Abstract:
:Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and the mutant proteins. This approach is found to give reliable results where all the solvent molecules are represented by Langevin dipoles and also when some bound water molecules are represented explicitly. A free energy perturbation method is also found to give reasonable results but at the expense of much more computer time. Finally, an approach that generates mutant structures from the native structure by molecular dynamics simulation and then uses these configurations in PDLD calculations is found to give a reasonable estimate of the effect of the mutation on the corresponding redox potential. The encouraging results obtained here and in a preliminary test case of the Phe82----Ser mutation indicates that the present strategies can provide a useful tool for structure-redox and sequence-redox correlation in proteins.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Langen R,Brayer GD,Berghuis AM,McLendon G,Sherman F,Warshel Adoi
10.1016/0022-2836(92)90546-vkeywords:
subject
Has Abstractpub_date
1992-04-05 00:00:00pages
589-600issue
3eissn
0022-2836issn
1089-8638pii
0022-2836(92)90546-Vjournal_volume
224pub_type
杂志文章abstract::Sparsomycin, a broad-spectrum antibiotic, acts at the peptidyl transferase centre of the ribosome, stabilizing peptidyl-tRNA binding at the P-site and weakening ternary complex binding. A sparsomycin-resistant mutant was isolated for the archaeon Halobacterium salinarium and shown to lack a post-transcriptional modifi...
journal_title:Journal of molecular biology
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abstract::Complexes of the type II restriction endonuclease EcoRV with a variety of short, selfcomplementary deoxyoligonucleotides have been crystallized. The best crystals diffract to about 2.7 A resolution and consist of 1:1 complexes between endonuclease dimers and duplexes of the cognate decamer GGGATATCCC containing the he...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1991-01-20 00:00:00
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更新日期:2001-11-16 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1996-01-26 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(84)90256-0
更新日期:1984-12-25 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2000.4016
更新日期:2000-08-25 00:00:00
abstract::Transcription regulation relies in the molecular interplay between the RNA polymerase (RNAP) and regulatory factors. Phage phi29 promoters A2c, A2b and A3 are coordinately regulated by the transcriptional regulator protein p4 and the histone-like protein p6. This study shows that protein p4 binds simultaneously to fou...
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journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1999-06-18 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1988-06-05 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
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