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Article ; Online: Effect on the conformations of the spike protein of SARS-CoV-2 due to mutation.

Gupta, Aayatti Mallick / Chakrabarti, Jaydeb

2022 Volume 70, Issue 3, Page(s) 979–991

Abstract: The spike protein of SARS-CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the ... ...

Abstract	The spike protein of SARS-CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations that appeared in the variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wild-type from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between the N-terminal domain and receptor binding domain, leading to an obtuse angle cosine θ distribution in the trimeric structure in spike protein. Thus, an increase in open state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for the host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming a linker loop where many residues undergo stabilization in the open state compared to the closed one.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Spike Glycoprotein, Coronavirus/genetics ; Mutation ; Protein Binding
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2022-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	883433-7
ISSN	1470-8744 ; 0885-4513
ISSN (online)	1470-8744
ISSN	0885-4513
DOI	10.1002/bab.2413
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Article ; Online: Conformational stability and order of Hoogsteen base pair induced by protein binding.

Kole, Kanika / Gupta, Aayatti Mallick / Chakrabarti, Jaydeb

Biophysical chemistry

2023 Volume 301, Page(s) 107079

Abstract: Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA ... ...

Abstract	Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA using all-atom molecular dynamics simulation in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson-Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the presence of proteins stabilizes and organizes the HG bp and the entire DNA duplex. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.
MeSH term(s)	Base Pairing ; Nucleic Acid Conformation ; Protein Binding ; DNA/chemistry ; Thermodynamics ; Sugars
Chemical Substances	DNA (9007-49-2) ; Sugars
Language	English
Publishing date	2023-07-25
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.2023.107079
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Article: Insights from the comparative genome analysis of natural rubber degrading

Sarkar, Biraj / Gupta, Aayatti Mallick / Mandal, Sukhendu

Bioinformation

2021 Volume 17, Issue 10, Page(s) 880–890

Abstract: ... ...

Abstract	Nocardia
Language	English
Publishing date	2021-10-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630017880
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Article ; Online: Distribution of sigma factors delineates segregation of virulent and avirulent Mycobacterium.

Mallick Gupta, Aayatti / Mandal, Sukhendu

Archives of microbiology

2021 Volume 203, Issue 4, Page(s) 1627–1640

Abstract: The genus Mycobacterium includes a wide range of species of both slow and rapid growth under major pathogens, opportunists, and saprophytes. The number and combination of sigma factors are extremely diversified among various species of Mycobacterium. The ...

Abstract	The genus Mycobacterium includes a wide range of species of both slow and rapid growth under major pathogens, opportunists, and saprophytes. The number and combination of sigma factors are extremely diversified among various species of Mycobacterium. The comparative genome analysis illustrates that SigC, SigD, SigG, SigH, SigK and SigI are dominant among the pathogens. Evolutionary analysis using Bayesian inference on 16S rRNA and MLST-based phylogeny using 14 housekeeping genes distinctly differentiate the slow-growing Mycobacterium from fast growers and segregate pathogens from opportunists and saprophytes. Based on the similarity coefficient upon the allotment of sigma factors in mycobacterial species through UPGMA dendrogram analysis, it is apparent that the pathogens are grouped separately following the similar trend observed from the evolutionary approach. Predominance of a set of sigma factors particularly the pathogenic Mycobacterium co-exists with the distribution of six well-known virulence factors of Mycobacterium (PhoP, PcaA, FbpA, Mce1B, KatG and PE_PGRS30). The pathogenicity responsible sigma factors elicit close resemblance with few notable characters of the known virulence factors. Thus the analysis renders that the distribution of sigma factors of different species of Mycobacterium can be a potential tool to predict their pathogenicity index.
MeSH term(s)	Bacterial Proteins/genetics ; Bayes Theorem ; Genes, Essential ; Multilocus Sequence Typing ; Mycobacterium/genetics ; Mycobacterium/pathogenicity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sigma Factor/genetics ; Species Specificity ; Virulence/genetics
Chemical Substances	Bacterial Proteins ; RNA, Ribosomal, 16S ; Sigma Factor
Language	English
Publishing date	2021-01-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-020-02172-8
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Article ; Online: The C-terminal domain of M. tuberculosis ECF sigma factor I (SigI) interferes in SigI-RNAP interaction.

