its symmetry axis. The dumbbell thus behaves as an Ornstein-Uhlenbeck walker, a prototype of active matter. Exploring the efficiency of this active motion, we show that in the over-damped limit, the persistence length l of the dumbbell is bound from above by half its mean size, while the propulsion speed v∥ is proportional to its inverse size. The persistence length can be increased by exploiting inertial effects beyond the over-damped regime, but this improvement always comes at the price of smaller propulsion speeds. This limitation is explained by noting that the diffusivity of a dumbbell, related to the product v∥l, is always less than that of its components, thus severely constraining the usefulness of passive dumbbells as active particles.
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Affiliation(s)
- Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia
| | - Mehran Kardar
- Massachusetts Institute of Technology, Department of Physics, Cambridge, Massachusetts 02139, USA
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7
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Dai L, Yu J. Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA. Biochem Biophys Res Commun 2020; 533:97-103. [PMID: 32933752 DOI: 10.1016/j.bbrc.2020.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Oncogenic protein Myc serves as a transcription factor to control cell metabolisms. Myc dimerizes via leucine zipper with its associated partner protein Max to form a heterodimer structure, which then binds target DNA sequences to regulate gene transcription. The regulation depends on Myc-Max binding to DNA and searching for target sequences via diffusional motions along DNA. Here, we conduct structure-based molecular dynamics (MD) simulations to investigate the diffusion dynamics of the Myc-Max heterodimer along DNA. We found that the heterodimer protein slides on the DNA in a rotation-uncoupled manner in coarse-grained simulations, as its two helical DNA binding basic regions (BRs) alternate between open and closed conformations via inchworm stepping motions. In such motions, the two BRs of the heterodimer step across the DNA strand one by one, with step sizes reaching about half of a DNA helical pitch length. Atomic MD simulations of the Myc-Max heterodimer in complex with DNA have also been conducted. Hydrogen bond interactions are revealed between the two BRs and two complementary DNA strands, respectively. In the non-specific DNA binding, the BR from Myc shows an onset of stepping on one association DNA strand and starts detaching from the other strand. Overall, our simulation studies suggest that the inchworm stepping motions of the Myc-Max heterodimer can be achieved during the protein diffusion along DNA.
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Affiliation(s)
- Liqiang Dai
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA, 92697, USA.
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8
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Davidson RB, Hendrix J, Geiss BJ, McCullagh M. Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations. PLoS Comput Biol 2018; 14:e1006103. [PMID: 29659571 PMCID: PMC5919694 DOI: 10.1371/journal.pcbi.1006103] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 04/26/2018] [Accepted: 03/22/2018] [Indexed: 12/29/2022] Open
Abstract
The C-terminus domain of non-structural 3 (NS3) protein of the Flaviviridae viruses (e.g. HCV, dengue, West Nile, Zika) is a nucleotide triphosphatase (NTPase) -dependent superfamily 2 (SF2) helicase that unwinds double-stranded RNA while translocating along the nucleic polymer. Due to these functions, NS3 is an important target for antiviral development yet the biophysics of this enzyme are poorly understood. Microsecond-long molecular dynamic simulations of the dengue NS3 helicase domain are reported from which allosteric effects of RNA and NTPase substrates are observed. The presence of a bound single-stranded RNA catalytically enhances the phosphate hydrolysis reaction by affecting the dynamics and positioning of waters within the hydrolysis active site. Coupled with results from the simulations, electronic structure calculations of the reaction are used to quantify this enhancement to be a 150-fold increase, in qualitative agreement with the experimental enhancement factor of 10–100. Additionally, protein-RNA interactions exhibit NTPase substrate-induced allostery, where the presence of a nucleotide (e.g. ATP or ADP) structurally perturbs residues in direct contact with the phosphodiester backbone of the RNA. Residue-residue network analyses highlight pathways of short ranged interactions that connect the two active sites. These analyses identify motif V as a highly connected region of protein structure through which energy released from either active site is hypothesized to move, thereby inducing the observed allosteric effects. These results lay the foundation for the design of novel allosteric inhibitors of NS3. Non-structural protein 3 (NS3) is a Flaviviridae (e.g. Hepatitis C, dengue, and Zika viruses) helicase that unwinds double stranded RNA while translocating along the nucleic polymer during viral genome replication. As a member of superfamily 2 (SF2) helicases, NS3 utilizes the free energy of nucleotide triphosphate (NTP) binding, hydrolysis, and product unbinding to perform its functions. While much is known about SF2 helicases, the pathways and mechanisms through which free energy is transduced between the NTP hydrolysis active site and RNA binding cleft remains elusive. Here we present a multiscale computational study to characterize the allosteric effects induced by the RNA and NTPase substrates (ATP, ADP, and Pi) as well as the pathways of short-range, residue-residue interactions that connect the two active sites. Results from this body of molecular dynamics simulations and electronic structure calculations are highlighted in context to the NTPase enzymatic cycle, allowing for development of testable hypotheses for validation of these simulations. Our insights, therefore, provide novel details about the biophysics of NS3 and guide the next generation of experimental studies.
