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Article ; Online: Structural investigations of the palmitoylated F13 envelope protein of Mpox virus.

Borkotoky, Subhomoi / Dey, Debajit

2023 Volume 95, Issue 5, Page(s) e28798

MeSH term(s)	Monkeypox virus ; Viral Envelope Proteins/chemistry
Chemical Substances	Viral Envelope Proteins
Language	English
Publishing date	2023-05-22
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28798
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Article ; Online: Strategies for rapid production of crystallization quality coatomer WD40 domains.

Dey, Debajit / Hasan, S Saif

Protein expression and purification

2023 Volume 212, Page(s) 106358

Abstract: The vesicular secretion of soluble cargo proteins from the endoplasmic reticulum (ER) is accompanied by the export of ER-resident membrane proteins that are co-packaged in secretory vesicles. The cytosolic coatomer protein complex I (COPI) utilizes the N- ...

Abstract	The vesicular secretion of soluble cargo proteins from the endoplasmic reticulum (ER) is accompanied by the export of ER-resident membrane proteins that are co-packaged in secretory vesicles. The cytosolic coatomer protein complex I (COPI) utilizes the N-terminal WD40 domains of α-COPI and β'-COPI subunits to bind these membrane protein "clients" for ER retrieval. These "αWD40" and "β'WD40" domains are structural homologs that demonstrate distinct selectivity for client proteins. However, elucidation of the atomic-level principles of coatomer-client interactions has been challenging due to the tendency of αWD40 domain to undergo aggregation during expression and purification. Here we describe a rapid recombinant production strategy from E. coli, which substantially enhances the quality of the purified αWD40 domain. The αWD40 purification and crystallization are completed within one day, which minimizes aggregation losses and yields a 1.9 Å resolution crystal structure. We demonstrate the versatility of this strategy by applying it to purify the β'WD40 domain, which yields crystal structures in the 1.2-1.3 Å resolution range. As an alternate recombinant production system, we develop a cost-effective strategy for αWD40 production in human Expi293 cells. Finally, we suggest a roadmap to simplify these protocols further, which is of significance for the production of WD40 mutants prone to rapid aggregation. The WD40 production strategies presented here are likely to have broad applications because the WD40 domain represents one of the largest families of biomolecular interaction modules in the eukaryotic proteome and is critical for trafficking of host as well as viral proteins such as the SARS-CoV-2 spike protein.
MeSH term(s)	Humans ; COVID-19 ; Crystallization ; Escherichia coli/genetics ; SARS-CoV-2
Chemical Substances	spike protein, SARS-CoV-2
Language	English
Publishing date	2023-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2023.106358
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Article: Chemical and biochemical characterization of

Saikia, Kangkon / Dey, Saurav / Hazarika, Shabiha Nudrat / Handique, Gautam Kumar / Thakur, Debajit / Handique, Arun Kumar

Frontiers in nutrition

2023 Volume 10, Page(s) 1304903

Abstract: Ipomea aquatica, ...

Abstract	Ipomea aquatica,
Language	English
Publishing date	2023-12-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2776676-7
ISSN	2296-861X
ISSN	2296-861X
DOI	10.3389/fnut.2023.1304903
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Article ; Online: Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective

Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved

Mol Biol Rep. 2023 Mar., v. 50, no. 3 p.2713-2721

2023

Abstract: BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to ... ...

Abstract	BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. METHODS: In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. CONCLUSION: Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; humans ; renin-angiotensin system ; therapeutics ; virus transmission ; viruses ; China
Language	English
Dates of publication	2023-03
Size	p. 2713-2721.
Publishing place	Springer Netherlands
Document type	Article ; Online
Note	Review
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-08193-4
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Article ; Online: Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective.

Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved

Molecular biology reports

2022 Volume 50, Issue 3, Page(s) 2713–2721

Abstract: Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to ... ...

Abstract	Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. Methods: In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. Conclusion: Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensins/metabolism ; Binding Sites ; COVID-19 ; Protein Binding/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Angiotensins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23)
Language	English
Publishing date	2022-12-23
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-08193-4
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Article ; Online: Addressing Biases in Ambient PM

Katoch, Varun / Kumar, Alok / Imam, Fahad / Sarkar, Debajit / Knibbs, Luke D / Liu, Yang / Ganguly, Dilip / Dey, Sagnik

Environmental science & technology

2023 Volume 57, Issue 48, Page(s) 19190–19201

Abstract: ... Ambient ... ...

Abstract	Ambient PM
MeSH term(s)	Particulate Matter/analysis ; Air Pollution/analysis ; Environmental Monitoring/methods ; Aerosols/analysis ; Bias ; India ; Air Pollutants/analysis
Chemical Substances	Particulate Matter ; Aerosols ; Air Pollutants
Language	English
Publishing date	2023-11-13
Publishing country	United States
Document type	Journal Article
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c03355
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Article ; Online: Unravelling viral dynamics through molecular dynamics simulations - A brief overview.

Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved / Joshi, Amit / Tripathi, Keshawanand

Biophysical chemistry

2022 Volume 291, Page(s) 106908

Abstract: Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A ... ...

