1
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Nishihara R, Dokainish HM, Kihara Y, Ashiba H, Sugita Y, Kurita R. Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin. ACS Cent Sci 2024; 10:283-290. [PMID: 38435535 PMCID: PMC10906034 DOI: 10.1021/acscentsci.3c00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/21/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024]
Abstract
Enzymatic reactions that involve a luminescent substrate (luciferin) and enzyme (luciferase) from luminous organisms enable a luminescence detection of target proteins and cells with high specificity, albeit that conventional assay design requires a prelabeling of target molecules with luciferase. Here, we report a luciferase-independent luminescence assay in which the target protein directly catalyzes the oxidative luminescence reaction of luciferin. The SARS-CoV-2 antigen (spike) protein catalyzes the light emission of Cypridina luciferin, whereas no such catalytic function was observed for salivary proteins. This selective luminescence reaction is due to the enzymatic recognition of the 3-(1-guanidino)propyl group in luciferin at the interfaces between the units of the spike protein, allowing a specific detection of the spike protein in human saliva without sample pretreatment. This method offers a novel platform to detect virus antigens simply and rapidly without genetic manipulation or antibodies.
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Affiliation(s)
- Ryo Nishihara
- National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Japan
Science and Technology Agency (JST), PREST, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hisham M. Dokainish
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Nishi 6 Kita12 Kita-ku, Sapporo 060-0812, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Kihara
- National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Faculty
of
Pure and Applied Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Hiroki Ashiba
- National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ryoji Kurita
- National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Faculty
of
Pure and Applied Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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2
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Dokainish HM, Sugita Y. Structural effects of spike protein D614G mutation in SARS-CoV-2. Biophys J 2023; 122:2910-2920. [PMID: 36397671 PMCID: PMC9671695 DOI: 10.1016/j.bpj.2022.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2. D614G mutation induces structural changes in the spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-loop rigidification on S-protein structure. The introduction of the mutation orders the 630-loop structure and thereby induces global structural changes toward the cryoelectron microscopy structure of the D614G S-protein. The ordered 630-loop weakens local interactions between the 614th residue and others in contrast to disordered structures in the wild-type protein. The mutation allosterically alters global interactions between receptor-binding domains, forming an asymmetric and mobile down conformation and facilitating transitions toward up conformation. The loss of salt bridge between D614 and K854 upon the mutation generally stabilizes S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding the molecular basis of D614G mutation is crucial as it dominates in all variants of concern, including Delta and Omicron.
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Affiliation(s)
- Hisham M Dokainish
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
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3
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Hashim PK, Dokainish HM, Tamaoki N. Chaperonin GroEL hydrolyses ortho-nitrophenyl β-galactoside. Org Biomol Chem 2023. [PMID: 37464895 DOI: 10.1039/d3ob00989k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We serendipitously found that chaperonin GroEL can hydrolyze ortho-nitrophenyl β-galactoside (ONPG), a well-known substrate of the enzyme β-galactosidase. The ONPG hydrolysis by GroEL follows typical enzyme kinetics. Our experiments and molecular docking studies suggest ONPG binding at the ATP binding site of GroEL.
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Affiliation(s)
- P K Hashim
- Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Hisham M Dokainish
- Center of Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Nobuyuki Tamaoki
- Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
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4
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Matsubara D, Kasahara K, Dokainish HM, Oshima H, Sugita Y. Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions. Molecules 2022; 27:molecules27175726. [PMID: 36080494 PMCID: PMC9457699 DOI: 10.3390/molecules27175726] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.
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Affiliation(s)
- Daiki Matsubara
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
| | - Kento Kasahara
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Osaka, Japan
| | - Hisham M. Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Saitama, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Saitama, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Hyogo, Japan
- Correspondence: ; Tel.: +81-48-462-1407
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5
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Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y. The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife 2022; 11:e75720. [PMID: 35323112 PMCID: PMC8963885 DOI: 10.7554/elife.75720] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding domains (RBDs) to enter the host cell. Here, we observe Down, one-Up, one-Open, and two-Up-like structures in enhanced molecular dynamics simulations, and characterize the transition pathways via inter-domain interactions. Transient salt-bridges between RBDA and RBDC and the interaction with glycan at N343B support RBDA motions from Down to one-Up. Reduced interactions between RBDA and RBDB in one-Up induce RBDB motions toward two-Up. The simulations overall agree with cryo-electron microscopy structure distributions and FRET experiments and provide hidden functional structures, namely, intermediates along Down-to-one-Up transition with druggable cryptic pockets as well as one-Open with a maximum exposed RBD. The inherent flexibility of S-protein thus provides essential information for antiviral drug rational design or vaccine development.
