Literature DB >> 19332020

Circular dichroism spectroscopy has intrinsic limitations for protein secondary structure analysis.

Sergei Khrapunov1.   

Abstract

Secondary structure content (SSC) cannot be calculated accurately from circular dichroism (CD) spectra for the majority of proteins whose three-dimensional structures have been solved. "Reliable" SSC that is significantly different from random SSC can be calculated from CD spectra only for all-alpha proteins and all-beta proteins with canonical beta-strand geometry.

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Year:  2009        PMID： 19332020      PMCID： PMC2696129          DOI： 10.1016/j.ab.2009.03.036

Source DB:  PubMed          Journal:  Anal Biochem        ISSN： 0003-2697            Impact factor:   3.365


  15 in total

1.  Analyses of circular dichroism spectra of membrane proteins.

Authors:  B A Wallace; J G Lees; A J W Orry; A Lobley; Robert W Janes
Journal:  Protein Sci       Date:  2003-04       Impact factor: 6.725

2.  DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.

Authors:  Lee Whitmore; B A Wallace
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

Review 3.  Computation and analysis of protein circular dichroism spectra.

Authors:  Narasimha Sreerama; Robert W Woody
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

4.  Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy.

Authors:  N Sreerama; S Y Venyaminov; R W Woody
Journal:  Protein Sci       Date:  1999-02       Impact factor: 6.725

5.  Bioinformatics analyses of circular dichroism protein reference databases.

Authors:  Robert W Janes
Journal:  Bioinformatics       Date:  2005-09-27       Impact factor: 6.937

6.  Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy.

Authors:  Koichi Matsuo; Ryuta Yonehara; Kunihiko Gekko
Journal:  J Biochem       Date:  2005-07       Impact factor: 3.387

7.  Solution structure and refolding of the Mycobacterium tuberculosis pentapeptide repeat protein MfpA.

Authors:  Sergei Khrapunov; Huiyong Cheng; Subray Hegde; John Blanchard; Michael Brenowitz
Journal:  J Biol Chem       Date:  2008-10-31       Impact factor: 5.157

8.  Structural patterns in globular proteins.

Authors:  M Levitt; C Chothia
Journal:  Nature       Date:  1976-06-17       Impact factor: 49.962

9.  Solvational tuning of the unfolding, aggregation and amyloidogenesis of insulin.

Authors:  Stefan Grudzielanek; Ralf Jansen; Roland Winter
Journal:  J Mol Biol       Date:  2005-08-26       Impact factor: 5.469

10.  Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.

Authors:  N Sreerama; R W Woody
Journal:  Anal Biochem       Date:  2000-12-15       Impact factor: 3.365
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  13 in total

1.  Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy.

Authors:  András Micsonai; Frank Wien; Linda Kernya; Young-Ho Lee; Yuji Goto; Matthieu Réfrégiers; József Kardos
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-02       Impact factor: 11.205

2.  Design of bioactive peptides derived from CART sequence isolated from the toadfish Thalassophryne nattereri.

Authors:  Katia Conceição; Gabrielle L de Cena; Verônica A da Silva; Xisto Antonio de Oliveira Neto; Vitor Martins de Andrade; Dayane Batista Tada; Michael Richardson; Sonia A de Andrade; Susana A Dias; Miguel A R B Castanho; Mônica Lopes-Ferreira
Journal:  3 Biotech       Date:  2020-03-06       Impact factor: 2.406

3.  High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations.

Authors:  L Michel Espinoza-Fonseca; Ameeta Kelekar
Journal:  Mol Biosyst       Date:  2015-07

4.  Xenobiotic-metabolizing enzymes in Bacillus anthracis: molecular and functional analysis of a truncated arylamine N-acetyltransferase isozyme.

Authors:  Xavier Kubiak; Romain Duval; Benjamin Pluvinage; Alain F Chaffotte; Jean-Marie Dupret; Fernando Rodrigues-Lima
Journal:  Br J Pharmacol       Date:  2016-11-12       Impact factor: 8.739

5.  Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance.

Authors:  Sergei Khrapunov; Michael Brenowitz
Journal:  Biophys Chem       Date:  2011-05-05       Impact factor: 2.352

6.  Binding of the inhibitor protein IF(1) to bovine F(1)-ATPase.

Authors:  John V Bason; Michael J Runswick; Ian M Fearnley; John E Walker
Journal:  J Mol Biol       Date:  2010-12-28       Impact factor: 5.469

7.  BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy.

Authors:  András Micsonai; Éva Moussong; Frank Wien; Eszter Boros; Henrietta Vadászi; Nikoletta Murvai; Young-Ho Lee; Tamás Molnár; Matthieu Réfrégiers; Yuji Goto; Ágnes Tantos; József Kardos
Journal:  Nucleic Acids Res       Date:  2022-05-11       Impact factor: 19.160

Review 8.  AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species.

Authors:  Francesco Simone Ruggeri; Johnny Habchi; Andrea Cerreta; Giovanni Dietler
Journal:  Curr Pharm Des       Date:  2016       Impact factor: 3.116

9.  BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

Authors:  András Micsonai; Frank Wien; Éva Bulyáki; Judit Kun; Éva Moussong; Young-Ho Lee; Yuji Goto; Matthieu Réfrégiers; József Kardos
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

10.  Elucidating the Binding Mechanism of a Novel Silica-Binding Peptide.

Authors:  Rachit Bansal; Zehra Elgundi; Andrew Care; Sophia C Goodchild; Megan S Lord; Alison Rodger; Anwar Sunna
Journal:  Biomolecules       Date:  2019-12-18
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