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Affiliation(s)
- Russell B. Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
| | - Josie Hendrix
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, United States of America
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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9
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Mhashal AR, Choudhury CK, Roy S. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation. J Mol Model 2016; 22:54. [PMID: 26860503 DOI: 10.1007/s00894-016-2922-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 01/24/2016] [Indexed: 11/26/2022]
Abstract
Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state.
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Affiliation(s)
- Anil R Mhashal
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India
| | | | - Sudip Roy
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India.
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10
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Yu J. Coordination and control inside simple biomolecular machines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:353-84. [PMID: 24446369 DOI: 10.1007/978-3-319-02970-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biomolecular machines can achieve physiological functions precisely and efficiently, though they always operate under fluctuations and noises. We review two types of simple machinery that we have recently studied. The machinery can be regarded as molecular motors. They transform chemical free energy from NTP hydrolysis to mechanical work. One type belongs to small monomeric helicases that move directionally along single-stranded nucleic acid, and may further unwind the duplex part for gene replication or repair. The other type belongs to ring-shaped NTPase motors that also move or transport nucleic acid or protein substrate in a directional manner, such as for genome packaging or protein degradation. The central issue in this review is on how the machinery coordinates essential degrees of freedom during the mechanochemical coupling process. Further concerns include how the coordination and control are manifested in experiments, and how they can be captured well in modeling and computational research. We employed atomistic molecular dynamics simulations, coarse-grained analyses, and stochastic modeling techniques to examine the molecular machines at multiple resolutions and timescales. Detailed descriptions on how the protein interacts with its substrate at interface, as well as how multiple protein subunits are coordinated are summarized.
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Affiliation(s)
- Jin Yu
- Beijing Computational Science Research Center, No 3 Heqing Road, Haidian District, Beijing, 100084, China,
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11
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Erie DA, Weninger KR. Single molecule studies of DNA mismatch repair. DNA Repair (Amst) 2014; 20:71-81. [PMID: 24746644 DOI: 10.1016/j.dnarep.2014.03.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/21/2014] [Accepted: 03/22/2014] [Indexed: 11/30/2022]
Abstract
DNA mismatch repair, which involves is a widely conserved set of proteins, is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair.