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Grants
- FLAGSHIP 2020 project Ministry of Education, Culture, Sports, Science and Technology
- 19K06532 Ministry of Education, Culture, Sports, Science and Technology
- Dynamic Structural Biology/Glycolipidologue Initiative/Biology of Intracellular Environments RIKEN
- Priority Issue on Post-K computer Ministry of Education, Culture, Sports, Science and Technology
- Program for Promoting Researches on the Supercomputer Fugaku Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200101 Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200201 Ministry of Education, Culture, Sports, Science and Technology
- 19H05645 Ministry of Education, Culture, Sports, Science and Technology
- 21H05249 Ministry of Education, Culture, Sports, Science and Technology
- 20K15737 Ministry of Education, Culture, Sports, Science and Technology
- 19K12229 Ministry of Education, Culture, Sports, Science and Technology
- 21H05157 Ministry of Education, Culture, Sports, Science and Technology
- hp200135 HPCI System Research project
- hp200153 HPCI System Research project
- hp200028 HPCI System Research project
- hp210107 HPCI System Research project
- hp210177 HPCI System Research project
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Affiliation(s)
- Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
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6
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Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y. Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets. Biophys J 2022. [PMCID: PMC8833025 DOI: 10.1016/j.bpj.2021.11.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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7
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Ren W, Dokainish HM, Shinobu A, Oshima H, Sugita Y. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. J Phys Chem B 2021; 125:2898-2909. [PMID: 33728914 PMCID: PMC10954230 DOI: 10.1021/acs.jpcb.0c11600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBPG134R) in solution. The free-energy landscape (FEL) of RBPG134R in the presence of a ribose at the binding site included the open and closed states and two intermediates, open-like and closed-like forms. Only the open and open-like forms existed in the FEL without a ribose. In the current study, the coupling between the conformational changes and ligand binding is further investigated using coarse-grained MD, multiple atomistic cMD, and free-energy calculations. The ribose is easily dissociated from the binding site of wild-type RBP and RBPG134R in the cMD simulations starting from the open and open-like forms. In contrast, it is stable at the binding site in the simulations from the closed and closed-like forms. The free-energy calculations provide the binding affinities of different structures, supporting the results of cMD simulations. Importantly, cMD simulations from the closed-like structures reveal transitions toward the closed one in the presence of a bound ribose. On the basis of the computational results, we propose a molecular mechanism in which conformational selection and induced fit happen in the first and second halves of the open-to-closed transition in RBP, respectively.
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Affiliation(s)
- Weitong Ren
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisham M. Dokainish
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Shinobu
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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8
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Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein. Biophys J 2021; 120:1060-1071. [PMID: 33484712 PMCID: PMC7825899 DOI: 10.1016/j.bpj.2021.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by the new coronavirus, SARS-CoV-2, calls for urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S-protein), which consists of trimeric polypeptide chains with glycosylated residues on the surface, triggers the virus entry into a host cell. Extensive structural and functional studies on this protein have rapidly advanced our understanding of the S-protein structure at atomic resolutions, although most of these structural studies overlook the effect of glycans attached to the S-protein on the conformational stability and functional motions between the inactive down and active up forms. Here, we performed all-atom molecular dynamics simulations of both down and up forms of a fully glycosylated S-protein in solution as well as targeted molecular dynamics simulations between them to elucidate key interdomain interactions for stabilizing each form and inducing the large-scale conformational transitions. The residue-level interaction analysis of the simulation trajectories detects distinct amino acid residues and N-glycans as determinants on conformational stability of each form. During the conformational transitions between them, interdomain interactions mediated by glycosylated residues are switched to play key roles on the stabilization of another form. Electrostatic interactions, as well as hydrogen bonds between the three receptor binding domains, work as driving forces to initiate the conformational transitions toward the active form. This study sheds light on the mechanisms underlying conformational stability and functional motions of the S-protein, which are relevant for vaccine and antiviral drug developments.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
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9
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Dokainish HM, Sugita Y. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. Int J Mol Sci 2020; 22:ijms22010270. [PMID: 33383937 PMCID: PMC7796230 DOI: 10.3390/ijms22010270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 11/26/2022] Open
Abstract
Conformational transitions in multidomain proteins are essential for biological functions. The Apo conformations are typically open and flexible, while the Holo states form more compact conformations stabilized by protein-ligand interactions. Unfortunately, the atomically detailed mechanisms for such open-closed conformational changes are difficult to be accessed experimentally as well as computationally. To simulate the transitions using atomistic molecular dynamics (MD) simulations, efficient conformational sampling algorithms are required. In this work, we propose a new approach based on generalized replica-exchange with solute tempering (gREST) for exploring the open-closed conformational changes in multidomain proteins. Wherein, selected surface charged residues in a target protein are defined as the solute region in gREST simulation and the solute temperatures are different in replicas and exchanged between them to enhance the domain motions. This approach is called gREST selected surface charged residues (gREST_SSCR) and is applied to the Apo and Holo states of ribose binding protein (RBP) in solution. The conformational spaces sampled with gREST_SSCR are much wider than those with the conventional MD, sampling open-closed conformational changes while maintaining RBP domains’ stability. The free-energy landscapes of RBP in the Apo and Holo states are drawn along with twist and hinge angles of the two moving domains. The inter-domain salt-bridges that are not observed in the experimental structures are also important in the intermediate states during the conformational changes.
