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10.1016/j.bpj.2021.05.022 http://scihub22266oqcxt.onion/10.1016/j.bpj.2021.05.022 34087207!8169235!34087207     free     free     free Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 217.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Biophys+J 2021 ; 120 (14): 2848-2858 Nephropedia Template TP {{tp|p=34087207|t=2021. Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein |pdf=|usr=}}{{34087207}} gab.com Text Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein JO: Biophys J http://www.kidney.de/pget.php?&tw=1&pmid=34087207 #FOAvip Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses. Twit Text FOAVip Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein ????Biophys J http://www.kidney.de/pget.php?&tw=1&pmid=34087207 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=34087207 #FOAvip English Wikipedia <ref>{{Cite pmid|34087207}}</ref> Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein #MMPMID34087207 Remington JM; McKay KT; Ferrell JB; Schneebeli ST; Li J Biophys J 2021[Jul]; 120 (14): 2848-2858 PMID34087207show ga Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses. |*COVID-19[MESH] |*Spike Glycoprotein, Coronavirus[MESH] |Humans[MESH] |Peptides[MESH] |SARS-CoV-2[MESH]Enhanced sampling protocol to elucidate fusion peptide opening of SARS(epmc).pdf DeepDyve Pubget Overpricing