Impact of emerging mutations on the dynamic properties the SARS-CoV-2 main protease: an in silico investigation
- Authors: Amamuddy, Olivier S , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163035 , vital:41006 , doi: 10.1021/acs.jcim.0c00634
- Description: The new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mpro dimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averaged betweenness centrality and geometry calculations. Domains from each Mpro protomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants.
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- Date Issued: 2020
The social dimensions of biological invasions in South Africa
- Authors: Shackleton, Ross T , Novoa, Ana , Shackleton, Charlie M , Kull, Christian A
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/176285 , vital:42681 , DOI 10.1007/978-3-030-32394-3
- Description: This chapter examines current knowledge relating to the human and social dimensions of biological invasions in South Africa. We do so by advancing 12 propositions and examining the evidence for or against each using South African literature. The propositions cover four broad issues: how people cause invasions; how they conceptualise them; effects of invasive species on people; and peoples’ responses to them.
- Full Text:
- Date Issued: 2020
The social dimensions of biological invasions in South Africa
- Authors: Shackleton, Ross T , Novoa, A , Shackleton, Charlie M
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/434000 , vital:73020 , ISBN 978-3-030-32394-3 , https://doi.org/10.1007/978-3-030-32394-3
- Description: This chapter examines current knowledge relating to the human and social dimensions of biological invasions in South Africa. We do so by advancing 12 propositions and examining the evidence for or against each using South African literature. The propositions cover four broad issues: how people cause invasions; how they conceptualise them; effects of invasive species on people; and peoples’ responses to them. The propositions we assess include:(1) intentional introductions were and continue to refiect the social ethos of the time;(2) people go to great lengths to ensure that newly introduced species establish themselves;(3) human-mediated modifications help invasive species to establish;(4) how people think about and study invasive species is strongly shaped by social-ecological contexts;(5) knowledge and awareness of invasive species is low amongst the general public;(6) personal values are the primary factor affecting perceptions of invasive alien species and their control;(7) specific social-ecological contexts mediate how invasive species affect people;(8) research on social effects of invasive species primarily focuses on negative impacts;(9) the negative social impacts of invasive species on local livelihoods are of more concern to people than impacts on biodiversity;(10) people are less willing to manage species regarded as ‘charismatic’;(11) social heterogeneity increases confiicts around the management of biological invasions; and (12) engagement with society is key to successful management. By advancing and questioning propositions, we were able to determine what is known, provide evidence for where gaps lie, and thus identify areas for future research.
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- Date Issued: 2020