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Affiliation(s)
- Hisham M. Dokainish
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- RIKEN Center for Computational Science, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Correspondence: ; Tel.: +81-48-462-1407
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10
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Dokainish HM, Kitao A. Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases. J Phys Chem B 2018; 122:8537-8547. [PMID: 30124048 DOI: 10.1021/acs.jpcb.8b07048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Photolyases are ancient enzymes that harvest sunlight to repair DNA pyrimidine lesions such as pyrimidine(6-4)pyrimidone and cyclobutane dimers. Particularly, (6-4) photolyase ((6-4)PHR) plays an important role in maintaining genetic integrity by repairing thymine(6-4)thymine (T(6-4)T) and thymine(6-4)cytosine (T(6-4)C) photolesions. The majority of (6-4)PHR studies have been performed on the basis of the former's activity and assuming the equivalence of the two repair mechanisms, although the latter's activity remains poorly studied. Here, we describe investigations of the repair process of the T(6-4)C dimer using several computational methods from molecular dynamics (MD) simulations to large quantum mechanical/molecular mechanical approaches. Two possible mechanisms, the historically proposed azetidine four-member ring intermediate and the free NH3 formation pathways, were considered. The MD results predicted that important active site histidine residues employed for the repair of the T(6-4)C dimer have protonation states similar to those seen in the (6-4)PHR/T(6-4)T complex. More importantly, despite chemical differences between the two substrates, a similar repair mechanism was identified: His365 protonates NH2, resulting in formation/activation mechanism of a free NH3, inducing NH2 transfer to the 5' base, and ultimately leading to pyrimidine restoration. This reaction is thermodynamically favorable with a rate-limiting barrier of 20.4 kcal mol-1. In contrast, the azetidine intermediate is unfeasible, possessing an energy barrier of 60 kcal mol-1; this barrier is similar to that predicted for the oxetane intermediate in T(6-4)T repair. Although both substrates are repaired with comparable quantum yields, the reactive complex in T(6-4)C was shown to be a 3' base radical with a lower driving force for back electron transfer combined with higher energy barrier for catalysis. These results showed the similarity in the general repair mechanisms between the two substrates while emphasizing differences in the electron dynamics in the repair cycle.
