1
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Rogoulenko E, Levy Y. Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic Acids Res 2024; 52:6763-6776. [PMID: 38721783 PMCID: PMC11229352 DOI: 10.1093/nar/gkae333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 07/09/2024] Open
Abstract
The kinetics of protein-DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shaping biological function. Protein-DNA recognition kinetics are characterized by two key elements: the time taken to locate the target site amid various nonspecific alternatives; and the kinetics involved in the recognition process, which may necessitate overcoming an energetic barrier. In this study, we developed a coarse-grained (CG) model to investigate interactions between a transcription factor called the sex-determining region Y (SRY) protein and DNA, in order to probe how DNA conformational changes affect SRY-DNA recognition and binding kinetics. We find that, not only does a requirement for such a conformational DNA transition correspond to a higher energetic barrier for binding and therefore slower kinetics, it may further impede the recognition kinetics by increasing unsuccessful binding events (skipping events) where the protein partially binds its DNA target site but fails to form the specific protein-DNA complex. Such skipping events impose the need for additional cycles protein search of nonspecific DNA sites, thus significantly extending the overall recognition time. Our results highlight a trade-off between the speed with which the protein scans nonspecific DNA and the rate at which the protein recognizes its specific target site. Finally, we examine molecular approaches potentially adopted by natural systems to enhance protein-DNA recognition despite its intrinsically slow kinetics.
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Affiliation(s)
- Elena Rogoulenko
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Simonsen S, Søgaard CK, Olsen JG, Otterlei M, Kragelund BB. The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery. Cell Mol Life Sci 2024; 81:245. [PMID: 38814467 PMCID: PMC11139829 DOI: 10.1007/s00018-024-05252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.
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Affiliation(s)
- Signe Simonsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Johan G Olsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Birthe B Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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3
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Kim H, Pak Y. Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level. J Chem Theory Comput 2024; 20:2666-2675. [PMID: 38451471 DOI: 10.1021/acs.jctc.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
DNA glycosylases play key roles in the maintenance of genomic integrity. These enzymes effectively find rare damaged sites in DNA and participate in subsequent base excision repair. Single-molecule and ensemble experiments have revealed key aspects of this damage-site searching mechanism and the involvement of facilitated diffusion. In this study, we describe free energy landscapes of enzyme translocation along nonspecific DNA obtained using a fully atomistic molecular dynamics (MD) simulation of a well-known DNA glycosylase, human 8-oxoguanine DNA glycosylase 1 (hOGG1). Based on an analysis of simulated free energy profiles, we propose a three-state model for the damage-site searching mechanism. In the three states, named the L1, L2, and L3 states, the L1 state is a helical sliding mode in close contact with DNA, whereas the L2 state is a major- or minor-groove tracking mode in loose contact with DNA and the L3 state is a two-dimensional freely diffusing mode during which hOGG1 is somewhat removed from the DNA surface (∼24 Å away from the surface). This three-state model well describes key experimental findings obtained from single-molecule and ensemble experiments and provides a unified molecular picture of the DNA lesion-searching mechanism of hOGG1.
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Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
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4
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Song Y, Kim JS. Structure and dynamics of double-stranded DNA rotaxanes. NANOSCALE 2024; 16:4317-4324. [PMID: 38353661 DOI: 10.1039/d3nr05846h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
A DNA rotaxane, with its unique mechanically interlocked architecture consisting of a circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental component for nanoscale functional devices. Nevertheless, its structural and dynamic behaviors, essential for advancing molecular machinery, remain largely unexplored. Using extensive all-atom molecular dynamics simulations, we investigated the behaviors of double-stranded DNA (dsDNA) rotaxanes, concentrating on the effects of shape distortion induced by torsional stress in small circular dsDNA containing 70-90 base pairs. We analyzed structural characteristics, including shape, intermolecular distances, and tilt angles, while also exploring dynamic properties such as translational diffusion and toroidal rotation. Our results indicate that shape distortion brings the circular and linear dsDNA components into closer proximity and causes a slight increase in translational diffusion yet a minor decrease in toroidal rotation. Nevertheless, there is no apparent evidence of coupling between translation and rotation. Overall, the insights from this study indicate that such shape distortion does not significantly alter their structure and dynamics. This finding provides flexibility for the design of DNA rotaxanes in nanoscale applications.
