Abstract：
:The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed (13)C(alpha) chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree-Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMR-derived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed (13)C(alpha) chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed (13)C(alpha) chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Vila JA,Villegas ME,Baldoni HA,Scheraga HAdoi
10.1007/s10858-007-9162-xsubject
Has Abstractpub_date
2007-07-01 00:00:00pages
221-35issue
3eissn
0925-2738issn
1573-5001journal_volume
38pub_type
杂志文章abstract：:We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T 2' times and a site-specific comparison of T 2' at 93 kHz versus 60 kHz MAS frequency....
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
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
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：10.1023/a:1026776721348
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00200435
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF01877224
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00174609
更新日期：1993-09-01 00:00:00
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journal_title：Journal of biomolecular NMR
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doi：10.1023/a:1012431013082
更新日期：2001-10-01 00:00:00
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doi：10.1007/s10858-011-9583-4
更新日期：2012-01-01 00:00:00
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doi：10.1007/s10858-009-9310-6
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journal_title：Journal of biomolecular NMR
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更新日期：2010-02-01 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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journal_title：Journal of biomolecular NMR
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journal_title：Journal of biomolecular NMR
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更新日期：2009-03-01 00:00:00
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journal_title：Journal of biomolecular NMR
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