FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2063820211> ?p ?o ?g. }

• W2063820211 endingPage "958" @default.
• W2063820211 startingPage "945" @default.
• W2063820211 abstract "The conformational flexibility of the tetrapyrrolic phytochromobilin (PPhiB) chromophore of the bacteriophytochrome Deinococcus radiodurans (DrCBD) in the Pr state has been investigated by molecular dynamics simulations. Because these simulations require accurate force field parameters for the prosthetic group, in the present work we developed new empirical force field parameters for the PPhiB molecule that are compatible with the CHARMM22 force field for proteins. For this reason, the new force field parameters for the nonbonded (partial atomic charges) and bonded (bonds, angles, dihedrals, improper) energy terms were derived by reproducing ab initio target data following the methodology used in the development of the CHARMM22 force field. This new set of parameters was employed to analyze structural and dynamical features of PPhiB inside DrCBD. The 45 ns all-atom molecular dynamics (MD) simulation reveals the existence of two stable conformational states of the chromophore characterized by distinct torsional angles around the C-C bond at the methine bridge connecting rings A and B of the tetrapyrrole. This result supports experimental observations derived from NMR and resonance Raman spectroscopy. Furthermore, statistical analysis of H-bonding events allowed us to identify (a) important H-bonds between the propionic side chains of the chromophore and the apoprotein which may be relevant for the signal transduction step during the photoinduced cycle and (b) a network of eight water molecules which remain in the vicinity of the chromophore during the entire 45 ns production run." @default.
• W2063820211 created "2016-06-24" @default.
• W2063820211 creator A5012078696 @default.
• W2063820211 creator A5013367017 @default.
• W2063820211 creator A5063958238 @default.
• W2063820211 date "2009-01-05" @default.
• W2063820211 modified "2023-09-30" @default.
• W2063820211 title "Molecular Dynamics Simulations of the Chromophore Binding Site of <i>Deinococcus radiodurans</i> Bacteriophytochrome Using New Force Field Parameters for the Phytochromobilin Chromophore" @default.
• W2063820211 cites W1967688689 @default.
• W2063820211 cites W1967737979 @default.
• W2063820211 cites W1972758026 @default.
• W2063820211 cites W1973501174 @default.
• W2063820211 cites W1976499671 @default.
• W2063820211 cites W1981589073 @default.
• W2063820211 cites W1982356449 @default.
• W2063820211 cites W1984073014 @default.
• W2063820211 cites W1987935024 @default.
• W2063820211 cites W2003674624 @default.
• W2063820211 cites W2015844604 @default.
• W2063820211 cites W2020572633 @default.
• W2063820211 cites W2027408247 @default.
• W2063820211 cites W2029667189 @default.
• W2063820211 cites W2036999324 @default.
• W2063820211 cites W2038758364 @default.
• W2063820211 cites W2067174909 @default.
• W2063820211 cites W2069893600 @default.
• W2063820211 cites W2089444699 @default.
• W2063820211 cites W2102376488 @default.
• W2063820211 cites W2103636724 @default.
• W2063820211 cites W2130662176 @default.
• W2063820211 cites W2150981663 @default.
• W2063820211 cites W2151334055 @default.
• W2063820211 cites W2162166182 @default.
• W2063820211 cites W2164389392 @default.
• W2063820211 cites W606051889 @default.
• W2063820211 doi "https://doi.org/10.1021/jp8047532" @default.
• W2063820211 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19123828" @default.
• W2063820211 hasPublicationYear "2009" @default.
• W2063820211 type Work @default.
• W2063820211 sameAs 2063820211 @default.
• W2063820211 citedByCount "25" @default.
• W2063820211 countsByYear W20638202112012 @default.
• W2063820211 countsByYear W20638202112013 @default.
• W2063820211 countsByYear W20638202112015 @default.
• W2063820211 countsByYear W20638202112016 @default.
• W2063820211 countsByYear W20638202112017 @default.
• W2063820211 countsByYear W20638202112018 @default.
• W2063820211 countsByYear W20638202112019 @default.
• W2063820211 countsByYear W20638202112020 @default.
• W2063820211 countsByYear W20638202112021 @default.
• W2063820211 countsByYear W20638202112022 @default.
• W2063820211 crossrefType "journal-article" @default.
• W2063820211 hasAuthorship W2063820211A5012078696 @default.
• W2063820211 hasAuthorship W2063820211A5013367017 @default.
• W2063820211 hasAuthorship W2063820211A5063958238 @default.
• W2063820211 hasConcept C104317684 @default.
• W2063820211 hasConcept C10803110 @default.
• W2063820211 hasConcept C121332964 @default.
• W2063820211 hasConcept C147597530 @default.
• W2063820211 hasConcept C159467904 @default.
• W2063820211 hasConcept C178790620 @default.
• W2063820211 hasConcept C185592680 @default.
• W2063820211 hasConcept C192468462 @default.
• W2063820211 hasConcept C2776519032 @default.
• W2063820211 hasConcept C32909587 @default.
• W2063820211 hasConcept C55493867 @default.
• W2063820211 hasConcept C59593255 @default.
• W2063820211 hasConcept C62520636 @default.
• W2063820211 hasConcept C75473681 @default.
• W2063820211 hasConceptScore W2063820211C104317684 @default.
• W2063820211 hasConceptScore W2063820211C10803110 @default.
• W2063820211 hasConceptScore W2063820211C121332964 @default.
• W2063820211 hasConceptScore W2063820211C147597530 @default.
• W2063820211 hasConceptScore W2063820211C159467904 @default.
• W2063820211 hasConceptScore W2063820211C178790620 @default.
• W2063820211 hasConceptScore W2063820211C185592680 @default.
• W2063820211 hasConceptScore W2063820211C192468462 @default.
• W2063820211 hasConceptScore W2063820211C2776519032 @default.
• W2063820211 hasConceptScore W2063820211C32909587 @default.
• W2063820211 hasConceptScore W2063820211C55493867 @default.
• W2063820211 hasConceptScore W2063820211C59593255 @default.
• W2063820211 hasConceptScore W2063820211C62520636 @default.
• W2063820211 hasConceptScore W2063820211C75473681 @default.
• W2063820211 hasIssue "4" @default.
• W2063820211 hasLocation W20638202111 @default.
• W2063820211 hasLocation W20638202112 @default.
• W2063820211 hasOpenAccess W2063820211 @default.
• W2063820211 hasPrimaryLocation W20638202111 @default.
• W2063820211 hasRelatedWork W1971265428 @default.
• W2063820211 hasRelatedWork W2004981350 @default.
• W2063820211 hasRelatedWork W2042638827 @default.
• W2063820211 hasRelatedWork W2089497916 @default.
• W2063820211 hasRelatedWork W2161972019 @default.
• W2063820211 hasRelatedWork W2225974560 @default.
• W2063820211 hasRelatedWork W2313914827 @default.
• W2063820211 hasRelatedWork W2501841583 @default.
• W2063820211 hasRelatedWork W2754244034 @default.
• W2063820211 hasRelatedWork W4382010728 @default.

• next