Mallick Gupta, Aayatti / Mandal, Sukhendu

Journal of molecular modeling

2020 Volume 26, Issue 4, Page(s) 77

Abstract: Mycobacterium tuberculosis is equipped with diversified ECF sigma factors that are generally expressed under adverse environmental conditions. Mtb-SigI belongs to the ECF41 family of sigma factor, and no information is available about their expression ... ...

Abstract	Mycobacterium tuberculosis is equipped with diversified ECF sigma factors that are generally expressed under adverse environmental conditions. Mtb-SigI belongs to the ECF41 family of sigma factor, and no information is available about their expression during stringent response. This study provides the structural insight of Mtb-SigI and the characterization of its C-terminal polypeptide extension. C-terminal site of Mtb-SigI is truncated in two ways: (a) conserved region of C-terminal extension is preserved while the rest of the portion is deleted and (b) complete deletion of C-terminal extension. Each of the wild-type and truncated Mtb-SigI is docked with a β subunit of core RNA polymerase and simulated for 100 ns. Relative binding strength calculated from trajectory analysis reflects that the complete deletion of the C-terminal extension of Mtb-SigI favors interaction with core RNA polymerase. It can be implicated that the C-terminal domain in the wild-type docked complex help flipping of domain 4 of Mtb-SigI and thereby impaired holoenzyme formation. When the C-terminal extension is partially deleted, such flipping of domain 4 of Mtb-SigI diminishes and complete deletion of C-terminal extension promotes holoenzyme formation. In the absence of any sigma factor antagonist, the C-terminal extension of Mtb-SigI might behave as a complex player in transcription regulation. Graphical abstract Role of Mtb-SigI in transcription regulation.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/genetics ; Humans ; Molecular Docking Simulation ; Mycobacterium tuberculosis/chemistry ; Mycobacterium tuberculosis/genetics ; Protein Domains ; Sigma Factor/chemistry ; Sigma Factor/genetics
Chemical Substances	Bacterial Proteins ; Sigma Factor ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2020-03-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-020-4322-y
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Article ; Online: Effect on the conformations of spike protein of SARS-CoV-2 due to mutation

Gupta, Aayatti Mallick / Chakrabarti, Jaydeb

bioRxiv

Abstract: The spike protein of SARS CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the ... ...

Abstract	The spike protein of SARS CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations appeared in variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wildtype from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between N-terminal domain and receptor binding domain leading to an obtuse angle cosine distribution in the trimeric structure in spike protein. Thus, increase in open-state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming linker loop where many residues undergo stabilization in the open state compared to the closed one.
Keywords	covid19
Language	English
Publishing date	2022-05-12
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.05.11.491583
Database	COVID19

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Article ; Online: Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2.

Mallick Gupta, Aayatti / Mandal, SasthiCharan / Mandal, Sukhendu / Chakrabarti, Jaydeb

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3542–3552

Abstract: Mutations drive viral evolution and genome variability that causes viruses to escape host immunity and to develop drug resistance. SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to ...

Abstract	Mutations drive viral evolution and genome variability that causes viruses to escape host immunity and to develop drug resistance. SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein. We consider the effects of mutations in some of the epitope region including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. We observe that the mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, we study the conformational stability of the epitope region and epitope:paratope interface under the mutation from the fluctuations in the dihedral angles. We observe that the mutation renders the epitope and the epitope:paratope interface unstable compared to the corresponding wild type ones. Thus, the mutations may help in escaping antibody mediated immunity of the hostCommunicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Epitopes/genetics ; COVID-19 ; Mutation ; RNA-Dependent RNA Polymerase/chemistry ; Molecular Docking Simulation ; Antiviral Agents/pharmacology
Chemical Substances	Epitopes ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Antiviral Agents
Language	English
Publishing date	2022-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2051746
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Article ; Online: Mycobacterium tuberculosis H37 Rv1222: structural insight in transcription inhibition.