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Affiliation(s)
- Dorothy A Erie
- Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, United States
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12
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Wang H, Hong W, Paterson IC, Pu J, Laughton CA. Identification of the PcrA DNA helicase reaction pathway by applying advanced targeted molecular dynamic simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.875170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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The study of interactions between DNA and PcrA DNA helicase by using targeted molecular dynamic simulations. J Mol Model 2013; 19:4997-5006. [PMID: 24068309 DOI: 10.1007/s00894-013-2008-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/08/2013] [Indexed: 10/26/2022]
Abstract
DNA helicases are important enzymes involved in all aspects of nucleic acid metabolism, ranging from DNA replication and repair to recombination, rescue of stalled replication and translation. DNA helicases are molecular motors. Through conformational changes caused by ATP hydrolysis and binding, they move along the template double helix, break the hydrogen bonds between the two strands and separate the template chains, so that the genetic information can be accessed. In this paper, targeted molecular dynamic simulations were performed to study the important interactions between DNA and PcrA DNA helicase, which can not be observed from the crystal structures. The key residues on PcrA DNA helicase that have strong interactions with both double stranded DNA (ds-DNA) and single stranded DNA (ss-DNA) have been identified, and it was found that such interactions mostly exist between the protein and DNA backbone, which indicates that the translocation of PcrA is independent of the DNA sequence. The simulations indicate that the ds-DNA is separated upon ATP rebinding, rather than ATP hydrolysis, which suggests that the two strokes in the mechanism have two different major roles. Firstly, in the power stroke (ATP hydrolysis), most of the translocations of the bases from one pocket to the next occur. In the relaxation stroke (ATP binding), most of the 'work' is being done to 'melt' the DNA at the separation fork. Therefore, we propose a mechanism whereby the translocation of the ss-DNA is powered by ATP hydrolysis and the separation of the ds-DNA is powered by ATP binding.
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14
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Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid. Biophys J 2013; 103:1343-53. [PMID: 22995507 DOI: 10.1016/j.bpj.2012.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/01/2012] [Accepted: 08/06/2012] [Indexed: 01/14/2023] Open
Abstract
The NS3 helicase of Hepatitis C virus is an ATP-fueled molecular motor that can translocate along single-stranded (ss) nucleic acid, and unwind double-stranded nucleic acids. It makes a promising antiviral target and an important prototype system for helicase research. Despite recent progress, the detailed mechanism of NS3 helicase remains unknown. In this study, we have combined coarse-grained (CG) and atomistic simulations to probe the translocation mechanism of NS3 helicase along ssDNA. At the residue level of detail, our CG simulations have captured functionally important interdomain motions of NS3 helicase and reproduced single-base translocation of NS3 helicase along ssDNA in the 3'-5' direction, which is in good agreement with experimental data and the inchworm model. By combining the CG simulations with residue-specific perturbations to protein-DNA interactions, we have identified a number of key residues important to the translocation machinery that agree with previous structural and mutational studies. Additionally, our atomistic simulations with targeted molecular dynamics have corroborated the findings of CG simulations and further revealed key protein-DNA hydrogen bonds that break/form during the transitions. This study offers, to our knowledge, the most detailed and realistic simulations of translocation mechanism of NS3 helicase. The simulation protocol established in this study will be useful for designing inhibitors that target the translocation machinery of NS3 helicase, and for simulations of a variety of nucleic-acid-based molecular motors.
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15
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Kim H, Ha T. Single-molecule nanometry for biological physics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:016601. [PMID: 23249673 PMCID: PMC3549428 DOI: 10.1088/0034-4885/76/1/016601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.
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Affiliation(s)
- Hajin Kim
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
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16
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Palla M, Chen CP, Zhang Y, Li J, Ju J, Liao JC. Mechanism of flexibility control for ATP access of hepatitis C virus NS3 helicase. J Biomol Struct Dyn 2012; 31:129-41. [PMID: 22870946 DOI: 10.1080/07391102.2012.698236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hepatitis C virus (HCV) NS3 helicase couples adenosine triphosphate (ATP) binding and hydrolysis to polynucleotide unwinding. Understanding the regulation mechanism of ATP binding will facilitate targeting of the ATP-binding site for potential therapeutic development for hepatitis C. T324, an amino acid residue connecting domains 1 and 2 of NS3 helicase, has been suggested as part of a flexible hinge for opening of the ATP-binding cleft, although the detailed mechanism remains largely unclear. We used computational simulation to examine the mutational effect of T324 on the dynamics of the ATP-binding site. A mutant model, T324A, of the NS3 helicase apo structure was created and energy was minimized. Molecular dynamics simulation was conducted for both wild type and the T324A mutant apo structures to compare their differences. For the mutant structure, histogram analysis of pairwise distances between residues in domains 1 and 2 (E291-Q460, K210-R464 and R467-T212) showed that separation between the two domains was reduced by ~10% and the standard deviation by ~33%. Root mean square fluctuation (RMSF) analysis demonstrated that residues in close proximity to residue 324 have at least 30% RMSF value reductions in the mutant structure. Solvent RMSF analysis showed that more water molecules were trapped near D290 and H293 in domain 1 to form an extensive interaction network constraining cleft opening. We also demonstrated that the T324A mutation established a new atomic interaction with V331, revealing that an atomic interaction cascade from T324 to residues in domains 1 and 2 controls the flexibility of the ATP-binding cleft.
