Estimating the accuracy of protein structures using residual dipolar couplings

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Estimating the accuracy of protein structures using residual dipolar couplings. / Simon, Katya; Xu, Jun; Kim, Chinpal; Skrynnikov, Nikolai R.

In: Journal of Biomolecular NMR, Vol. 33, No. 2, 10.2005, p. 83-93.

Research output: Contribution to journal › Article › peer-review

Author

Simon, Katya ; Xu, Jun ; Kim, Chinpal ; Skrynnikov, Nikolai R. / Estimating the accuracy of protein structures using residual dipolar couplings. In: Journal of Biomolecular NMR. 2005 ; Vol. 33, No. 2. pp. 83-93.

BibTeX

@article{54b3ad05cd084ed0ae3fba8d26c5ff8d,

title = "Estimating the accuracy of protein structures using residual dipolar couplings",

abstract = "It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable {\~R} values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable {\~R} values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.",

keywords = "NMR, PALES software, PDZ2 domain from human phosphatase hPTP1E, Precisionand accuracy of protein structures, Residual dipolar couplings, X-ray crystallography",

author = "Katya Simon and Jun Xu and Chinpal Kim and Skrynnikov, {Nikolai R.}",

year = "2005",

month = oct,

doi = "10.1007/s10858-005-2601-7",

language = "English",

volume = "33",

pages = "83--93",

journal = "Journal of Biomolecular NMR",

issn = "0925-2738",

publisher = "Springer Nature",

number = "2",

}

RIS

TY - JOUR

T1 - Estimating the accuracy of protein structures using residual dipolar couplings

AU - Simon, Katya

AU - Xu, Jun

AU - Kim, Chinpal

AU - Skrynnikov, Nikolai R.

PY - 2005/10

Y1 - 2005/10

N2 - It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R̃ values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R̃ values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

AB - It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R̃ values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R̃ values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

KW - NMR

KW - PALES software

KW - PDZ2 domain from human phosphatase hPTP1E

KW - Precisionand accuracy of protein structures

KW - Residual dipolar couplings

KW - X-ray crystallography

UR - http://www.scopus.com/inward/record.url?scp=25844509280&partnerID=8YFLogxK

U2 - 10.1007/s10858-005-2601-7

DO - 10.1007/s10858-005-2601-7

M3 - Article

C2 - 16258827

VL - 33

SP - 83

EP - 93

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 2

ER -

ID: 74232612