Skip to main content
SpringerLink
Log in

RETRACTED ARTICLE: Overestimated accuracy of circular dichroism in determining protein secondary structure

  • Original Paper
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

This article was retracted on 14 March 2014

Abstract

Circular dichroism (CD) is a spectroscopic technique widely used for estimating protein secondary structures in aqueous solution, but its accuracy has been doubted in recent work. In the present paper, the contents of nine globular proteins with known secondary structures were determined by CD spectroscopy and Fourier transform infrared spectroscopy (FTIR) in aqueous solution. A large deviation was found between the CD spectra and X-ray data, even when the experimental conditions were optimized. The content determined by FTIR was in good agreement with the X-ray crystallography data. Therefore, CD spectra are not recommended for directly calculating the content of a protein’s secondary structure.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Adler AJ, Greenfield NJ, Fasman GD (1973) Circular dichroism and optical rotatory dispersion of proteins and polypeptides. Methods Enzymol 27:675–735

    Article  CAS  PubMed  Google Scholar 

  • Anderson DG, Hammes GG, Walz FG (1968) Binding of phosphate ligands to ribonuclease A. Biochemistry 7:1637–1645

    Article  CAS  PubMed  Google Scholar 

  • Andrade MA, Chacon P, Merelo JJ, Moran F (1993) Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng 6:383–390

    Article  CAS  PubMed  Google Scholar 

  • Arrondo JLR, Goñi FM (1999) Structure and dynamics of membrane proteins as studied by infrared spectroscopy. Prog Biophys Mol Biol 72:367–405

    Article  CAS  PubMed  Google Scholar 

  • Barth A (2007) Infrared spectroscopy of proteins. Biochim Biophy Acta-Bioenergetics 1767:1073–1101

    Article  CAS  Google Scholar 

  • Byler DM, Susi H (1986) Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25:469–487

    Article  CAS  PubMed  Google Scholar 

  • Chou PY, Fasman GD (1974) Prediction of protein conformation. Biochemistry 13:222–245

    Article  CAS  PubMed  Google Scholar 

  • Chou PY, Fasman GD (1978) Empirical predictions of protein conformation. Annu Rev Biochem 47:251–276

    Article  CAS  PubMed  Google Scholar 

  • Cowieson NP, Miles AJ, Robin G, Forwood JK, Kobe B, Martin JL, Wallace BA (2008) Evaluating protein: protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins 70:1142–1146

    Article  CAS  PubMed  Google Scholar 

  • Dong A, Caughey WS (1994) Infrared methods for study of hemoglobin reactions and structures. Methods Enzymol 232:139–175

    Article  CAS  PubMed  Google Scholar 

  • Dong A, Huang P, Caughey WS (1990) Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29:3303–3308

    Article  CAS  PubMed  Google Scholar 

  • Dong A, Malecki JM, Lee L, Carpenter JF, Lee JC (2002) Ligand-induced conformational and structural dynamics changes in Escherichia coli cyclic AMP receptor protein. Biochemistry 41:6660–6667

    Article  CAS  PubMed  Google Scholar 

  • Ganesan A, Moore BD, Kelly SM, Price NC, Rolinski OJ, Birch DJS, Dunkin IR, Halling PJ (2009) Optical spectroscopic methods for probing the conformational stability of immobilised enzymes. ChemPhysChem 10:1492–1499

    Article  CAS  PubMed  Google Scholar 

  • Gao Z, Li F, Wu G, Zhu Y, Yu T, Yu S (2012) Roles of hinge region, loops 3 and 4 in the activation of Escherichia coli cyclic AMP receptor protein. Int J Biol Macromol 50:1–6

    Article  PubMed  Google Scholar 

  • Garnier C, Lafitte D, Tsvetkov PO, Barbier P, Leclerc-Devin J, Millot JM, Briand C, Makarov AA, Catelli MG, Peyrot V (2002) Binding of ATP to heat shock protein 90: evidence for an ATP-binding site in the C-terminal domain. J Biol Chem 277:12208–12214