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Affiliation(s)
- Yeonho Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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5
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Abstract
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
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Affiliation(s)
- Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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6
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Korkmazhan E, Dunn AR. The membrane-actin linker ezrin acts as a sliding anchor. SCIENCE ADVANCES 2022; 8:eabo2779. [PMID: 35930643 PMCID: PMC9355349 DOI: 10.1126/sciadv.abo2779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein linkages to filamentous (F)-actin provide the cell membrane with mechanical stability and support intricate membrane architectures. However, the actin cytoskeleton is highly dynamic and undergoes rapid changes in shape during cell motility and other processes. The molecular mechanisms that generate a mechanically robust yet fluid connection between the membrane and actin cytoskeleton remain poorly understood. Here, we adapted a single-molecule optical trap assay to examine how the prototypical membrane-actin linker ezrin acts to anchor F-actin to the cell membrane. We find that ezrin forms a complex that slides along F-actin over micrometer distances while resisting detachment by forces oriented perpendicular to the filament axis. The ubiquity of ezrin and analogous proteins suggests that sliding anchors such as ezrin may constitute an important but overlooked element in the construction of the actin cytoskeleton.
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Affiliation(s)
- Elgin Korkmazhan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305 USA
- Graduate Program in Biophysics, Stanford University, Stanford, CA 94305 USA
| | - Alexander R. Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305 USA
- Corresponding author.
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7
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Chu X, Suo Z, Wang J. Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide. JACS AU 2022; 2:341-356. [PMID: 35252985 PMCID: PMC8889613 DOI: 10.1021/jacsau.1c00368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 06/14/2023]
Abstract
During DNA polymerization, the Y-family DNA polymerases are capable of bypassing various DNA damage, which can stall the replication fork progression. It has been well acknowledged that the structures of the Y-family DNA polymerases have been naturally evolved to undertake this vital task. However, the mechanisms of how these proteins utilize their unique structural and conformational dynamical features to perform the translesion DNA synthesis are less understood. Here, we developed structure-based models to study the precatalytic DNA polymerization process, including DNA and nucleotide binding to DPO4, a paradigmatic Y-family polymerase from Sulfolobus solfataricus. We studied the interplay between the folding and the conformational dynamics of DPO4 and found that DPO4 undergoes first unraveling (unfolding) and then folding for accomplishing the functional "open-to-closed" conformational transition. DNA binding dynamically modulates the conformational equilibrium in DPO4 during the stepwise binding through different types of interactions, leading to different conformational distributions of DPO4 at different DNA binding stages. We observed that nucleotide binding induces modulation of a few contacts surrounding the active site of the DPO4-DNA complex associated with a high free energy barrier. Our simulation results resonate with the experimental evidence that the conformational change at the active site led by nucleotide is the rate-limiting step of nucleotide incorporation. In combination with localized frustration analyses, we underlined the importance of DPO4 conformational dynamics and fluctuations in facilitating DNA and nucleotide binding. Our findings offer mechanistic insights into the processes of DPO4 conformational dynamics associated with the substrate binding and contribute to the understanding of the "structure-dynamics-function" relationship in the Y-family DNA polymerases.
