Abstract
Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures.Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al.(2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 143-153 |
| Number of pages | 11 |
| Journal | Journal of biomolecular NMR. |
| Volume | 30 |
| Issue number | 2 |
| State | Published - Oct 2004 |
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ASJC Scopus subject areas
- Spectroscopy
- Biochemistry, Genetics and Molecular Biology(all)
- Biochemistry
Cite this
An evaluation of chemical shift index-based secondary structure determination in proteins : influence of random coil chemical shifts. / Mielke, S. P.; Krishnan, Viswanathan V.
In: Journal of biomolecular NMR., Vol. 30, No. 2, 10.2004, p. 143-153.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - An evaluation of chemical shift index-based secondary structure determination in proteins
T2 - influence of random coil chemical shifts.
AU - Mielke, S. P.
AU - Krishnan, Viswanathan V
PY - 2004/10
Y1 - 2004/10
N2 - Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures.Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al.(2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.
AB - Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures.Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al.(2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.
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UR - http://www.scopus.com/inward/citedby.url?scp=32944464105&partnerID=8YFLogxK
M3 - Article
C2 - 15666561
AN - SCOPUS:32944464105
VL - 30
SP - 143
EP - 153
JO - Journal of Biomolecular NMR
JF - Journal of Biomolecular NMR
SN - 0925-2738
IS - 2
ER -