    Article  CAS  PubMed  Google Scholar 

  • Goormaghtigh E, Raussens V, Ruysschaert JM (1999) Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim Biophys Acta 1422:105–185

    Article  CAS  PubMed  Google Scholar 

  • Goormaghtigh E, Ruysschaert JM, Raussens V (2006) Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys J 90:2946–2957

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gottarelli G, Lena S, Masiero S, Pieraccini S, Spada GP (2008) The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: an overview. Chirality 20:471–485

    Article  CAS  PubMed  Google Scholar 

  • Greenfield NJ (1996) Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal Biochem 235:1–10

    Article  CAS  PubMed  Google Scholar 

  • Greenfield N, Fasman GD (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8:4108–4116

    Article  CAS  PubMed  Google Scholar 

  • Holzwarth G, Doty P (1965) The ultraviolet circular dichroism of polypeptides1. J Am Chem Soc 87:218–228

    Article  CAS  PubMed  Google Scholar 

  • Janes RW (2005) Bioinformatics analyses of circular dichroism protein reference databases. Bioinformatics 21:4230–4238

    Article  CAS  PubMed  Google Scholar 

  • Johnson WC Jr (1985) Circular dichroism and its empirical application to biopolymers. Methods Biochem Anal 31:61–163

    Article  CAS  PubMed  Google Scholar 

  • Johnson WC Jr (1990) Protein secondary structure and circular dichroism: a practical guide. Proteins 7:205–214

    Article  CAS  PubMed  Google Scholar 

  • Jung C (2000) Insight into protein structure and protein–ligand recognition by Fourier transform infrared spectroscopy. J Mol Recognit 13:325–351

    Article  CAS  PubMed  Google Scholar 

  • Kalnin NN, Baikalov IA, Venyaminov S (1990) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure. Biopolymers 30:1273–1280

    Article  CAS  PubMed  Google Scholar 

  • Kauppinen JK, Moffatt DJ, Mantsch HH, Cameron DG (1981) Fourier self-deconvolution: a method for resolving intrinsically overlapped bands. Appl Spectrosc 35:271–276

    Article  CAS  Google Scholar 

  • Kelly SM, Price NC (2000) The use of circular dichroism in the investigation of protein structure and function. Curr Protein Pept Sci 1:349–384

    Article  CAS  PubMed  Google Scholar 

  • Kelly SM, Jess TJ, Price NC (2005) How to study proteins by circular dichroism. Biochim Biophys Acta 1751:119–139

    Article  CAS  PubMed  Google Scholar 

  • Kong J, Yu S (2007) Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Bioch Bioph Sin 39:549–559

    Article  CAS  Google Scholar 

  • Lee DC, Haris PI, Chapman D, Mitchell RC (1990) Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry 29:9185–9193

    Article  CAS  PubMed  Google Scholar 

  • Levitt M, Greer J (1977) Automatic identification of secondary structure in globular proteins. J Mol Biol 114:181–239

    Article  CAS  PubMed  Google Scholar 

  • Li F, Yu T, Zhao Y, Yu S (2012) Probing the catalytic allosteric mechanism of rabbit muscle pyruvate kinase by tryptophan fluorescence quenching. Eur Biophys J 41:607–614

    Article  PubMed  Google Scholar 

  • Liu KZ, Shaw RA, Man A, Dembinski TC, Mantsch HH (2002) Reagent-free, simultaneous determination of serum cholesterol in HDL and LDL by infrared spectroscopy. Clin Chem 48:499–506

    CAS  PubMed  Google Scholar 

  • Matsuo K, Yonehara R, Gekko K (2005) Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy. J Biochem 138:79–88

    Article  CAS  PubMed  Google Scholar 

  • Maune JF, Klee CB, Beckingham K (1992) Ca2+ binding and conformational change in two series of point mutations to the individual Ca(2+)-binding sites of calmodulin. J Biol Chem 267:5286–5295

    CAS  PubMed  Google Scholar 

  • Navea S, Tauler R, Goormaghtigh E, de Juan A (2006) Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements. Proteins 63:527–541

