Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

Adhikari, Puja; Ching, W. Y.

doi:10.1039/d0ra08222h

Cited by 27 publications

(64 citation statements)

References 44 publications

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“…(3) RBD The calculation and analysis of AABP in RBD has been reported in ref. 34 in excruciating detail. Here we recapture most of them as part of the presentation for the seven structural domains in Sprotein.…”

Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 98%

“…Strictly speaking, assigning a distance of separation between AAs in a protein in order to describe their interactions, is a vague and arbitrary parameter. However, with the quantum mechanically based OLCAO method and with the interatomic interaction between all atoms available, we can define the bonding between two AAs u and v with no ambiguity, which we dub as amino acid bond pair (AABP) 34 :…”

Section: Extension To Amino Acid Interactions In Proteinsmentioning

confidence: 99%

“…Recently, we have demonstrated AABP analysis of two specific structural domains RBD and SD1 34 . This is the first time that the non-local 3-dimensional (3D) AA interactions were carefully demonstrated and analyzed beyond the traditional approach based only on the amino acid primary sequence or their nearest neighbors in the sequences based on which the conventional sequence conservation are characterized.…”

Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 99%

“…It is possible to provide more detailed inter-amino acids interactions at atomic level as shown in Fig.6 of ref. 34 for RBD including the involvement of HBs and the unique role of S-S bonds in Cys. However, in this article the analysis of such nature for all seven structural domains will be exceptionally demanding and time consuming and deemed not necessary.…”

Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 99%

“…The complete Chain A in S-protein shown in Figure 3 and Figure 4 with these seven structural domains is obviously a spectacularly complex biomolecular system. Although the RBD and SD1 parts have been extensively discuss by us recently [33][34] , discussions of the other structural domains NTD, SD2, and FP, HR1-CH and CD in S2 were relatively limited despite the results presented in Section 3. Here we will relate and attempt to connect these structural domains.…”

Section: Interaction Between Seven Structural Domains In Spike Proteinmentioning

confidence: 99%

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Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

Ching

Adhikari²,

Jawad³

et al. 2020

Preprint

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The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

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Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 98%

Section: Extension To Amino Acid Interactions In Proteinsmentioning

confidence: 99%

Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 99%

Section: Three-dimensional Aa-aa Interactionmentioning

confidence: 99%

Section: Interaction Between Seven Structural Domains In Spike Proteinmentioning

confidence: 99%

See 3 more Smart Citations

Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

Ching

Adhikari²,

Jawad³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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COVID‐19 into Chemical Science Perspective: Chemical Preventive Measures and Drug Development

Adhikari

Sahu

2021

ChemistrySelect

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COVID‐19 facts and literature are discussed into chemical science intuition highlighting the direct role of chemistry to the ongoing global pandemic by covering structural identification of the virus, chemical preventive measures and development of drugs. We reviewed the four most promising repurposed drugs which are presently being investigated in mass clinical trials on COVID‐19 infected persons and synthetic routes of these drugs with their recent advancement. Chemical preventive measures such as soap water, hand sanitizer and disinfectant are the only available options in the arsenal to fight against COVID‐19, till an effective medicine or vaccine will be made available. As such the present review will focus on the mode of action of the major chemical preventives.

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Molecular Level Dissection of Critical Spike Mutations in SARS‐CoV‐2 Variants of Concern (VOCs): A Simplified Review

2021

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SARS-CoV-2 virus during its spread in the last one and half year has picked up critical changes in its genetic code i.e. mutations, which have leads to deleterious epidemiological characteristics. Due to critical role of spike protein in cell entry and pathogenesis, mutations in spike regions have been reported to enhance transmissibility, disease severity, possible escape from vaccine-induced immune response and reduced diagnostic sensitivity/specificity. Considering the structure-function impact of mutations, understanding the molecular details of these key mutations of newly emerged variants/lineages is of urgent concern. In this review, we have explored the literature on key spike mutations harbored by alpha, beta, gamma and delta 'variants of concern' (VOCs) and discussed their molecular consequences in the context of resultant virus biology.

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Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

Abstract: Gly504 interacting with two nearest neighbor and one non-local amino acids.

Cited by 27 publications

References 44 publications

Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

COVID‐19 into Chemical Science Perspective: Chemical Preventive Measures and Drug Development

Molecular Level Dissection of Critical Spike Mutations in SARS‐CoV‐2 Variants of Concern (VOCs): A Simplified Review

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