Literature DB >> 12495031

A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics.

Mario Schubert1, Dirk Labudde, Hartmut Oschkinat, Peter Schmieder.   

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.

Entities:  

Mesh：

Substances：

Year:  2002        PMID： 12495031     DOI： 10.1023/a:1020997118364

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  13 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  New features and enhancements in the X-PLOR computer program.

Authors:  J Badger; R A Kumar; P Yip; S Szalma
Journal:  Proteins       Date:  1999-04-01

3.  Automated assignment of ambiguous nuclear overhauser effects with ARIA.

Authors:  J P Linge; S I O'Donoghue; M Nilges
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

4.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

5.  Peptide bonds revisited.

Authors:  M S Weiss; A Jabs; R Hilgenfeld
Journal:  Nat Struct Biol       Date:  1998-08

6.  Non-proline cis peptide bonds in proteins.

Authors:  A Jabs; M S Weiss; R Hilgenfeld
Journal:  J Mol Biol       Date:  1999-02-12       Impact factor: 5.469

7.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

8.  Torsion angle dynamics for NMR structure calculation with the new program DYANA.

Authors:  P Güntert; C Mumenthaler; K Wüthrich
Journal:  J Mol Biol       Date:  1997-10-17       Impact factor: 5.469

9.  Ab initio quantum mechanical calculations of the variation of the 1H and 13C nuclear magnetic shielding constants in proline as a function of the angle psi.

Authors:  C Giessner-Prettre; M T Cung; M Marraud
Journal:  Eur J Biochem       Date:  1987-02-16

10.  Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations.

Authors:  E J Milner-White; L H Bell; P H Maccallum
Journal:  J Mol Biol       Date:  1992-12-05       Impact factor: 5.469
View more
  116 in total

1.  A procedure to validate and correct the 13C chemical shift calibration of RNA datasets.

Authors:  Thomas Aeschbacher; Mario Schubert; Frédéric H-T Allain
Journal:  J Biomol NMR       Date:  2012-01-18       Impact factor: 2.835

2.  NMR structure note: N-terminal domain of Thermus thermophilus CdnL.

Authors:  Aranzazu Gallego-García; Yasmina Mirassou; Montserrat Elías-Arnanz; S Padmanabhan; M Angeles Jiménez
Journal:  J Biomol NMR       Date:  2012-07-11       Impact factor: 2.835

3.  Solution structure of the zinc finger domain of human RNF144A ubiquitin ligase.

Authors:  Kazuhide Miyamoto; Kaori Migita; Kazuki Saito
Journal:  Protein Sci       Date:  2020-07-13       Impact factor: 6.725

4.  Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR.

Authors:  Dwaipayan Mukhopadhyay; Chitrak Gupta; Theint Theint; Christopher P Jaroniec
Journal:  J Magn Reson       Date:  2018-10-30       Impact factor: 2.229

5.  Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.

Authors:  David Pantoja-Uceda; Blanca López-Méndez; Seizo Koshiba; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama; Peter Güntert
Journal:  Protein Sci       Date:  2004-12-02       Impact factor: 6.725

6.  Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold.

Authors:  Hua Li; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Emi Nunokawa; Yoko Motoda; Atsuo Kobayashi; Takaho Terada; Mikako Shirouzu; Seizo Koshiba; Yi-Jan Lin; Peter Güntert; Harukazu Suzuki; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
Journal:  J Biomol NMR       Date:  2005-08       Impact factor: 2.835

7.  Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes.

Authors:  Anna Scott; David Pantoja-Uceda; Seizo Koshiba; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Sumio Sugano; Shigeyuki Yokoyama; Peter Güntert
Journal:  J Biomol NMR       Date:  2005-04       Impact factor: 2.835

8.  Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2.

Authors:  Hans Wienk; Simona Tomaselli; Cédric Bernard; Roberto Spurio; Delia Picone; Claudio O Gualerzi; Rolf Boelens
Journal:  Protein Sci       Date:  2005-08-04       Impact factor: 6.725

9.  Solution structure of the RNA binding domain in the human muscleblind-like protein 2.

Authors:  Fahu He; Weirong Dang; Chikage Abe; Kengo Tsuda; Makoto Inoue; Satoru Watanabe; Naohiro Kobayashi; Takanori Kigawa; Takayoshi Matsuda; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takushi Harada; Yuri Tomabechi; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Peter Güntert; Yutaka Muto; Shigeyuki Yokoyama
Journal:  Protein Sci       Date:  2009-01       Impact factor: 6.725

10.  p15PAF is an intrinsically disordered protein with nonrandom structural preferences at sites of interaction with other proteins.

Authors:  Alfredo De Biasio; Alain Ibáñez de Opakua; Tiago N Cordeiro; Maider Villate; Nekane Merino; Nathalie Sibille; Moreno Lelli; Tammo Diercks; Pau Bernadó; Francisco J Blanco
Journal:  Biophys J       Date:  2014-02-18       Impact factor: 4.033
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.