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dc.contributor.authorKandeel, Mahmoud
dc.contributor.authorAl-Taher, Abdulla
dc.contributor.authorLi, Huifang
dc.contributor.authorSchwingenschlögl, Udo
dc.contributor.authorAlnazawi, Mohamed
dc.date.accessioned2018-05-22T09:46:15Z
dc.date.available2018-05-22T09:46:15Z
dc.date.issued2018-05-17
dc.identifier.citationKandeel M, Al-Taher A, Li H, Schwingenschlogl U, Alnazawi M (2018) Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers. Computational Biology and Chemistry. Available: http://dx.doi.org/10.1016/j.compbiolchem.2018.05.020.
dc.identifier.issn1476-9271
dc.identifier.doi10.1016/j.compbiolchem.2018.05.020
dc.identifier.urihttp://hdl.handle.net/10754/627937
dc.description.abstractStructural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lowest root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HR, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer were modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the “a” and “d” positions of HR helices stabilize the whole system, having minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three different energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at a and d position of HR helix were strong stabilizers of HRs recognition.
dc.description.sponsorshipThis work was supported by a research grant from King Faisal University, Deanship of Scientific Research under grant number 171001. We thank the faculty of Veterinary Medicine at King Faisal University for providing computational facilities from the PC labs. The research reported in this publication was supported by funding from King Abdullah University (KAUST). For computer time, this research used the resources of the Supercomputing Laboratory at KAUST.
dc.publisherElsevier BV
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S1476927118300926
dc.rightsNOTICE: this is the author’s version of a work that was accepted for publication in Computational Biology and Chemistry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Computational Biology and Chemistry, [, , (2018-05-17)] DOI: 10.1016/j.compbiolchem.2018.05.020 . © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectCoronavirus
dc.subjectmolecular dynamics
dc.subjectviral membrane fusion
dc.subjectbioinformatics
dc.subjectcontact score
dc.titleMolecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers
dc.typeArticle
dc.contributor.departmentComputational Physics and Materials Science (CPMS)
dc.contributor.departmentKAUST Solar Center (KSC)
dc.contributor.departmentMaterial Science and Engineering Program
dc.contributor.departmentPhysical Science and Engineering (PSE) Division
dc.identifier.journalComputational Biology and Chemistry
dc.eprint.versionPost-print
dc.contributor.institutionDepartment of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
dc.contributor.institutionDepartment of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa, Saudi Arabia
kaust.personLi, Huifang
kaust.personSchwingenschlögl, Udo
dc.date.published-online2018-05-17
dc.date.published-print2018-08


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NOTICE: this is the author’s version of a work that was accepted for publication in Computational Biology and Chemistry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Computational Biology and Chemistry, [, , (2018-05-17)] DOI: 10.1016/j.compbiolchem.2018.05.020 . © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
Except where otherwise noted, this item's license is described as NOTICE: this is the author’s version of a work that was accepted for publication in Computational Biology and Chemistry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Computational Biology and Chemistry, [, , (2018-05-17)] DOI: 10.1016/j.compbiolchem.2018.05.020 . © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/