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Affiliation(s)
- Xiakun Chu
- Department
of Chemistry, State University of New York
at Stony Brook, Stony
Brook, New York 11794, United States
| | - Zucai Suo
- Department
of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Jin Wang
- Department
of Chemistry, State University of New York
at Stony Brook, Stony
Brook, New York 11794, United States
- Department
of Physics and Astronomy, State University
of New York at Stony Brook, Stony Brook, New York 11794, United States
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8
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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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9
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Schaudy E, Lietard J, Somoza MM. Sequence Preference and Initiator Promiscuity for De Novo DNA Synthesis by Terminal Deoxynucleotidyl Transferase. ACS Synth Biol 2021; 10:1750-1760. [PMID: 34156829 PMCID: PMC8291772 DOI: 10.1021/acssynbio.1c00142] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The untemplated activity
of terminal deoxynucleotidyl transferase
(TdT) represents its most appealing feature. Its use is well established
in applications aiming for extension of a DNA initiator strand, but
a more recent focus points to its potential in enzymatic de
novo synthesis of DNA. Whereas its low substrate specificity
for nucleoside triphosphates has been studied extensively, here we
interrogate how the activity of TdT is modulated by the nature of
the initiating strands, in particular their length, chemistry, and
nucleotide composition. Investigation of full permutational libraries
of mono- to pentamers of d-DNA, l-DNA, and 2′O-methyl-RNA
of differing directionality immobilized to glass surfaces, and generated via photolithographic in situ synthesis,
shows that the efficiency of extension strongly depends on the nucleobase
sequence. We also show TdT being catalytically active on a non-nucleosidic
substrate, hexaethylene glycol. These results offer new perspectives
on constraints and strategies for de novo synthesis
of DNA using TdT regarding the requirements for initiation of enzymatic
generation of DNA.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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10
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Crocker K, London J, Medina A, Fishel R, Bundschuh R. Evolutionary advantage of a dissociative search mechanism in DNA mismatch repair. Phys Rev E 2021; 103:052404. [PMID: 34134264 PMCID: PMC8514111 DOI: 10.1103/physreve.103.052404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 04/08/2021] [Indexed: 01/10/2023]
Abstract
Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use a dissociative mechanism, in which two proteins, while continuously remaining attached to the DNA, sometimes associate into a single complex sliding on the DNA and sometimes dissociate into two independently sliding proteins. Here, we study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the sliding complexes. We compare such probabilities to those obtained using a nondissociative diffusive scan in the space of physically realistic diffusion constants, hemimethylated site distances, and total search times to determine the regions in which dissociative searching is more or less efficient than nondissociative searching. We conclude that the dissociative search mechanism is advantageous in the majority of the physically realistic parameter space, suggesting that the dissociative search mechanism confers an evolutionary advantage.
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Affiliation(s)
- Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Andrés Medina
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ralf Bundschuh
- Department of Physics, Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Bigman LS, Greenblatt HM, Levy Y. What Are the Molecular Requirements for Protein Sliding along DNA? J Phys Chem B 2021; 125:3119-3131. [PMID: 33754737 PMCID: PMC8041311 DOI: 10.1021/acs.jpcb.1c00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
DNA-binding proteins rely on linear
diffusion along the longitudinal
DNA axis, supported by their nonspecific electrostatic affinity for
DNA, to search for their target recognition sites. One may therefore
expect that the ability to engage in linear diffusion along DNA is
universal to all DNA-binding proteins, with the detailed biophysical
characteristics of that diffusion differing between proteins depending
on their structures and functions. One key question is whether the
linear diffusion mechanism is defined by translation coupled with
rotation, a mechanism that is often termed sliding. We conduct coarse-grained
and atomistic molecular dynamics simulations to investigate the minimal
requirements for protein sliding along DNA. We show that coupling,
while widespread, is not universal. DNA-binding proteins that slide
along DNA transition to uncoupled translation–rotation (i.e.,
hopping) at higher salt concentrations. Furthermore, and consistently
with experimental reports, we find that the sliding mechanism is the
less dominant mechanism for some DNA-binding proteins, even at low
salt concentrations. In particular, the toroidal PCNA protein is shown
to follow the hopping rather than the sliding mechanism.
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Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Pal A, Greenblatt HM, Levy Y. Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6. Biochemistry 2020; 59:4822-4832. [PMID: 33319999 PMCID: PMC7872316 DOI: 10.1021/acs.biochem.0c00669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA
mismatch repair (MMR) is an important postreplication process
that eliminates mispaired or unpaired nucleotides to ensure genomic
replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two
mismatch repair initiation factors that recognize DNA lesions. While
X-ray crystal structures exist for these proteins in complex with
DNA lesions, little is known about their structures during the initial
search along nonspecific double-stranded DNA, because they are short-lived
and difficult to determine experimentally. In this study, various
computational approaches were used to sidestep these difficulties.