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Affiliation(s)
- Mirkó Palla
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
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17
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Wang H, Laughton CA. The inhibitory effects of vinylphosphonate-linked thymidine dimers on the unidirectional translocation of PcrA helicase along DNA: a molecular modelling study. Phys Chem Chem Phys 2012; 14:12230-7. [PMID: 22864246 DOI: 10.1039/c2cp41193h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The PcrA DNA helicases are important bacterial enzymes and quintessential examples of molecular motors. Through conformational changes caused by ATP hydrolysis, they move along the template double helix, breaking the hydrogen bonds holding the two strands together, and separating the template chains so that the genetic information can be accessed. The flexibility of the DNA backbone is essential for the unidirectional translocation of PcrA. A modified DNA substrate with reduced backbone rotational flexibility (via an incorporated vinylphosphonate linkage) has previously been designed and tested as a helicase substrate. The results show that a single modification on the backbone is sufficient to inhibit the activity of PcrA. In this paper a range of molecular simulation methods have been applied to examine the structural origins of this inhibitory effect, as it tests our theories of the mechanism of action of this motor. We observe that the chemical modification has different effects on the energetics of DNA translocation through the protein as it reaches different sub-sites.
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Affiliation(s)
- Hao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, P. R. China.
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18
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Abstract
Helicases are a ubiquitous and abundant group of motor proteins that couple NTP binding and hydrolysis to processive unwinding of nucleic acids. By targeting this activity to a wide range of specific substrates, and by coupling it with other catalytic functionality, helicases fulfil diverse roles in virtually all aspects of nucleic acid metabolism. The present review takes a look back at our efforts to elucidate the molecular mechanisms of UvrD-like DNA helicases. Using these well-studied enzymes as examples, we also discuss how helicases are programmed by interactions with partner proteins to participate in specific cellular functions.
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19
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Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations. Proc Natl Acad Sci U S A 2010; 107:20875-80. [PMID: 21081697 DOI: 10.1073/pnas.1014631107] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated.
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20
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Coupling translocation with nucleic acid unwinding by NS3 helicase. J Mol Biol 2010; 404:439-55. [PMID: 20887735 DOI: 10.1016/j.jmb.2010.09.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/27/2010] [Accepted: 09/20/2010] [Indexed: 11/20/2022]
Abstract
We present a semiquantitative model for translocation and unwinding activities of monomeric nonstructural protein 3 (NS3) helicase. The model is based on structural, biochemical, and single-molecule measurements. The model predicts that the NS3 helicase actively unwinds duplex by reducing more than 50% the free energy that stabilizes base pairing/stacking. The unwinding activity slows the movement of the helicase in a sequence-dependent manner, lowering the average unwinding efficiency to less than 1 bp per ATP cycle. When bound with ATP, the NS3 helicase can display significant translocational diffusion. This increases displacement fluctuations of the helicase, decreases the average unwinding efficiency, and enhances the sequence dependence. Also, interactions between the helicase and the duplex stabilize the helicase at the junction, facilitating the helicase's unwinding activity while preventing it from dissociating. In the presence of translocational diffusion during active unwinding, the dissociation rate of the helicase also exhibits sequence dependence. Based on unwinding velocity fluctuations measured from single-molecule experiments, we estimate the diffusion rate to be on the order of 10 s(-1). The generic features of coupling single-stranded nucleic acid translocation with duplex unwinding presented in this work may apply generally to a class of helicases.
