FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4366996461> ?p ?o ?g. }

• W4366996461 endingPage "e1011054" @default.
• W4366996461 startingPage "e1011054" @default.
• W4366996461 abstract "Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm's volume. Viral enzymes in the host cell also encounter such crowded conditions as they often function at the endoplasmic reticulum membranes. We focus on an enzyme encoded by the hepatitis C virus, the NS3/4A protease, which is crucial for viral replication. We have previously found experimentally that synthetic crowders, polyethylene glycol (PEG) and branched polysucrose (Ficoll), differently affect the kinetic parameters of peptide hydrolysis catalyzed by NS3/4A. To gain understanding of the reasons for such behavior, we perform atomistic molecular dynamics simulations of NS3/4A in the presence of either PEG or Ficoll crowders and with and without the peptide substrates. We find that both crowder types make nanosecond long contacts with the protease and slow down its diffusion. However, they also affect the enzyme structural dynamics; crowders induce functionally relevant helical structures in the disordered parts of the protease cofactor, NS4A, with the PEG effect being more pronounced. Overall, PEG interactions with NS3/4A are slightly stronger but Ficoll forms more hydrogen bonds with NS3. The crowders also interact with substrates; we find that the substrate diffusion is reduced much more in the presence of PEG than Ficoll. However, contrary to NS3, the substrate interacts more strongly with Ficoll than with PEG crowders, with the substrate diffusion being similar to crowder diffusion. Importantly, crowders also affect the substrate-enzyme interactions. We observe that both PEG and Ficoll enhance the presence of substrates near the active site, especially near catalytic H57 but Ficoll crowders increase substrate binding more than PEG molecules." @default.
• W4366996461 created "2023-04-27" @default.
• W4366996461 creator A5061800523 @default.
• W4366996461 creator A5088500200 @default.
• W4366996461 creator A5090446172 @default.
• W4366996461 date "2023-04-25" @default.
• W4366996461 modified "2023-09-30" @default.
• W4366996461 title "Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease" @default.
• W4366996461 cites W1630238018 @default.
• W4366996461 cites W1877659824 @default.
• W4366996461 cites W1964391817 @default.
• W4366996461 cites W1964547135 @default.
• W4366996461 cites W1969493239 @default.
• W4366996461 cites W1970948529 @default.
• W4366996461 cites W1976488701 @default.
• W4366996461 cites W1980374511 @default.
• W4366996461 cites W1984233626 @default.
• W4366996461 cites W1984318965 @default.
• W4366996461 cites W1998712158 @default.
• W4366996461 cites W1999613945 @default.
• W4366996461 cites W2004984389 @default.
• W4366996461 cites W2005202913 @default.
• W4366996461 cites W2012500478 @default.
• W4366996461 cites W2014468790 @default.
• W4366996461 cites W2016934983 @default.
• W4366996461 cites W2027918314 @default.
• W4366996461 cites W2028455456 @default.
• W4366996461 cites W2029667189 @default.
• W4366996461 cites W2032919483 @default.
• W4366996461 cites W2038758364 @default.
• W4366996461 cites W2042287552 @default.
• W4366996461 cites W2054655080 @default.
• W4366996461 cites W2055337326 @default.
• W4366996461 cites W2056734463 @default.
• W4366996461 cites W2057089150 @default.
• W4366996461 cites W2060872711 @default.
• W4366996461 cites W2062853403 @default.
• W4366996461 cites W2064569009 @default.
• W4366996461 cites W2066736364 @default.
• W4366996461 cites W2067174909 @default.
• W4366996461 cites W2069262457 @default.
• W4366996461 cites W2085229813 @default.
• W4366996461 cites W2091560747 @default.
• W4366996461 cites W2105573149 @default.
• W4366996461 cites W2106140689 @default.
• W4366996461 cites W2117318478 @default.
• W4366996461 cites W2123681603 @default.
• W4366996461 cites W2124195135 @default.
• W4366996461 cites W2132262459 @default.
• W4366996461 cites W2132629607 @default.
• W4366996461 cites W2141920771 @default.
• W4366996461 cites W2150766477 @default.
• W4366996461 cites W2150981663 @default.
• W4366996461 cites W2154553490 @default.
• W4366996461 cites W2156458781 @default.
• W4366996461 cites W2328490316 @default.
• W4366996461 cites W2332893388 @default.
• W4366996461 cites W2409577334 @default.
• W4366996461 cites W2523214233 @default.
• W4366996461 cites W2542660070 @default.
• W4366996461 cites W2555870966 @default.
• W4366996461 cites W2724359247 @default.
• W4366996461 cites W2761541116 @default.
• W4366996461 cites W2768469871 @default.
• W4366996461 cites W2806946242 @default.
• W4366996461 cites W2900552445 @default.
• W4366996461 cites W2949223833 @default.
• W4366996461 cites W2970696575 @default.
• W4366996461 cites W2970750990 @default.
• W4366996461 cites W3014308339 @default.
• W4366996461 cites W3044083479 @default.
• W4366996461 cites W3047269537 @default.
• W4366996461 cites W3087634998 @default.
• W4366996461 cites W3176856228 @default.
• W4366996461 cites W3181315599 @default.
• W4366996461 cites W3187018774 @default.
• W4366996461 cites W3213940527 @default.
• W4366996461 cites W4214942036 @default.
• W4366996461 doi "https://doi.org/10.1371/journal.pcbi.1011054" @default.
• W4366996461 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37098073" @default.
• W4366996461 hasPublicationYear "2023" @default.
• W4366996461 type Work @default.
• W4366996461 citedByCount "1" @default.
• W4366996461 countsByYear W43669964612023 @default.
• W4366996461 crossrefType "journal-article" @default.
• W4366996461 hasAuthorship W4366996461A5061800523 @default.
• W4366996461 hasAuthorship W4366996461A5088500200 @default.
• W4366996461 hasAuthorship W4366996461A5090446172 @default.
• W4366996461 hasBestOaLocation W43669964611 @default.
• W4366996461 hasConcept C10138342 @default.
• W4366996461 hasConcept C12554922 @default.
• W4366996461 hasConcept C132379496 @default.
• W4366996461 hasConcept C137061746 @default.
• W4366996461 hasConcept C162324750 @default.
• W4366996461 hasConcept C181199279 @default.
• W4366996461 hasConcept C185592680 @default.
• W4366996461 hasConcept C202751555 @default.
• W4366996461 hasConcept C204389451 @default.

• next