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Affiliation(s)
- Hisham M Dokainish
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
| | - Akio Kitao
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
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11
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Dokainish HM, Simard DJ, Gauld JW. A Pseudohypervalent Sulfur Intermediate as an Oxidative Protective Mechanism in the Archaea Peroxiredoxin Enzyme ApTPx. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b04671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hisham M. Dokainish
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Daniel J. Simard
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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12
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Dokainish HM, Yamada D, Iwata T, Kandori H, Kitao A. Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisham M. Dokainish
- Institute
of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Daichi Yamada
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Akio Kitao
- Institute
of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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13
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Dokainish HM, Kitao A. Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hisham M. Dokainish
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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14
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Yamada D, Dokainish HM, Iwata T, Yamamoto J, Ishikawa T, Todo T, Iwai S, Getzoff ED, Kitao A, Kandori H. Functional Conversion of CPD and (6-4) Photolyases by Mutation. Biochemistry 2016; 55:4173-83. [PMID: 27431478 DOI: 10.1021/acs.biochem.6b00361] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet (UV) light from the sun damages DNA by forming a cyclobutane pyrimidine dimer (CPD) and pyrimidine(6-4)pyrimidone photoproducts [(6-4) PP]. Photolyase (PHR) enzymes utilize near-UV/blue light for DNA repair, which is initiated by light-induced electron transfer from the fully reduced flavin adenine dinucleotide chromophore. Despite similar structures and repair mechanisms, the functions of PHR are highly selective; CPD PHR repairs CPD, but not (6-4) PP, and vice versa. In this study, we attempted functional conversion between CPD and (6-4) PHRs. We found that a triple mutant of (6-4) PHR is able to repair the CPD photoproduct, though the repair efficiency is 1 order of magnitude lower than that of wild-type CPD PHR. Difference Fourier transform infrared spectra for repair demonstrate the lack of secondary structural alteration in the mutant, suggesting that the triple mutant gains substrate binding ability while it does not gain the optimized conformational changes from light-induced electron transfer to the release of the repaired DNA. Interestingly, the (6-4) photoproduct is not repaired by the reverse mutation of CPD PHR, and eight additional mutations (total of 11 mutations) introduced into CPD PHR are not sufficient. The observed asymmetric functional conversion is interpreted in terms of a more complex repair mechanism for (6-4) repair, which was supported by quantum chemical/molecular mechanical calculation. These results suggest that CPD PHR may represent an evolutionary origin for photolyase family proteins.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Hisham M Dokainish
- Institute of Molecular and Cellular Biosciences, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Tomoko Ishikawa
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University , Osaka 565-0871, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University , Osaka 565-0871, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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15
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Dokainish HM, Ion BF, Gauld JW. Computational investigations on the catalytic mechanism of maleate isomerase: the role of the active site cysteine residues. Phys Chem Chem Phys 2015; 16:12462-74. [PMID: 24827730 DOI: 10.1039/c4cp01342e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The maleate isomerase (MI) catalysed isomerization of maleate to fumarate has been investigated using a wide range of computational modelling techniques, including small model DFT calculations, QM-cluster approach, quantum mechanical/molecular mechanical approach (QM/MM in the ONIOM formalism) and molecular dynamics simulations. Several fundamental questions regarding the mechanism were answered in detail, such as the activation and stabilization of the catalytic Cys in a rather hydrophobic active site. The two previously proposed mechanisms were considered, where either enediolate or succinyl-Cys intermediate forms. Small model calculations as well as an ONIOM-based approach suggest that an enediolate intermediate is too unstable. Furthermore, the formation of succinyl-Cys intermediate via the nucleophilic attack of Cys76(-) on the substrate C2 (as proposed experimentally) was found to be energetically unfeasible in both QM-cluster and ONIOM approaches. Instead, our results show that Cys194, upon activation via the substrate, acts as a nucleophile and Cys76 acts as an acid/base catalyst, forming a succinyl-Cys intermediate in a concerted fashion. Indeed, the calculated PA of Cys76 is always higher than that of Cys194 before or upon substrate binding in the active site. Furthermore, the mechanism proceeds via multiple steps by substrate rotation around C2-C3 with the assistance of the now negatively charged Cys76, leading to the formation of fumarate. Finally, our calculated barrier is in good agreement with experiment. These findings represent a novel mechanism in the racemase superfamily.
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Affiliation(s)
- Hisham M Dokainish
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.
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16
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Dokainish HM, Gauld JW. Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B). ACS Catal 2015. [DOI: 10.1021/cs501707h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisham M. Dokainish
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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17
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Dokainish HM, Gauld JW. A Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study of the Catalytic Reductase Mechanism of Methionine Sulfoxide Reductase A: Formation and Reduction of a Sulfenic Acid. Biochemistry 2013; 52:1814-27. [DOI: 10.1021/bi301168p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hisham M. Dokainish
- Department of Chemistry
and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry
and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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18
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Mattar SM, Dokainish HM. Assignment of the 6,6′-Dioxo-3,3′-biverdazyl Ground State by Using Broken Symmetry and Spectroscopy Oriented Configuration Interaction Techniques. J Phys Chem A 2010; 114:2010-21. [DOI: 10.1021/jp910643e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saba M. Mattar
- University of New Brunswick, Department of Chemistry and Centre for Laser, Atomic, and Molecular Sciences, Fredericton, New Brunswick, Canada E3B 6E2
| | - Hisham M. Dokainish
- University of New Brunswick, Department of Chemistry and Centre for Laser, Atomic, and Molecular Sciences, Fredericton, New Brunswick, Canada E3B 6E2
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