Abstract:
:We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field (employed in standard refinement to supplement experimental data) for a site of interest by quantum chemical calculations. This way, we obtain an accurate description of the site, even if a molecular-mechanics force field does not exist for this site, or if there is little experimental information about the site. Moreover, the site may change its bonding during the refinement, which often is the case for metal sites. The second method is to extract a molecular mechanics potential for the site of interest from a quantum chemical geometry optimisation and frequency calculation. We apply both methods to the two Ca2+ sites in the epidermal growth factor-like domains 3 and 4 in the vitamin K-dependent protein S and compare them to various methods to treat these sites in standard refinement. We show that both methods perform well and have their advantages and disadvantages. We also show that the glutamate Ca2+ ligand is unlikely to bind in a bidentate mode, in contrast to the crystal structure of an EGF domain of factor IX.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Hsiao YW,Drakenberg T,Ryde Udoi
10.1007/s10858-004-6729-7subject
Has Abstractpub_date
2005-02-01 00:00:00pages
97-114issue
2eissn
0925-2738issn
1573-5001journal_volume
31pub_type
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-013-9754-6
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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更新日期:2007-08-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF02192848
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1024768328860
更新日期:2003-09-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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更新日期:2019-11-01 00:00:00
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journal_title:Journal of biomolecular NMR
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journal_title:Journal of biomolecular NMR
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