All-atom and coarse-grained simulations based on the crystal structures
of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting
that the initial search conformation differs from the lesion-bound
crystal structure. We modeled probable search-mode structures of MSH
proteins and showed, using coarse-grained molecular dynamics simulations,
that they can perform rotation-coupled diffusion on DNA, which is
a suitable and efficient search mechanism for their function and one
predicted earlier by fluorescence resonance energy transfer and fluorescence
microscopy studies. This search mechanism is implemented by electrostatic
interactions among the mismatch-binding domain (MBD), the clamp domains,
and the DNA backbone. During simulations, their diffusion rate did
not change significantly with an increasing salt concentration, which
is consistent with observations from experimental studies. When the
gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused
mostly via the clamp domains while Msh2-Msh6 still diffused using
the MBD, reproducing the experimentally measured lower diffusion coefficient
of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating
from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex.
This is consistent with the experimental observation that Msh2-Msh3,
unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our
models provide a molecular picture of the different mismatch search
mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity
of their structures.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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Does PCNA diffusion on DNA follow a rotation-coupled translation mechanism? Nat Commun 2020; 11:5000. [PMID: 33020481 PMCID: PMC7536400 DOI: 10.1038/s41467-020-18855-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/29/2020] [Indexed: 01/25/2023] Open
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14
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You S, Lee HG, Kim K, Yoo J. Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA. J Chem Theory Comput 2020; 16:4006-4013. [PMID: 32543861 DOI: 10.1021/acs.jctc.0c00241] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As the field of molecular dynamics simulation utilizing the force fields is moving toward more complex systems, the accuracy of intermolecular interactions has become a central issue of the field. Here, we quantitatively evaluate the accuracy of the protein-DNA interactions in AMBER and CHARMM force fields by comparing experimental and simulated diffusion coefficients of proliferating cell nuclear antigen. We find that both force fields underestimate diffusion coefficients by at least an order of magnitude because the interactions between basic amino acids and DNA phosphate groups are too attractive. Then, we propose Lennard-Jones parameters optimized using the experimental osmotic pressure data of model chemicals, by using which one can reproduce the experimental diffusion coefficients. Newly optimized parameters will have a broad impact on general protein-DNA interactions.
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Affiliation(s)
- Seonju You
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hong-Guen Lee
- Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.,Center for Self-Assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea
| | - Kimoon Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.,Center for Self-Assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea
| | - Jejoong Yoo
- Center for Self-Assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea.,Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
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15
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Bigman LS, Levy Y. Protein Diffusion on Charged Biopolymers: DNA versus Microtubule. Biophys J 2020; 118:3008-3018. [PMID: 32492371 DOI: 10.1016/j.bpj.2020.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target sites, and protein diffusion on microtubules is important for proper cell division and neuronal development. On the one hand, these linear diffusion processes are mediated by long-range electrostatic interactions between positively charged proteins and negatively charged biopolymers and have similar characteristic diffusion coefficients. On the other hand, DNA and microtubules have different structural properties. Here, using computational approaches, we studied the mechanism of protein diffusion along DNA and microtubules by exploring the diffusion of both protein types on both biopolymers. We found that DNA-binding and microtubule-binding proteins can diffuse on each other's substrates; however, the adopted diffusion mechanism depends on the molecular properties of the diffusing proteins and the biopolymers. On the protein side, only DNA-binding proteins can perform rotation-coupled diffusion along DNA, with this being due to their higher net charge and its spatial organization at the DNA recognition helix. By contrast, the lower net charge on microtubule-binding proteins enables them to diffuse more quickly than DNA-binding proteins on both biopolymers. On the biopolymer side, microtubules possess intrinsically disordered, negatively charged C-terminal tails that interact with microtubule-binding proteins, thus supporting their diffusion. Thus, although both DNA-binding and microtubule-binding proteins can diffuse on the negatively charged biopolymers, the unique molecular features of the biopolymers and of their natural substrates are essential for function.
