Matches in SemOpenAlex for { <https://semopenalex.org/work/W2000787542> ?p ?o ?g. }
- W2000787542 abstract "We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150 000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW91∕6-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal “active site.” To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53kcalmol−1 and eliminates the enormous 115kcalmol−1 energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the “special pair” of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered." @default.
- W2000787542 created "2016-06-24" @default.
- W2000787542 creator A5018647545 @default.
- W2000787542 creator A5044085579 @default.
- W2000787542 creator A5079865740 @default.
- W2000787542 creator A5088911718 @default.
- W2000787542 date "2006-01-09" @default.
- W2000787542 modified "2023-10-17" @default.
- W2000787542 title "Density-functional geometry optimization of the 150 000-atom photosystem-I trimer" @default.
- W2000787542 cites W1965416725 @default.
- W2000787542 cites W1966620930 @default.
- W2000787542 cites W1974871313 @default.
- W2000787542 cites W1980725587 @default.
- W2000787542 cites W1983148800 @default.
- W2000787542 cites W1994565127 @default.
- W2000787542 cites W1997173539 @default.
- W2000787542 cites W2007176314 @default.
- W2000787542 cites W2016322349 @default.
- W2000787542 cites W2023271753 @default.
- W2000787542 cites W2030971064 @default.
- W2000787542 cites W2037808893 @default.
- W2000787542 cites W2042267228 @default.
- W2000787542 cites W2043219059 @default.
- W2000787542 cites W2049079467 @default.
- W2000787542 cites W2058821322 @default.
- W2000787542 cites W2061903313 @default.
- W2000787542 cites W2071255097 @default.
- W2000787542 cites W2072741235 @default.
- W2000787542 cites W2109919880 @default.
- W2000787542 cites W2114788392 @default.
- W2000787542 cites W2115339329 @default.
- W2000787542 cites W2115458478 @default.
- W2000787542 cites W2127336290 @default.
- W2000787542 cites W2130479394 @default.
- W2000787542 cites W2132717858 @default.
- W2000787542 cites W2138629368 @default.
- W2000787542 cites W2141704677 @default.
- W2000787542 cites W2141956573 @default.
- W2000787542 cites W2155358697 @default.
- W2000787542 cites W2155524113 @default.
- W2000787542 cites W2157165549 @default.
- W2000787542 cites W2162789008 @default.
- W2000787542 cites W2169193736 @default.
- W2000787542 cites W2592457075 @default.
- W2000787542 cites W2953003901 @default.
- W2000787542 doi "https://doi.org/10.1063/1.2148956" @default.
- W2000787542 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16422577" @default.
- W2000787542 hasPublicationYear "2006" @default.
- W2000787542 type Work @default.
- W2000787542 sameAs 2000787542 @default.
- W2000787542 citedByCount "62" @default.
- W2000787542 countsByYear W20007875422012 @default.
- W2000787542 countsByYear W20007875422013 @default.
- W2000787542 countsByYear W20007875422014 @default.
- W2000787542 countsByYear W20007875422015 @default.
- W2000787542 countsByYear W20007875422016 @default.
- W2000787542 countsByYear W20007875422017 @default.
- W2000787542 countsByYear W20007875422018 @default.
- W2000787542 countsByYear W20007875422019 @default.
- W2000787542 countsByYear W20007875422020 @default.
- W2000787542 countsByYear W20007875422021 @default.
- W2000787542 countsByYear W20007875422022 @default.
- W2000787542 countsByYear W20007875422023 @default.
- W2000787542 crossrefType "journal-article" @default.
- W2000787542 hasAuthorship W2000787542A5018647545 @default.
- W2000787542 hasAuthorship W2000787542A5044085579 @default.
- W2000787542 hasAuthorship W2000787542A5079865740 @default.
- W2000787542 hasAuthorship W2000787542A5088911718 @default.
- W2000787542 hasConcept C121332964 @default.
- W2000787542 hasConcept C147597530 @default.
- W2000787542 hasConcept C14961307 @default.
- W2000787542 hasConcept C149635348 @default.
- W2000787542 hasConcept C152365726 @default.
- W2000787542 hasConcept C159467904 @default.
- W2000787542 hasConcept C178790620 @default.
- W2000787542 hasConcept C184779094 @default.
- W2000787542 hasConcept C185592680 @default.
- W2000787542 hasConcept C2776165824 @default.
- W2000787542 hasConcept C2776403692 @default.
- W2000787542 hasConcept C2779546866 @default.
- W2000787542 hasConcept C32909587 @default.
- W2000787542 hasConcept C41008148 @default.
- W2000787542 hasConcept C41999313 @default.
- W2000787542 hasConcept C58312451 @default.
- W2000787542 hasConcept C86025842 @default.
- W2000787542 hasConceptScore W2000787542C121332964 @default.
- W2000787542 hasConceptScore W2000787542C147597530 @default.
- W2000787542 hasConceptScore W2000787542C14961307 @default.
- W2000787542 hasConceptScore W2000787542C149635348 @default.
- W2000787542 hasConceptScore W2000787542C152365726 @default.
- W2000787542 hasConceptScore W2000787542C159467904 @default.
- W2000787542 hasConceptScore W2000787542C178790620 @default.
- W2000787542 hasConceptScore W2000787542C184779094 @default.
- W2000787542 hasConceptScore W2000787542C185592680 @default.
- W2000787542 hasConceptScore W2000787542C2776165824 @default.
- W2000787542 hasConceptScore W2000787542C2776403692 @default.
- W2000787542 hasConceptScore W2000787542C2779546866 @default.
- W2000787542 hasConceptScore W2000787542C32909587 @default.
- W2000787542 hasConceptScore W2000787542C41008148 @default.
- W2000787542 hasConceptScore W2000787542C41999313 @default.