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Titolo:
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations
Autore:
Nielsen, JE; Vriend, G;
Indirizzi:
European Mol Biol Lab, D-69117 Heidelberg, Germany European Mol Biol Lab Heidelberg Germany D-69117 117 Heidelberg, Germany
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 4, volume: 43, anno: 2001,
pagine: 403 - 412
SICI:
0887-3585(20010601)43:4<403:OTHNIP>2.0.ZU;2-Y
Fonte:
ISI
Lingua:
ENG
Soggetto:
CONTINUUM ELECTROSTATIC MODEL; A BETA-LACTAMASES; CONFORMATIONAL FLEXIBILITY; PROTEIN-STRUCTURE; IONIZABLE GROUPS; SELF-CONSISTENT; PH; SITE; TITRATION; RESIDUES;
Keywords:
pK(a) calculations; hydrogen-bond network optimization; electrostatics; Poisson-Boltzmann 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, D-69117 Heidelberg, Germany European Mol Biol Lab Meyerhofstr 1 Heidelberg Germany D-69117
Citazione:
J.E. Nielsen e G. Vriend, "Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations", PROTEINS, 43(4), 2001, pp. 403-412

Abstract

pK(a) calculation methods that are based on finite difference solutions tothe Poisson-Boltzmann 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 FDPB-based pK(a) calculation method in which the hydrogen-bond 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 X-ray structures that are corrected for crystalartifacts. Proteins 2001;43:403-412. (C) 2001 Wiley-Liss, Inc.

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Documento generato il 24/01/20 alle ore 12:22:54