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Affiliation(s)
- Lavi S Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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16
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:7130-7142. [PMID: 31334814 PMCID: PMC6649754 DOI: 10.1093/nar/gkz551] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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17
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De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magaña A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A. p15PAF binding to PCNA modulates the DNA sliding surface. Nucleic Acids Res 2019; 46:9816-9828. [PMID: 30102405 PMCID: PMC6182140 DOI: 10.1093/nar/gky723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF–PCNA–DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η–PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Susana Barrera-Vilarmau
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | | | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alfredo De Biasio
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy.,Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
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18
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Piatt SC, Loparo JJ, Price AC. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophys J 2019; 116:2367-2377. [PMID: 31113551 PMCID: PMC6588823 DOI: 10.1016/j.bpj.2019.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of a 1D search by quantum dot-labeled EcoRI. Our data supports the view that proteins search DNA via rotation-coupled sliding over a corrugated energy landscape. We observed that whereas EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations, its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites, which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence-independent energy landscape during fast search but rapidly interconverts with a "hemispecific" binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding, which can then lead to target recognition.
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Affiliation(s)
- Sadie C Piatt
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.
| | - Allen C Price
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts.
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Kanada R, Terakawa T, Kenzaki H, Takada S. Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins. Biophys J 2019; 116:2285-2295. [PMID: 31151739 DOI: 10.1016/j.bpj.2019.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023] Open
Abstract
Dynamics of nuclear proteins in crowded chromatin has only been poorly understood. Here, we address the diffusion, target search, and structural dynamics of three proteins in a model chromatin using coarse-grained molecular simulations run on the K computer. We prepared two structures of chromatin made of 20 nucleosomes with different nucleosome densities and investigated dynamics of two transcription factors, HMGB1 and p53, and one signaling protein, ERK, embedded in the chromatin. We found fast and normal diffusion of the nuclear proteins in the low-density chromatins and slow and subdiffusional movements in the high-density chromatin. The diffusion of the largest transcription factor, p53, is slowed by high-density chromatin most markedly. The on rates and off rates for DNA binding are increased and decreased, respectively, in the high-density chromatin. To our surprise, the DNA sequence search was faster in chromatin with high nucleosome density, though the diffusion is slower. We also found that the three nuclear proteins preferred to bind on the linker DNA and the entry and exit regions of nucleosomal DNA. In addition to these regions, HMGB1 and p53 also bound to the dyad.
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Affiliation(s)
- Ryo Kanada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan; Compass to Healthy Life Research Complex Program, Cluster for Science, Technology and Innovation Hub, RIKEN, Kobe, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroo Kenzaki
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan; Information Systems Division, Head Office for Information Systems and Cybersecurity, RIKEN, Saitama, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
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Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
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21
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Weßbecher IM, Brieger A. Phosphorylation meets DNA mismatch repair. DNA Repair (Amst) 2018; 72:107-114. [PMID: 30249411 DOI: 10.1016/j.dnarep.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
DNA mismatch repair (MMR) is a highly conserved process and ensures the removal of mispaired DNA bases and insertion-deletion loops right after replication. For this, a MutSα or MutSβ protein complex recognizes the DNA damage, MutLα nicks the erroneous strand, exonuclease 1 removes the wrong nucleotides, DNA polymerase δ refills the gap and DNA ligase I joins the fragments to seal the nicks and complete the repair process. The failure to accomplish these functions is associated with higher mutation rates and may lead to cancer, which highlights the importance of MMR by the maintenance of genomic stability. The post-replicative MMR implies that involved proteins are regulated at several levels, including posttranslational modifications (PTMs). Phosphorylation is one of the most common and major PTMs. Suitable with its regulatory force phosphorylation was shown to influence MMR factors thereby adjusting eukaryotic MMR activity. In this review, we summarized the current knowledge of the role of phosphorylation of MMR process involved proteins and their functional relevance.
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Affiliation(s)
| | - Angela Brieger
- Medical Clinic I, Biomedical Research Laboratory, Goethe-University, Frankfurt a.M., Germany.
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