Assessing the chemical accuracy of protein structures via peptide acidity.
Assessing the chemical accuracy of protein structures via peptide acidity.
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DOI：
10.1016/j.bpc.2012.10.005
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发表时间：
2013-01
影响因子：
3.8
通讯作者：
LeMaster, David M.
中科院分区：
文献类型：
--
作者：
Anderson, Janet S.;Hernandez, Griselda;LeMaster, David M.
Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses.
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影响因子：
2.7
作者：
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通讯作者：
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影响因子：
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作者：
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作者：
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通讯作者：
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DOI：
10.1073/pnas.0404050101
发表时间：
2004-07-27
影响因子：
11.1
作者：
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通讯作者：
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