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21
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Bowling AP, Palmer AF, Wilhelm L. Contact and impact in the multibody dynamics of motor protein locomotion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:12974-12981. [PMID: 19739622 DOI: 10.1021/la901812k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper presents the development of a rigid multibody dynamics approach to modeling, simulation, and analysis of motor proteins. A key element of this new model is that it retains the mass properties, in contrast to many commonly used models that do not. The mass properties are usually omitted because their inclusion yields a model with multiple time scales whose simulation requires a significant amount of time. However, the proposed model can be numerically integrated in a reasonable amount of time. Thus this approach represents a new method for treating multiple scale models. In addition, retaining the mass properties allows a detailed study of contact and impact between the protein and substrate, which is critical for protein processivity. The new model also provides insights into the characteristics of the protein and its environment, specifically, the effective damping experienced by the protein moving through its fluid environment may be quite small yielding under or critically damped motion. This conclusion runs contrary to the widely accepted notion that the protein's motion is strictly over damped. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of Myosin V.
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Affiliation(s)
- Alan P Bowling
- Department of Mechanical and Aerospace Engineering, The University of Texas at Arlington, Arlington, Texas 76019, USA.
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22
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Liu H, Shi Y, Chen XS, Warshel A. Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases. Proc Natl Acad Sci U S A 2009; 106:7449-54. [PMID: 19383795 PMCID: PMC2678657 DOI: 10.1073/pnas.0900532106] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Indexed: 11/18/2022] Open
Abstract
The molecular origin of the action of helicases is explored, starting with a model built based on the different X-ray structures of the large tumor antigen (LTag) hexameric helicase and a simplified model containing the ionized phosphate backbones of a single-strand DNA. The coupling between the protein structural changes and the translocation process is quantified using an effective electrostatic free-energy surface for the protein/DNA complex. This surface is then used in Langevin dynamics simulations of the time dependence of the translocation process. Remarkably, the simulated motion along the free-energy surface results in a vectorial translocation of the DNA, consistent with the biological process. The electrostatic energy of the system appears to reproduce the directionality of this process. Thus, we are able to provide a consistent structure-based molecular description of the energetic and dynamics of the translocation process. This analysis may have general implications for relating structural models to translocation directionality in helicases and other DNA translocases.
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Affiliation(s)
| | - Yemin Shi
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
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23
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Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proc Natl Acad Sci U S A 2009; 106:1039-44. [PMID: 19151156 DOI: 10.1073/pnas.0806908106] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RecQ-like helicases, which include 5 members in the human genome, are important in maintaining genome integrity. We present a crystal structure of a truncated form of the human RECQ1 protein with Mg-ADP. The truncated protein is active in DNA fork unwinding but lacks other activities of the full-length enzyme: disruption of Holliday junctions and DNA strand annealing. The structure of human RECQ1 resembles that of Escherichia coli RecQ, with some important differences. All structural domains are conserved, including the 2 RecA-like domains and the RecQ-specific zinc-binding and winged-helix (WH) domains. However, the WH domain is positioned at a different orientation from that of the E. coli enzyme. We identify a prominent beta-hairpin of the WH domain as essential for DNA strand separation, which may be analogous to DNA strand-separation features of other DNA helicases. This hairpin is significantly shorter in the E. coli enzyme and is not required for its helicase activity, suggesting that there are significant differences between the modes of action of RecQ family members.
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24
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Withers IM, Mazanetz MP, Wang H, Fischer PM, Laughton CA. Active site pressurization: a new tool for structure-guided drug design and other studies of protein flexibility. J Chem Inf Model 2008; 48:1448-54. [PMID: 18553961 DOI: 10.1021/ci7004725] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a new molecular dynamics methodology to assist in structure-based drug design and other studies that seek to predict protein deformability. Termed Active Site Pressurization (ASP), the new methodology simply injects a resin into the ligand binding-site of a protein during the course of a molecular dynamics simulation such that novel, energetically reasonable protein conformations are generated in an unbiased way that may be better representations of the ligand binding conformation than are currently available. Here we apply two different versions of the ASP methodology to three proteins, cytochrome P450cam, PcrA helicase, and glycogen synthase kinase 3beta (GSK3beta), and show that the method is capable of inducing significant conformational changes when compared to the X-ray crystal structures. Application of the ASP methodology therefore provides a view of binding site flexibility that is a rich source of data for inclusion in a variety of further investigations, including high-throughput virtual screening, lead hopping, revealing alternative modes of deformation, and revealing hidden exit and entrance tunnels.
