Catalogo Articoli (Spogli Riviste)
OPAC HELP
Titolo: Optimizing the hydrogenbond network in PoissonBoltzmann equationbased pK(a) calculations
Autore: Nielsen, JE; Vriend, G;
 Indirizzi:
 European Mol Biol Lab, D69117 Heidelberg, Germany European Mol Biol Lab Heidelberg Germany D69117 117 Heidelberg, Germany
 Titolo Testata:
 PROTEINSSTRUCTURE FUNCTION AND GENETICS
fascicolo: 4,
volume: 43,
anno: 2001,
pagine: 403  412
 SICI:
 08873585(20010601)43:4<403:OTHNIP>2.0.ZU;2Y
 Fonte:
 ISI
 Lingua:
 ENG
 Soggetto:
 CONTINUUM ELECTROSTATIC MODEL; A BETALACTAMASES; CONFORMATIONAL FLEXIBILITY; PROTEINSTRUCTURE; IONIZABLE GROUPS; SELFCONSISTENT; PH; SITE; TITRATION; RESIDUES;
 Keywords:
 pK(a) calculations; hydrogenbond network optimization; electrostatics; PoissonBoltzmann equation; protein structure optimization; crystal artifacts;
 Tipo documento:
 Article
 Natura:
 Periodico
 Settore Disciplinare:
 Life Sciences
 Citazioni:
 51
 Recensione:
 Indirizzi per estratti:
 Indirizzo: Nielsen, JE European Mol Biol Lab, Meyerhofstr 1, D69117 Heidelberg, Germany European Mol Biol Lab Meyerhofstr 1 Heidelberg Germany D69117



 Citazione:
 J.E. Nielsen e G. Vriend, "Optimizing the hydrogenbond network in PoissonBoltzmann equationbased pK(a) calculations", PROTEINS, 43(4), 2001, pp. 403412
Abstract
pK(a) calculation methods that are based on finite difference solutions tothe PoissonBoltzmann equation (FDPB) require that energy calculations be performed for a large number of different protonation states of the protein. Normally, the differences between these protonation states are modeled bychanging the charges on a few atoms, sometimes the differences are modeledby adding or removing hydrogens, and in a few cases the positions of thesehydrogens are optimized locally. We present an FDPBbased pK(a) calculation method in which the hydrogenbond network is globally optimized for everysingle protonation state used. This global optimization gives a significant improvement in the accuracy of calculated pK(a) values, especially for buried residues. It is also shown that large errors in calculated pK(a) values are often due to structural artifacts induced by crystal packing. Optimization of the force fields and parameters used in pK(a) calculations should therefore be performed with Xray structures that are corrected for crystalartifacts. Proteins 2001;43:403412. (C) 2001 WileyLiss, Inc.
ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 24/01/20 alle ore 12:22:54