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Article ; Online: The distal-proximal relationships among the human moonlighting proteins: Evolutionary hotspots and Darwinian checkpoints.

Nawn, Debaleena / Hassan, Sk Sarif / Sil, Moumita / Ghosh, Ankita / Goswami, Arunava / Basu, Pallab / Dayhoff, Guy W / Lundstrom, Kenneth / Uversky, Vladimir N

International journal of biological macromolecules

2024 Volume 259, Issue Pt 1, Page(s) 128998

Abstract: Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained ... ...

Abstract	Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.
MeSH term(s)	Humans ; Phylogeny ; Proteins/chemistry ; Protein Processing, Post-Translational ; Genome
Chemical Substances	Proteins
Language	English
Publishing date	2024-01-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.128998
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Article: Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes.

Hassan, Sk Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Meta gene

2021 Volume 28, Page(s) 100873

Abstract: A total number of 3080 SARS-CoV-2 genomes from all continents are considered from the NCBI database. Every accessory protein ORF6, ORF7b, and ORF10 of SARS-CoV-2 possess a single missense mutation in less than 1.5% of the 3080 genomes. It has now been ... ...

Abstract	A total number of 3080 SARS-CoV-2 genomes from all continents are considered from the NCBI database. Every accessory protein ORF6, ORF7b, and ORF10 of SARS-CoV-2 possess a single missense mutation in less than 1.5% of the 3080 genomes. It has now been observed that different non-synonymous mutations occurred in these three accessory proteins. Most of these rare mutations are changing the amino acids such as hydrophilic to hydrophobic, acidic or basic to hydrophobic, and vice versa etc. So these highly conserved proteins might play an essential role in virus pathogenicity. This study opens a question whether it carries some messages about the virus rapid replications, and virulence.
Language	English
Publishing date	2021-02-18
Publishing country	Netherlands
Document type	Journal Article
ISSN	2214-5400
ISSN	2214-5400
DOI	10.1016/j.mgene.2021.100873
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Book ; Online: Fractality in a delayed-prey-predator ecological system with Allee effects

Goldar, Sujay / Hassan, Sk. Sarif

2021

Abstract: A delayed, discrete-time, prey-predator model with Allee effects imposed on prey and predator populations is defined, and dynamics of the system is characterized computationally. The parametric conditions for local asymptotic stability of equilibria are ... ...

Abstract	A delayed, discrete-time, prey-predator model with Allee effects imposed on prey and predator populations is defined, and dynamics of the system is characterized computationally. The parametric conditions for local asymptotic stability of equilibria are investigated with several illustrating examples. In addition, several periodic solutions were achieved. Furthermore, high degree of fractality of the prey-predator population trajectories is observed when the system is sufficiently delayed. This system has turned out to be a cooperative system, which is depicted using fractal dimension.
Keywords	Quantitative Biology - Populations and Evolution ; Mathematics - Dynamical Systems
Publishing date	2021-06-24
Publishing country	us
Document type	Book ; Online
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Article ; Online: Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs.

Sengupta, Antara / Hassan, Sk Sarif / Choudhury, Pabitra Pal

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2021 Volume 89, Page(s) 104724

Abstract: Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different ... ...

Abstract	Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence" hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
MeSH term(s)	Asia ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
Language	English
Publishing date	2021-01-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.104724
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Article ; Online: SARS-CoV2 envelope protein

Hassan, Sk. Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Genomics

non-synonymous mutations and its consequences

2020 Volume 112, Issue 6, Page(s) 3890–3892

Keywords	Genetics ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.001
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Article ; Online: Molecular phylogeny and missense mutations at envelope proteins across coronaviruses.

Hassan, Sk Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Genomics

2020 Volume 112, Issue 6, Page(s) 4993–5004

Abstract: Envelope (E) protein is one of the structural viroporins (76-109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the ... ...

Abstract	Envelope (E) protein is one of the structural viroporins (76-109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the β-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV-2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.
MeSH term(s)	Animals ; Camelus/virology ; Cats ; Cattle ; Chiroptera/virology ; Coronavirus/genetics ; Coronavirus Envelope Proteins/genetics ; Coronavirus Infections/virology ; Humans ; Mutation, Missense ; Phylogeny
Chemical Substances	Coronavirus Envelope Proteins ; envelope protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.09.014
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Article: Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs

Sengupta, Antara / Hassan, Sk. Sarif / Choudhury, Pabitra Pal

Infection, genetics, and evolution. 2021 Apr., v. 89

2021

Abstract	Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence” hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
Keywords	amino acids ; ancestry ; genome ; infection ; lead ; light ; monophyly ; mortality ; mutation ; nucleotide sequences ; proteins ; shade ; vaccines ; virulence ; viruses ; Asia
Language	English
Dates of publication	2021-04
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-light
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.104724
Database	NAL-Catalogue (AGRICOLA)

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Article: Molecular phylogeny and missense mutations at envelope proteins across coronaviruses

Hassan, Sk. Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Genomics. 2020 Nov., v. 112, no. 6

2020

Abstract: Envelope (E) protein is one of the structural viroporins (76–109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the ... ...

Abstract	Envelope (E) protein is one of the structural viroporins (76–109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the β-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV-2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.
Keywords	Orthocoronavirinae ; amino acids ; databases ; genome ; missense mutation ; phylogeny ; proteins ; sequence homology
Language	English
Dates of publication	2020-11
Size	p. 4993-5004.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.09.014
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: SARS-CoV2 envelope protein: non-synonymous mutations and its consequences.

Hassan, Sk Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Genomics

2020 Volume 112, Issue 6, Page(s) 3890–3892

Abstract: In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus ... ...

Abstract	In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus domains in 15 (0.414%) genomes among 3617 SARS-CoV2 genomes, analyzed. More precisely, 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contained the missense mutations over the E-protein of SARS-CoV2 genomes. The C-terminus motif DLLV has been to DFLV and YLLV in the proteins from QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.
MeSH term(s)	COVID-19/virology ; Coronavirus Envelope Proteins/chemistry ; Coronavirus Envelope Proteins/genetics ; Coronavirus Envelope Proteins/metabolism ; Genome, Viral ; Humans ; Membrane Proteins/metabolism ; Mutation ; Nucleoside-Phosphate Kinase/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
Chemical Substances	Coronavirus Envelope Proteins ; Membrane Proteins ; envelope protein, SARS-CoV-2 ; Nucleoside-Phosphate Kinase (EC 2.7.4.4) ; MPP5 protein, human (EC 2.7.4.8)
Keywords	covid19
Language	English
Publishing date	2020-07-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.001
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Article: SARS-CoV2 envelope protein: non-synonymous mutations and its consequences

Hassan, Sk. Sarif / Choudhury, Pabitra Pal / Roy, Bidyut

Genomics. 2020 Nov., v. 112, no. 6

2020

Abstract	In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus domains in 15 (0.414%) genomes among 3617 SARS-CoV2 genomes, analyzed. More precisely, 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contained the missense mutations over the E-protein of SARS-CoV2 genomes. The C-terminus motif DLLV has been to DFLV and YLLV in the proteins from QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; databases ; genome ; missense mutation ; nucleotide sequences ; viral envelope proteins ; China ; Europe ; Pacific Ocean Islands ; United States ; Victoria (Australia)
Language	English
Dates of publication	2020-11
Size	p. 3890-3892.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.001
Database	NAL-Catalogue (AGRICOLA)

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