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Article ; Online: Structural effects of spike protein D614G mutation in SARS-CoV-2.

Dokainish, Hisham M / Sugita, Yuji

2022 Volume 122, Issue 14, Page(s) 2910–2920

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 ... ...

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 614
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Cryoelectron Microscopy ; Spike Glycoprotein, Coronavirus/genetics ; Mutation
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2022-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.11.025
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Article ; Online: Chaperonin GroEL hydrolyses

Hashim, P K / Dokainish, Hisham M / Tamaoki, Nobuyuki

Organic & biomolecular chemistry

2023 Volume 21, Issue 30, Page(s) 6120–6123

Abstract: We serendipitously found that chaperonin GroEL can ... ...

Abstract	We serendipitously found that chaperonin GroEL can hydrolyze
MeSH term(s)	Molecular Docking Simulation ; Binding Sites ; Galactosides ; Chaperonins/metabolism ; Adenosine Triphosphate/metabolism ; Protein Folding ; Hydrolysis
Chemical Substances	beta-galactoside ; Galactosides ; Chaperonins (EC 3.6.1.-) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-08-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d3ob00989k
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for

Nishihara, Ryo / Dokainish, Hisham M / Kihara, Yoshiki / Ashiba, Hiroki / Sugita, Yuji / Kurita, Ryoji

ACS central science

2024 Volume 10, Issue 2, Page(s) 283–290

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 ... ...

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
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.3c00887
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Article ; Online: Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

Hisham M Dokainish / Yuji Sugita

International Journal of Molecular Sciences, Vol 22, Iss 270, p

2021 Volume 270

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. ... ...

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.
Keywords	molecular dynamics ; enhanced conformational sampling algorithm ; ribose binding protein ; gREST_SSCR ; free energy landscapes ; hinge and twist angles ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2

Dokainish, Hisham M. / Sugita, Yuji

bioRxiv

Abstract: A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). D614G mutation induces structural changes in the Spike (S) protein that strengthen the ...

Abstract	A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-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 wild-type structure. The introduction of mutation with ordered 630-loop induces structural changes toward S-G614 Cryo-EM structure. An ordered 630-loop weakens the stabilizing interactions of the anionic D614, suggesting its disorder in wild-type. The mutation allosterically alters the receptor binding domain (RBD) forming an asymmetric and mobile Down conformation, which facilitate Up transition. The loss of D614_K854 salt-bridge upon mutation, generally stabilize S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding of the molecular basis of D614G is crucial as it dominates in all variants of concern including Delta and Omicron.
Keywords	covid19
Language	English
Publishing date	2022-01-25
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.01.24.477651
Database	COVID19

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Article ; Online: Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.

Dokainish, Hisham M / Sugita, Yuji

International journal of molecular sciences

2020 Volume 22, Issue 1

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.
MeSH term(s)	Carrier Proteins ; Hydrogen Bonding ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Protein Domains ; Proteins/chemistry
Chemical Substances	Carrier Proteins ; Proteins
Language	English
Publishing date	2020-12-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22010270
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Article ; Online: The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein.

Dokainish, Hisham M / Re, Suyong / Mori, Takaharu / Kobayashi, Chigusa / Jung, Jaewoon / Sugita, Yuji

eLife

2022 Volume 11

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 ( ...

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 RBD
MeSH term(s)	COVID-19 ; Cryoelectron Microscopy ; Humans ; Protein Domains ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-03-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.75720
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Article ; Online: Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.

Matsubara, Daiki / Kasahara, Kento / Dokainish, Hisham M / Oshima, Hiraku / Sugita, Yuji

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 17

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 ... ...

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)
MeSH term(s)	Intrinsically Disordered Proteins/chemistry ; Molecular Dynamics Simulation ; Peptides ; Thermodynamics ; Water/chemistry
Chemical Substances	Intrinsically Disordered Proteins ; Peptides ; Water (059QF0KO0R)
Language	English
Publishing date	2022-09-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27175726
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Article ; Online: Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases.

Dokainish, Hisham M / Kitao, Akio

The journal of physical chemistry. B

2018 Volume 122, Issue 36, Page(s) 8537–8547

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 ... ...

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 NH
MeSH term(s)	Animals ; Azetidines/chemistry ; Catalysis ; Catalytic Domain ; Cytosine/chemistry ; DNA Repair ; Deoxyribodipyrimidine Photo-Lyase/chemistry ; Drosophila melanogaster/enzymology ; Histidine/chemistry ; Lysine/chemistry ; Models, Chemical ; Molecular Dynamics Simulation ; Pyrimidine Dimers/chemistry ; Quantum Theory ; Thermodynamics ; Thymine/chemistry
Chemical Substances	Azetidines ; Pyrimidine Dimers ; Histidine (4QD397987E) ; Cytosine (8J337D1HZY) ; pyrimidine(6-4)pyrimidone photolyase (EC 4.1.99.-) ; Deoxyribodipyrimidine Photo-Lyase (EC 4.1.99.3) ; Lysine (K3Z4F929H6) ; Thymine (QR26YLT7LT)
Language	English
Publishing date	2018-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.8b07048
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Similarities and Differences between Thymine(6–4)Thymine/Cytosine DNA Lesion Repairs by Photolyases

Dokainish, Hisham M / Akio Kitao

Journal of physical chemistry. 2018 Aug. 20, v. 122, no. 36

2018

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 ... ...

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.
Keywords	active sites ; ammonia ; catalytic activity ; computational methodology ; cytosine ; DNA damage ; electron transfer ; energy ; enzymes ; genetic stability ; histidine ; molecular dynamics ; quantum mechanics ; solar radiation ; thermodynamics ; thymine
Language	English
Dates of publication	2018-0820
Size	p. 8537-8547.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.8b07048
Database	NAL-Catalogue (AGRICOLA)

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