Matches in SemOpenAlex for { <https://semopenalex.org/work/W3119150888> ?p ?o ?g. }
- W3119150888 abstract "Proteins’ biological function and folding mechanisms are often guided by large-scale, slow motions, which involve crossing high energy barriers. In a simulation trajectory, these slow fluctuations are commonly identified using a principal component analysis (PCA). Despite the popularity of this method, a complete analysis of its predictions based on the physics of protein motion has been so far limited. This study formally connects the PCA to a Langevin model of protein dynamics and analyzes the contributions of energy barriers and hydrodynamic interactions to the slow PCA modes of motion. To do so, we introduce an anisotropic extension of the Langevin Equation for Protein Dynamics, called the LE4PD-XYZ, which formally connects to the PCA ‘essential dynamics’. The LE4PD-XYZ is an accurate coarse-grained diffusive method to model protein motion, which describes anisotropic fluctuations in the protein’s alpha-carbons. The LE4PD accounts for hydrodynamic effects and mode-dependent free-energy barriers. This study compares large-scale anisotropic fluctuations identified by the LE4PD-XYZ to the mode-dependent PCA’s predictions, starting from a microsecond-long alpha-carbon molecular dynamics atomistic trajectory of the protein ubiquitin. We observe that the inclusion of free-energy barriers and hydrodynamic interactions has important effects on the identification and timescales of ubiquitin’s slow modes." @default.
- W3119150888 created "2021-01-18" @default.
- W3119150888 creator A5009994990 @default.
- W3119150888 creator A5087430767 @default.
- W3119150888 date "2021-01-08" @default.
- W3119150888 modified "2023-10-16" @default.
- W3119150888 title "Comparison between slow, anisotropic LE4PD fluctuations and the Principal Component Analysis modes of Ubiquitin" @default.
- W3119150888 cites W1031578623 @default.
- W3119150888 cites W1559535630 @default.
- W3119150888 cites W1597577535 @default.
- W3119150888 cites W1979863594 @default.
- W3119150888 cites W1986614779 @default.
- W3119150888 cites W1997870466 @default.
- W3119150888 cites W1998093640 @default.
- W3119150888 cites W1998412941 @default.
- W3119150888 cites W2001773296 @default.
- W3119150888 cites W2007995903 @default.
- W3119150888 cites W2018748094 @default.
- W3119150888 cites W2024423406 @default.
- W3119150888 cites W2025899185 @default.
- W3119150888 cites W2030542905 @default.
- W3119150888 cites W2031822741 @default.
- W3119150888 cites W2036178765 @default.
- W3119150888 cites W2043701535 @default.
- W3119150888 cites W2052126651 @default.
- W3119150888 cites W2055516113 @default.
- W3119150888 cites W2056467595 @default.
- W3119150888 cites W2058167083 @default.
- W3119150888 cites W2066962978 @default.
- W3119150888 cites W2068265376 @default.
- W3119150888 cites W2070437391 @default.
- W3119150888 cites W2071656198 @default.
- W3119150888 cites W2078828682 @default.
- W3119150888 cites W2081231020 @default.
- W3119150888 cites W2085266415 @default.
- W3119150888 cites W2085550698 @default.
- W3119150888 cites W2085569207 @default.
- W3119150888 cites W2088647884 @default.
- W3119150888 cites W2091701505 @default.
- W3119150888 cites W2094795801 @default.
- W3119150888 cites W2111339528 @default.
- W3119150888 cites W2112033855 @default.
- W3119150888 cites W2115416706 @default.
- W3119150888 cites W2132589721 @default.
- W3119150888 cites W2142595184 @default.
- W3119150888 cites W2146332813 @default.
- W3119150888 cites W2147917253 @default.
- W3119150888 cites W2154253928 @default.
- W3119150888 cites W2154319440 @default.
- W3119150888 cites W2156012420 @default.
- W3119150888 cites W2158323088 @default.
- W3119150888 cites W2161605421 @default.
- W3119150888 cites W2212440680 @default.
- W3119150888 cites W2323434174 @default.
- W3119150888 cites W2532797789 @default.
- W3119150888 cites W2554489021 @default.
- W3119150888 cites W2611479621 @default.
- W3119150888 cites W2761995952 @default.
- W3119150888 cites W2895395073 @default.
- W3119150888 cites W2902028108 @default.
- W3119150888 cites W2963426504 @default.
- W3119150888 cites W2982650029 @default.
- W3119150888 cites W2991513044 @default.
- W3119150888 cites W3023486351 @default.
- W3119150888 cites W3102735881 @default.
- W3119150888 cites W4246043393 @default.
- W3119150888 cites W4255420656 @default.
- W3119150888 cites W585413800 @default.
- W3119150888 doi "https://doi.org/10.1101/2021.01.06.425617" @default.
- W3119150888 hasPublicationYear "2021" @default.
- W3119150888 type Work @default.
- W3119150888 sameAs 3119150888 @default.
- W3119150888 citedByCount "0" @default.
- W3119150888 crossrefType "posted-content" @default.
- W3119150888 hasAuthorship W3119150888A5009994990 @default.
- W3119150888 hasAuthorship W3119150888A5087430767 @default.
- W3119150888 hasBestOaLocation W31191508881 @default.
- W3119150888 hasConcept C121332964 @default.
- W3119150888 hasConcept C121864883 @default.
- W3119150888 hasConcept C13662910 @default.
- W3119150888 hasConcept C154945302 @default.
- W3119150888 hasConcept C186060115 @default.
- W3119150888 hasConcept C27438332 @default.
- W3119150888 hasConcept C2775981520 @default.
- W3119150888 hasConcept C2777577648 @default.
- W3119150888 hasConcept C41008148 @default.
- W3119150888 hasConcept C59593255 @default.
- W3119150888 hasConcept C62520636 @default.
- W3119150888 hasConcept C85725439 @default.
- W3119150888 hasConcept C86803240 @default.
- W3119150888 hasConceptScore W3119150888C121332964 @default.
- W3119150888 hasConceptScore W3119150888C121864883 @default.
- W3119150888 hasConceptScore W3119150888C13662910 @default.
- W3119150888 hasConceptScore W3119150888C154945302 @default.
- W3119150888 hasConceptScore W3119150888C186060115 @default.
- W3119150888 hasConceptScore W3119150888C27438332 @default.
- W3119150888 hasConceptScore W3119150888C2775981520 @default.
- W3119150888 hasConceptScore W3119150888C2777577648 @default.
- W3119150888 hasConceptScore W3119150888C41008148 @default.
- W3119150888 hasConceptScore W3119150888C59593255 @default.