Gupta, Aayatti Mallick / Mandal, Sukhendu

Journal of biomolecular structure & dynamics

2017 Volume 35, Issue 7, Page(s) 1574–1581

Language	English
Publishing date	2017
Publishing country	England
Document type	Letter
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2016.1189357
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Article: Distribution of sigma factors delineates segregation of virulent and avirulent Mycobacterium

Mallick Gupta, Aayatti / Mandal, Sukhendu

Archives of microbiology. 2021 May, v. 203, no. 4

2021

Abstract	The genus Mycobacterium includes a wide range of species of both slow and rapid growth under major pathogens, opportunists, and saprophytes. The number and combination of sigma factors are extremely diversified among various species of Mycobacterium. The comparative genome analysis illustrates that SigC, SigD, SigG, SigH, SigK and SigI are dominant among the pathogens. Evolutionary analysis using Bayesian inference on 16S rRNA and MLST-based phylogeny using 14 housekeeping genes distinctly differentiate the slow-growing Mycobacterium from fast growers and segregate pathogens from opportunists and saprophytes. Based on the similarity coefficient upon the allotment of sigma factors in mycobacterial species through UPGMA dendrogram analysis, it is apparent that the pathogens are grouped separately following the similar trend observed from the evolutionary approach. Predominance of a set of sigma factors particularly the pathogenic Mycobacterium co-exists with the distribution of six well-known virulence factors of Mycobacterium (PhoP, PcaA, FbpA, Mce1B, KatG and PE_PGRS30). The pathogenicity responsible sigma factors elicit close resemblance with few notable characters of the known virulence factors. Thus the analysis renders that the distribution of sigma factors of different species of Mycobacterium can be a potential tool to predict their pathogenicity index.
Keywords	Bayesian theory ; Mycobacterium ; microbiology ; phylogeny ; saprophytes ; sequence analysis ; virulence
Language	English
Dates of publication	2021-05
Size	p. 1627-1640.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-020-02172-8
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Article ; Online: Unraveling DPP4 Receptor Interactions with SARS-CoV-2 Variants and MERS-CoV: Insights into Pulmonary Disorders via Immunoinformatics and Molecular Dynamics.

Roy, Arpan Narayan / Gupta, Aayatti Mallick / Banerjee, Deboshmita / Chakrabarti, Jaydeb / Raghavendra, Pongali B

Viruses

2023 Volume 15, Issue 10

Abstract: Human coronaviruses like MERS CoV are known to utilize dipeptidyl peptidase 4 (DPP4), apart from angiotensin-converting enzyme 2(ACE2) as a potential co-receptor for viral cell entry. DPP4, the ubiquitous membrane-bound aminopeptidase, is closely ... ...

Abstract	Human coronaviruses like MERS CoV are known to utilize dipeptidyl peptidase 4 (DPP4), apart from angiotensin-converting enzyme 2(ACE2) as a potential co-receptor for viral cell entry. DPP4, the ubiquitous membrane-bound aminopeptidase, is closely associated with elevation of disease severity in comorbidities. In SARS-CoV-2, there is inadequate evidence for combination of spike protein variants with DPP4, and underlying adversity in COVID-19. To elucidate this mechanistic basis, we have investigated interaction of spike protein variants with DPP4 through molecular docking and simulation studies. The possible binding interactions between the receptor binding domain (RBD) of different spike variants of SARS-CoV-2 and DPP4 have been compared with interactions observed in the experimentally determined structure of the complex of MERS-CoV with DPP4. Comparative binding affinity confers that Delta-CoV-2: DPP4 shows close proximity with MERS-CoV:DPP4, as depicted from accessible surface area, radius of gyration and number of hydrogen bonding in the interface. Mutations in the delta variant, L452R and T478K directly participate in DPP4 interaction, enhancing DPP4 binding. E484K in alpha and gamma variants of spike protein is also found to interact with DPP4. Hence, DPP4 interaction with spike protein becomes more suitable due to mutation, especially due to L452R, T478K and E484K. Furthermore, perturbation in the nearby residues Y495, Q474 and Y489 is evident due to L452R, T478K and E484K, respectively. Virulent strains of spike protein are more susceptible to DPP4 interaction and are prone to be victimized in patients due to comorbidities. Our results will aid the rational optimization of DPP4 as a potential therapeutic target to manage COVID-19 disease severity.
MeSH term(s)	Humans ; COVID-19/metabolism ; Dipeptidyl Peptidase 4/metabolism ; Middle East Respiratory Syndrome Coronavirus/genetics ; Middle East Respiratory Syndrome Coronavirus/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Dipeptidyl Peptidase 4 (EC 3.4.14.5) ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-10-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15102056
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