Evolution of camel CYP2E1 and its associated power of binding toxic industrial chemicals and drugs

Kandeel, Mahmoud; Altaher, Abdullah; Kitade, Yukio; Abdelaziz, Magdi; Alnazawi, Mohamed; Elshazli, Kamal

doi:10.1016/j.compbiolchem.2016.07.009

Computational Biology and Chemistry

2016

DOI: 10.1016/j.compbiolchem.2016.07.009

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Evolution of camel CYP2E1 and its associated power of binding toxic industrial chemicals and drugs

Mahmoud Kandeel

Abdullah Altaher

Yukio Kitade

et al.

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Cited by 6 publications

(2 citation statements)

References 25 publications

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“…[15][16][17] Understanding the gene's composition and subsequent analysis of codon usage is indispensable in understanding virus replication and evolution and targeting the unique aspects of virus biology. 18,19) For the 20 amino acids, 61 genetic codes are used.…”

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confidence: 99%

Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Kandeel

Altaher

2017

Biological & Pharmaceutical Bulletin

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Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro.

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confidence: 99%

Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Kandeel

Altaher

2017

Biological & Pharmaceutical Bulletin

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“…[13][14][15][16][17] In this work, we performed MD analysis of the interaction of NSP3 Plpro with ubiquitin and Ubl among important viruses that pose serious health risks, such as SARS and MERS CoV. Investigation of the detailed interaction at the protein-protein interface will contribute to our knowledge about the interaction of viral proteins with host innate immunity proteins.…”

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confidence: 99%

Molecular Dynamic Studies of Interferon and Innate Immunity Resistance in MERS CoV Non-Structural Protein 3

Alfuwaires

Altaher

Kandeel

2017

Biological & Pharmaceutical Bulletin

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The new emerging Middle East Respiratory Syndrome Coronavirus (MERS CoV) encodes several resistance proteins against the innate immune response of the host, including interferon (IFN) resistance. Monitoring of the status of such proteins will be important to track viral pathogenicity. In this study, molecular dynamics approaches were used to investigate MERS CoV Non-Structural Protein 3 (NSP3) specific proteins that resist host innate immunity. MERS CoV papain-like protease (Plpro) was more conformationally flexible than Severe Acute Respiratory Syndrome CoV (SARS) CoV Plpro. This flexibility was evident in either the free form or when bound with ubiquitin. There were marked changes in the root-mean-square deviation (RMSD) in the ubiquitin like domain (Ubl) and the fingers subdomain of the catalytic domain of Plpro. An interesting feature is the dynamic change in Ubl, which shows a rigid conformation in the free form of Plpro but is fully flexible upon the binding of ubiquitin. This increased flexibility could be important for the downstream effects of the interaction with other proteins and the inhibition of the innate immunity. Four major residues involved in deubiquitination, L106, P163, R168 and F265, were conserved in all MERS CoVs and differed from other Beta CoVs. These conserved CoV residues were associated with lower deubiquitinating activity and render MERS CoV Plpro with less potent deubiquitinating potential. The number of residues and total interactions with ubiquitin were lower for the MERS CoV Plpro than for the SARS CoV. These factors contribute to the lower deubiquitinating actions of MERS CoV NSP3 and its subsequently lower interaction with the host immune system.

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Cefotaxime pharmacokinetics in Arabian camel (Camelus dromedarius) calves after single intravenous injection

Altayban

Kandeel

Tahoun

et al. 2019

Trop Anim Health Prod

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Evolution of camel CYP2E1 and its associated power of binding toxic industrial chemicals and drugs

Cited by 6 publications

References 25 publications

Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Molecular Dynamic Studies of Interferon and Innate Immunity Resistance in MERS CoV Non-Structural Protein 3

Cefotaxime pharmacokinetics in Arabian camel (Camelus dromedarius) calves after single intravenous injection

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