Abstract	Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A virus structure is metastable and highly responsive to environmental changes. Although major events of a virus life cycle are well characterized, several important questions with respect to how the nucleocapsid assemble/disassemble remain to be explored. In recent years due to enhanced computational power, molecular dynamics (MD) simulations have become an attractive alternative for addressing these questions since it is challenging to probe dynamic behavior with in vitro experimentation. The ability to simulate a complete virus particle provides an unprecedented atomic level resolution which can be used to understand its behavior under specific conditions. The current review outlines contributions made by all-atom and coarse-grained MD simulations towards understanding the mechanics and dynamics of virus structure and function. Databases and programs which facilitate such in silico investigations have also been discussed.
MeSH term(s)	Molecular Dynamics Simulation ; Proteins ; RNA ; Viruses ; DNA
Chemical Substances	Proteins ; RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2022-10-12
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2022.106908
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Article ; Online: Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion.

Borkotoky, Subhomoi / Dey, Debajit / Banerjee, Manidipa

Journal of chemical information and modeling

2021 Volume 61, Issue 1, Page(s) 423–431

Abstract: Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded ... ...

Abstract	Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, we attempted to identify the correct fusion peptide region in the Spike protein of SARS-CoV-2 by all-atom molecular dynamics simulations of dual membrane systems with varied oligomeric units of putative candidate peptides. Of all of the systems tested, only a trimeric unit of a 40-amino-acid region (residues 816-855 of SARS-CoV-2 Spike) was effective in triggering the initial stages of membrane fusion, within 200 ns of simulation time. Association of this trimeric unit with dual membranes resulted in the migration of lipids from the upper leaflet of the lower bilayer toward the lower leaflet of the upper bilayer to create a structural unit reminiscent of a fusion bridge. We submit that residues 816-855 of Spike represent the bona fide fusion peptide of SARS-CoV-2 and that computational methods represent an effective way to identify fusion peptides in viral glycoproteins.
MeSH term(s)	Amino Acid Sequence ; COVID-19/metabolism ; COVID-19/virology ; Host-Pathogen Interactions ; Humans ; Membrane Fusion ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/metabolism ; Protein Multimerization ; SARS-CoV-2/chemistry ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Internalization
Chemical Substances	Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.0c01231
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Article: The Structural Biology of Eastern Equine Encephalitis Virus, an Emerging Viral Threat.

Hasan, S Saif / Dey, Debajit / Singh, Suruchi / Martin, Matthew

Pathogens (Basel, Switzerland)

2021 Volume 10, Issue 8

Abstract: Alphaviruses are arboviruses that cause arthritis and encephalitis in humans. Eastern Equine Encephalitis Virus (EEEV) is a mosquito-transmitted alphavirus that is implicated in severe encephalitis in humans with high mortality. However, limited insights ...

Abstract	Alphaviruses are arboviruses that cause arthritis and encephalitis in humans. Eastern Equine Encephalitis Virus (EEEV) is a mosquito-transmitted alphavirus that is implicated in severe encephalitis in humans with high mortality. However, limited insights are available into the fundamental biology of EEEV and residue-level details of its interactions with host proteins. In recent years, outbreaks of EEEV have been reported mainly in the United States, raising concerns about public safety. This review article summarizes recent advances in the structural biology of EEEV based mainly on single-particle cryogenic electron microscopy (cryoEM) structures. Together with functional analyses of EEEV and related alphaviruses, these structural investigations provide clues to how EEEV interacts with host proteins, which may open avenues for the development of therapeutics.
Language	English
Publishing date	2021-07-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10080973
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Article ; Online: Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid.

Shrivastav, Gourav / Borkotoky, Subhomoi / Dey, Debajit / Singh, Bhumika / Malhotra, Nidhi / Azad, Kimi / Jayaram, B / Agarwal, Manish / Banerjee, Manidipa

Biophysical chemistry

2023 Volume 305, Page(s) 107152

Abstract: Although virus capsids appear as rigid, symmetric particles in experimentally determined structures; biochemical studies suggest a significant degree of structural flexibility in the particles. We carried out all-atom simulations on the icosahedral ... ...

Abstract	Although virus capsids appear as rigid, symmetric particles in experimentally determined structures; biochemical studies suggest a significant degree of structural flexibility in the particles. We carried out all-atom simulations on the icosahedral capsid of an insect virus, Flock House Virus, which show intriguing differences in the degree of flexibility of quasi-equivalent capsid subunits consistent with previously described biological behaviour. The flexibility of all the β and γ subunits of the protein and RNA fragments is analysed and compared. Both γ
MeSH term(s)	Capsid/chemistry ; Capsid/metabolism ; Interleukin Receptor Common gamma Subunit/analysis ; Interleukin Receptor Common gamma Subunit/metabolism ; Capsid Proteins/analysis ; Capsid Proteins/metabolism ; RNA/metabolism ; Water/metabolism
Chemical Substances	Interleukin Receptor Common gamma Subunit ; Capsid Proteins ; RNA (63231-63-0) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-12-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2023.107152
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