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Affiliation(s)
- Ian M Withers
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
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25
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Lohman TM, Tomko EJ, Wu CG. Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 2008; 9:391-401. [PMID: 18414490 DOI: 10.1038/nrm2394] [Citation(s) in RCA: 272] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Helicases and nucleic acid translocases are motor proteins that have essential roles in nearly all aspects of nucleic acid metabolism, ranging from DNA replication to chromatin remodelling. Fuelled by the binding and hydrolysis of nucleoside triphosphates, helicases move along nucleic acid filaments and separate double-stranded DNA into their complementary single strands. Recent evidence indicates that the ability to simply translocate along single-stranded DNA is, in many cases, insufficient for helicase activity. For some of these enzymes, self assembly and/or interactions with accessory proteins seem to regulate their translocase and helicase activities.
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Affiliation(s)
- Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA.
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26
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Mackerell AD, Nilsson L. Molecular dynamics simulations of nucleic acid-protein complexes. Curr Opin Struct Biol 2008; 18:194-9. [PMID: 18281210 DOI: 10.1016/j.sbi.2007.12.012] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/17/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulation studies of protein-nucleic acid complexes are more complicated than studies of either component alone-the force field has to be properly balanced, the systems tend to become very large, and a careful treatment of solvent and of electrostatic interactions is necessary. Recent investigations into several protein-DNA and protein-RNA systems have shown the feasibility of the simulation approach, yielding results of biological interest not readily accessible to experimental methods.
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Affiliation(s)
- Alexander D Mackerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
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27
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Kumar KV, Ramaswamy S, Rao M. Active elastic dimers: self-propulsion and current reversal on a featureless track. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:020102. [PMID: 18351968 DOI: 10.1103/physreve.77.020102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Indexed: 05/26/2023]
Abstract
We present a Brownian inchworm model of a self-propelled elastic dimer in the absence of an external potential. Nonequilibrium noise together with a stretch-dependent damping form the propulsion mechanism. Our model connects three key nonequilibrium features -- position-velocity correlations, a nonzero mean internal force, and a drift velocity. Our analytical results, including striking current reversals, compare very well with numerical simulations. The model unifies the propulsion mechanisms of DNA helicases, polar rods on a vibrated surface, crawling keratocytes and Myosin VI. We suggest experimental realizations and tests of the model.
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Affiliation(s)
- K Vijay Kumar
- CCMT, Department of Physics, Indian Institute of Science, Bangalore, India.
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28
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Yu J, Ha T, Schulten K. How directional translocation is regulated in a DNA helicase motor. Biophys J 2007; 93:3783-97. [PMID: 17704159 PMCID: PMC2084242 DOI: 10.1529/biophysj.107.109546] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2007] [Accepted: 07/18/2007] [Indexed: 11/18/2022] Open
Abstract
PcrA helicase from Bacillus stearothermophilus is one of the smallest motor proteins structurally known in full atomic detail. It translocates progressively from the 3' end to the 5' end of single-stranded DNA utilizing the free energy from ATP hydrolysis. The similarities in structure and reaction pathway between PcrA helicase and F1-ATPase suggest a similar mechanochemical mechanism at work in both systems. Previous studies of PcrA translocation demonstrated a domain stepping mechanism in which, during one ATP hydrolysis cycle, the pulling together and pushing apart of two translocation domains is synchronized with alternating mobilities of the individual domains such that PcrA moves unidirectionally along single-stranded DNA. To substantiate this translocation mechanism, this study applies molecular dynamics simulations, elastic network theory, and multiple sequence alignment to analyze the system. The analysis provides further evidence that directional translocation of PcrA is regulated allosterically through synchronization of ATP hydrolysis and domain mobilities. We identify a set of essential residues coevolutionarily coupled in related helicases that should be involved in the allosteric regulation of these motor proteins.