    Article  CAS  PubMed  Google Scholar 

  • Oberfelder RW, Lee LL, Lee JC (1984) Thermodynamic linkages in rabbit muscle pyruvate kinase: kinetic, equilibrium, and structural studies. Biochemistry 23:3813–3821

    Article  CAS  PubMed  Google Scholar 

  • Pribić R, van Stokkum IH, Chapman D, Haris PI, Bloemendal M (1993) Protein secondary structure from Fourier transform infrared and/or circular dichroism spectra. Anal Biochem 214:366–378

    Article  PubMed  Google Scholar 

  • Provencher SW, Glockner J (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20:33–37

    Article  CAS  PubMed  Google Scholar 

  • Qiu R, Wang F, Liu M, Yang Z, Wu T, Ji C (2011) Crystallization and preliminary X-ray analysis of the yeast tRNA-thiouridine modification protein 1 (Tum1p). Acta Crystallogr Sect F Struct Biol Cryst Commun 67:953–955

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sarver RW Jr, Krueger WC (1991) Protein secondary structure from Fourier transform infrared spectroscopy: a data base analysis. Anal Biochem 194:89–100

    Article  CAS  PubMed  Google Scholar 

  • Sreerama N, Woody RW (1993) A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal Biochem 209:32–44

    Article  CAS  PubMed  Google Scholar 

  • Sreerama N, Woody RW (2000) Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 287:252–260

    Article  CAS  PubMed  Google Scholar 

  • Susi H, Byler DM (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol 130:290–311

    Article  CAS  PubMed  Google Scholar 

  • van Stokkum IH, Spoelder HJ, Bloemendal M, van Grondelle R, Groen FC (1990) Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal Biochem 191:110–118

    Article  PubMed  Google Scholar 

  • Venyaminov SY, Baikalov IA, Shen ZM, Wu CSC, Yang JT (1993) Circular dichroic analysis of denatured proteins: inclusion of denatured proteins in the reference set. Anal Biochem 214:17–24

    Article  CAS  PubMed  Google Scholar 

  • Whitmore L, Wallace BA (2008) Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers 89:392–400

    Article  CAS  PubMed  Google Scholar 

  • Wu G, Gao Z, Dong A, Yu S (2012) Calcium-induced changes in calmodulin structural dynamics and thermodynamics. Int J Biol Macromol 50:1011–1017

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This project was supported in part by grants from the National Natural Science Foundation of China (No. 21275032 and 30970631) and Shanghai Leading Academic Discipline Project (No. B109).

Author information

Authors and Affiliations

  1. Department of Chemistry, Fudan University, Shanghai, 200433, China

    Kailei Lin, Huayan Yang, Zhengya Gao, Feng Li & Shaoning Yu

Authors
  1. Kailei Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huayan Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhengya Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Feng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shaoning Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shaoning Yu.

Additional information

Kailei Lin and Huayan Yang are equally contributed to this work.

After publication of this article, concerns were raised regarding accuracy and interpretation of the presented Circular Dichroism data. To investigate these claims, the article was checked again by two additional referees, and was also discussed by members of the European Circular Dichroism Society. The investigation revealed that the Circular Dichroism aspects of the article are invalid, because the measured protein Circular Dichroism spectra are highly inaccurate, and contradict numerous published studies. Hence, the conclusions of the authors regarding the unreliability of using Circular Dichroism for protein secondary structure determination are unjustified and misleading. When confronted with these findings, the authors were unable to dispel the doubts in their experimental methods and refused to withdraw the article themselves. It could also not be clarified, why the Circular Dichroism spectra presented in this paper have anomalously low amplitudes. As a result of these findings and the subsequent discussions, the Managing Editor of the European Biophysics Journal, Anthony Watts, has now retracted this article.

About this article

Cite this article

Lin, K., Yang, H., Gao, Z. et al. RETRACTED ARTICLE: Overestimated accuracy of circular dichroism in determining protein secondary structure. Eur Biophys J 42, 455–461 (2013). https://doi.org/10.1007/s00249-013-0896-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-013-0896-y

Keywords

Search

Navigation