The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics
Abstract
The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.
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“For trans-proline residues, the differences between the Cβ and Cγ chemical shifts are close to 4.5 p.p.m., whereas corresponding values for cis-proline residues are near 9.6 p.p.m. [53].”
From Differential conformational dynamics in the closely homologous FK506-binding domains of FKBP51 and FKBP52 (2014) · cites this paper as [53]
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
NMR of Proteins and Nucleic Acids
(2006) · Royal Society of Chemistry eBooks · doi:10.1039/9781847555236-00336 · Cited by 5,874
X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
Brünger, A. T. (1992) · Medical Entomology and Zoology · Cited by 3,424
Conformation of Polypeptides and Proteins
Ramachandran, G. N., & Sasisekharan, V. (1968) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60402-7 · Cited by 2,953
Torsion angle dynamics for NMR structure calculation with the new program Dyana
Güntert, P., Mumenthaler, C., & Kurt Wüthrich, A. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1284 · Cited by 2,781
Herrmann, T., Güntert, P., & Wüthrich, K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00241-3 · Cited by 1,472
Bronshtein, I. N., & Semendjaev, K. A. (1966) · CERN Document Server (European Organization for Nuclear Research) · Cited by 1,467
Nilges, M., Macías, M. J., O’Donoghue, S. I., & Oschkinat, H. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1044 · Cited by 429
A relational database for sequence-specific protein NMR data
Seavey, B. R., Farr, E. A., Westler, W. M., & Markley, J. L. (1991) · Journal of Biomolecular NMR · doi:10.1007/bf01875516 · Cited by 353
Automated Assignment of Ambiguous Nuclear Overhauser Effects with ARIA
Linge, J. P., O’Donoghue, S. I., & Nilges, M. (2001) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(01)39310-2 · Cited by 349
Non-proline Cis peptide bonds in proteins
Jabs, A., Weiss, M. S., & Hilgenfeld, R. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2459 · Cited by 319
Carbon-13 magnetic resonance spectroscopy. Spectrum of proline in oligopeptides
Dorman, D. E., & BOVEY, F. A. (1973) · The Journal of Organic Chemistry · doi:10.1021/jo00953a021 · Cited by 281
Weiss, M. S., Jabs, A., & Hilgenfeld, R. (1998) · Nature Structural & Molecular Biology · doi:10.1038/1368 · Cited by 188
Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides
Milner‐White, E. J., Bell, L. H., & Maccallum, P. H. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90859-i · Cited by 148
HAASNOOT, C. A. G., de Leeuw, F. A. A. M., de Leeuw, H. P. M., & Altona, C. (1981) · Biopolymers · doi:10.1002/bip.1981.360200610 · Cited by 133
The interpretation of carbon-13 spin-lattice relaxation resulting from ring puckering in proline
London, R. E. (1978) · Journal of the American Chemical Society · doi:10.1021/ja00477a018 · Cited by 97
Schmidt, J. M., Brüschweiler, R., Ernst, R. R., Dunbrack, R. L., Joseph‐McCarthy, D., & Karplus, M. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00072a030 · Cited by 65
Einfluß der Distanz des Prolincarbonyls vom β- und γ-Kohlenstoff auf die Lage der13C-NMR-Signale
Siemion, I. Z., Wieland, T., & Pook, K. (1975) · Angewandte Chemie · doi:10.1002/ange.19750871911 · Cited by 49
Ab Initio Molecular Orbital Calculations on Low-Energy Conformers ofN-Acetyl-N‘-methylprolineamide
Kang, Y. K. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp960381w · Cited by 38
New features and enhancements in the X-PLOR computer program
Badger, J., Kumar, R. A., Yip, P. F., & Szalma, S. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990401)35:1 · Cited by 32
Torchia, D. A., Sparks, S. W., Young, P. E., & Bax, A. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00203a063 · Cited by 27
GIESSNER‐PRETTRE, C., Cung, M. T., & Marraud, M. (1987) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1987.tb10739.x · Cited by 15
Stanczyk, S. M., Bolton, P. H., Dell’Acqua, M. L., & Gerlt, J. A. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00203a064 · Cited by 13
Research works printed but not linked: 1
- Ramachandran, G. N. and Sasisekharan, V. (1968) Adv. Prot. Chem., 23,283–437.
Cited by
Combined automated NOE assignment and structure calculation with CYANA
Güntert, P., & Buchner, L. (2015) · Journal of Biomolecular NMR · doi:10.1007/s10858-015-9924-9 · Cited by 403
Functional aspects of protein flexibility
Teilum, K., Olsen, J. G., & Kragelund, B. B. (2009) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-009-0014-6 · Cited by 280
Interpreting protein chemical shift data
Wishart, D. S. (2010) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2010.07.004 · Cited by 258
PREDITOR: a web server for predicting protein torsion angle restraints
Berjanskii, M. V., Neal, S., & Wishart, D. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl341 · Cited by 195
Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein
Sarkar, P., Reichman, C., Saleh, T., Birge, R. B., & Kalodimos, C. G. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.01.004 · Cited by 189
Metadata
- Authors
- Schubert, M., Labudde, D., Oschkinat, H., & Schmieder, P.
- Affiliations
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (DE)
- Corresponding author
- Labudde, Dirk
- Venue
- Journal of Biomolecular NMR
- Published
- 2002-10
- Volume
- 24
- Issue
- 2
- Pages
- 149-154
- ISSN
- 0925-2738 (ISSN-L)
- 1573-5001
- OpenAlex
- W2127886370
- Cited by
- 351
- References
- 24
- Citations by year
- 2026: 18 · 2025: 8 · 2024: 15 · 2023: 9 · 2022: 12 · 2021: 28 · 2020: 16 · 2019: 17 · 2018: 21 · 2017: 18 · 2016: 14 · 2015: 15 · 2014: 12 · 2013: 11 · 2012: 13
- FWCI
- 3.36
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Biomolecular NMR (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Molecular spectroscopy and chirality
- Keywords
- cis-trans conformation, 13C NMR chemical shifts, chemical shift differences, proline, conformational prediction, NMR resonance assignment, peptide conformation
- MeSH terms
- Amino Acids, Carbon Isotopes, Hydrogen Bonding, Models, Molecular, Peptides, Proline, Protein Conformation, Proteins, Software, Stereoisomerism, Thermodynamics, Computational Biology, Nuclear Magnetic Resonance, Biomolecular
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