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Affiliation(s)
- Jin Yu
- Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois; and Howard Hughes Medical Institute, Urbana, Illinois, USA
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29
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Tomko EJ, Fischer CJ, Niedziela-Majka A, Lohman TM. A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. Mol Cell 2007; 26:335-47. [PMID: 17499041 PMCID: PMC2041850 DOI: 10.1016/j.molcel.2007.03.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Revised: 03/15/2007] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
E. coli UvrD is an SF1 helicase involved in several DNA metabolic processes. Although a UvrD dimer is needed for helicase activity, a monomer can translocate with 3' to 5' directionality along single-stranded DNA, and this ATP-dependent translocation is likely involved in RecA displacement. In order to understand how the monomeric translocase functions, we have combined fluorescence stopped-flow kinetic methods with recently developed analysis methods to determine the kinetic mechanism, including ATP coupling stoichiometry, for UvrD monomer translocation along ssDNA. Our results suggest that the macroscopic rate of UvrD monomer translocation is not limited by each ATPase cycle but rather by a slow step (pause) in each translocation cycle that occurs after four to five rapid 1 nt translocation steps, with each rapid step coupled to hydrolysis of one ATP. These results suggest a nonuniform stepping mechanism that differs from either a Brownian motor or previous structure-based inchworm mechanisms.
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Affiliation(s)
| | | | | | - Timothy M. Lohman
- *Address correspondence to: T. M. Lohman, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid, St. Louis, MO 63110, 314-362-4393, FAX: 314-362-7183,
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30
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Xie P. On translocation mechanism of ring-shaped helicase along single-stranded DNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:737-48. [PMID: 17499029 DOI: 10.1016/j.bbapap.2007.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 03/16/2007] [Accepted: 04/05/2007] [Indexed: 11/28/2022]
Abstract
The ring-shaped helicases represent one important group of helicases that can translocate along single-stranded (ss) DNA and unwinding double-stranded (ds) DNA by using the energy derived from NTP binding and hydrolysis. Despite intensive studies, the mechanism by which the ring-shaped helicase translocates along ssDNA and unwinds dsDNA remains undetermined. In order to understand their chemomechanical-coupling mechanism, two models on NTPase activities of the hexamers in the presence of DNA have been studied here. One model is assumed that, of the six nucleotide-binding sites, three are noncatalytic and three are catalytic. The other model is assumed that all the six nucleotide-binding sites are catalytic. In terms of the sequential NTPase activity around the ring and the previous determined crystal structure of bacteriophage T7 helicase it is shown that the obtained mechanical behaviors such as the ssDNA-translocation size and DNA-unwinding size per dTTPase cycle using the former model are in good quantitative agreement with the previous experimental results for T7 helicase. Moreover, the acceleration of DNA unwinding rate with the stimulation of DNA synthesis by DNA polymerase can also be well explained by using the former model. In contrast, the ssDNA-translocation size and DNA-unwinding size per dTTPase cycle obtained by using the latter model are not consistent with the experimental results for T7 helicase. Thus it is preferred that the former model is the appropriate one for the T7 helicase. Furthermore, using the former model some dynamic behaviors such as the rotational speeds of DNA relative to the T7 helicase when translocation along ssDNA and when unwinding dsDNA have been predicted, which are expected to test in order to further verify the model.
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Affiliation(s)
- Ping Xie
- Department of Physics, Renmin University of China, Beijing 100872, China.
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31
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Hyeon C, Onuchic JN. Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc Natl Acad Sci U S A 2007; 104:2175-80. [PMID: 17287347 PMCID: PMC1892953 DOI: 10.1073/pnas.0610939104] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Indexed: 11/18/2022] Open
Abstract
In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Because the processivity of kinesin is much higher than other motor proteins, it has been speculated that there exists a mechanism for allosteric regulation between the two monomers. Recent experiments suggest that ATP binding to the leading head (L) domain in kinesin is regulated by the rearward strain built on the neck-linker. We test this hypothesis by explicitly modeling a Calpha-based kinesin structure whose motor domains are bound on the tubulin binding sites. The equilibrium structures of kinesin on the microtubule show disordered and ordered neck-linker configurations for the L and trailing head, respectively. The comparison of the structures between the two heads shows that several native contacts present at the nucleotide binding site in the L are less intact than those in the binding site of the rear head. The network of native contacts obtained from this comparison provides the internal tension propagation pathway, which leads to the disruption of the nucleotide binding site in the L. Also, using an argument based on polymer theory, we estimate the internal tension built on the neck-linker to be f approximately 12-15 pN. Both of these conclusions support the experimental hypothesis.
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Affiliation(s)
- Changbong Hyeon
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374
| | - José N. Onuchic
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374
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32
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Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. PLoS Comput Biol 2007; 3:e21. [PMID: 17291159 PMCID: PMC1796662 DOI: 10.1371/journal.pcbi.0030021] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 12/21/2006] [Indexed: 12/28/2022] Open
Abstract
Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP), the recovery stroke in the conventional myosin has been shown to be dependent on the hydrolysis of ATP. To obtain a clearer mechanistic picture for such "mechanochemical coupling" in myosin, equilibrium active-site simulations with explicit solvent have been carried out to probe the behavior of the motor domain as functions of the nucleotide chemical state and conformation of the converter/relay helix. In conjunction with previous studies of ATP hydrolysis with different active-site conformations and normal mode analysis of structural flexibility, the results help establish an energetics-based framework for understanding the mechanochemical coupling. It is proposed that the activation of hydrolysis does not require the rotation of the lever arm per se, but the two processes are tightly coordinated because both strongly couple to the open/close transition of the active site. The underlying picture involves shifts in the dominant population of different structural motifs as a consequence of changes elsewhere in the motor domain. The contribution of this work and the accompanying paper [] is to propose the actual mechanism behind these "population shifts" and residues that play important roles in the process. It is suggested that structural flexibilities at both the small and large scales inherent to the motor domain make it possible to implement tight couplings between different structural motifs while maintaining small free-energy drops for processes that occur in the detached states, which is likely a feature shared among many molecular motors. The significantly different flexibility of the active site in different X-ray structures with variable level arm orientations supports the notation that external force sensed by the lever arm may transmit into the active site and influence the chemical steps (nucleotide hydrolysis and/or binding).
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Affiliation(s)
- Haibo Yu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Liang Ma
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Yang Yang
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin, United States of America
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33
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Hunter P. A quantum leap in biology. One inscrutable field helps another, as quantum physics unravels consciousness. EMBO Rep 2006; 7:971-4. [PMID: 17016453 PMCID: PMC1618371 DOI: 10.1038/sj.embor.7400802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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34
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Dittrich M, Schulten K. PcrA helicase, a prototype ATP-driven molecular motor. Structure 2006; 14:1345-53. [PMID: 16962966 DOI: 10.1016/j.str.2006.06.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 06/19/2006] [Accepted: 06/22/2006] [Indexed: 11/19/2022]
Abstract
Despite extensive studies, the mechanisms underlying molecular motor function are still poorly understood. Key to the mechanisms is the coupling of ATP hydrolysis to conformational changes of the motor protein. To investigate this coupling, we have conducted combined quantum mechanical/molecular mechanical simulations of PcrA helicase, a strikingly simple motor that translocates unidirectionally along single-stranded DNA (ssDNA). Our results reveal a close similarity in catalytic site structure and reaction pathway to those of F1-ATPase, and these similarities include a proton relay mechanism important for efficient ATP hydrolysis and an "arginine finger" residue that is key to the coupling of the chemical reaction to protein conformational changes. By means of in silico mutation studies, we identified the residue Q254 as being crucial for the coupling of ssDNA translocation to the actual catalytic event. Based on the present result for PcrA helicase and previous findings for F1-ATPase, we propose a general mechanism of ATP-driven molecular motor function.
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Affiliation(s)
- Markus Dittrich
- Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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