Abstract
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Notes
The bold numbers represent the value used and fixed for each parameter during the variation of the other data collection parameters.
References
Anthis NJ, Clore GM (2013) Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm. Protein Sci 22(6):851–858. https://doi.org/10.1002/pro.2253
Bürck J, Wadhwani P, Fanghänel S, Ulrich AS (2016) Oriented circular dichroism: a method to characterize membrane-active peptides in oriented lipid bilayers. Acc Chem Res 49(2):184–192. https://doi.org/10.1021/acs.accounts.5b00346
Compton LA, Johnson WC Jr (1986) Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal Biochem 155(1):155–167. https://doi.org/10.1016/0003-2697(86)90241-1
Di Giuseppe AMA, Russo L, Russo R, Ragucci S, Caso JV, Isernia C (1865) Di Maro A (2017) Molecular characterization of myoglobin from Sciurus vulgaris meridionalis: primary structure, kinetics and spectroscopic studies. Biochim Biophys Acta 5:499–509. https://doi.org/10.1016/j.bbapap.2017.02.011
Drew ED, Janes RW (2019) 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. Nucleic Acids Res 47(W1):W477–W481. https://doi.org/10.1093/nar/gkz456
Drew ED, Janes RW (2020) PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. Nucleic Acids Res 48(W1):W17–W24. https://doi.org/10.1093/nar/gkaa296
Evans SV, Brayer GD (1990) High-resolution study of the three-dimensional structure of horse heart metmyoglobin. J Mol Biol 213(4):885–897. https://doi.org/10.1016/S0022-2836(05)80270-0
Fasman GD (1996) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York
Hales BJ (2011) Magnetic circular dichroism spectroscopy. Methods Mol Biol 766:207–219. https://doi.org/10.1007/978-1-61779-194-9_14
Heumann C, Schomaker M (2016) Introduction to statistics and data analysis. Springer International Publishing, Switzerland
Janes RW, Wallace BA (2009) An introduction to circular dichroism and synchrotron radiation circular dichroism spectroscopy. In: Wallace BA, Janes RW (eds) Modern techniques for circular dichroism and synchrotron radiation circular dichroism, vol 1. IOS Press, Amsterdam, pp 1–18
Jones C, Schiffmann D, Knight A, Windsor S (2004) Val-CID best practice guide: CD spectroscopy for the quality control of biopharmaceuticals. National Physical Laboratory, Teddington
Kelly SM, Price NC (2009) Sample preparation and good practice in circular dichroism spectroscopy. In: Wallace BA, Janes RW (eds) Modern techniques for circular dichroism and synchrotron radiation circular dichroism. IOS Press, Amsterdam, pp 91–107
Kelly SM, Jess TJ, Price NC (2005) How to study proteins by circular dichroism. Biochem Biophys Acta 1751(2):119–139. https://doi.org/10.1016/j.bbapap.2005.06.005
Kumagai PS, Araujo APU, Lopes JLS (2017a) Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy. Biophys Rev 9(5):517–527. https://doi.org/10.1007/s12551-017-0314-2
Kumagai PS, DeMarco R, Lopes JLS (2017b) Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins. Eur Biophys J 46(7):599–606. https://doi.org/10.1007/s00249-017-1202-1
Lees JG, Wallace BA (2002) Synchrotron radiation circular dichroism and conventional circular dichroism spectroscopy: a comparison. Spectroscopy 16:121–125
Lees JG, Miles AJ, Wien F, Wallace BA (2006) A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 22(16):1955–1962. https://doi.org/10.1093/bioinformatics/btl327
Manavalan P, Johnson WC (1987) Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal Biochem 167(1):76–85. https://doi.org/10.1016/0003-2697(87)90135-7
Matsuo K, Gekko K (2018) Synchrotron-radiation vacuum-ultraviolet circular-dichroism spectroscopy for characterizing the structure of saccharides. Adv Exp Med Biol 1104:101–117. https://doi.org/10.1007/978-981-13-2158-0_6
Micsonai A, Wien F, Kernya L, Lee YH, Goto Y, Refregiers M, Kardos J (2015) Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy. Proc Natl Acad Sci USA 112(24):E3095–E3103. https://doi.org/10.1073/pnas.1500851112
Micsonai A, Wien F, Bulyáki É, Kun J, Moussong É, Lee YH, Goto Y, Réfrégiers M, Kardos J (2018) BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res 46(W1):W315–W322. https://doi.org/10.1093/nar/gky497
Miles AJ, Wallace BA (2009) Calibration techniques for circular dichroism and synchrotron radiation circular dichroism spectroscopy. In: Modern techniques for circular dichroism and synchrotron radiation circular dichroism spectroscopy. IOS Press, Amsterdam. https://doi.org/10.3233/978-1-60750-000-1-73
Miles AJ, Wallace BA (2018) CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data. Protein Sci 27(9):1717–1722. https://doi.org/10.1002/pro.3474
Miles AJ, Whitmore L, Wallace BA (2005a) Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data. Protein Sci 14(2):368–374. https://doi.org/10.1110/ps.041019905
Miles AJ, Wien F, Lees JG, Wallace BA (2005b) Calibration and standardisation of synchrotron radiation and conventional circular dichroism spectrometers. Part 2: factors affecting magnitude and wavelength. Spectroscopy 19:43–51. https://doi.org/10.1039/B316168B
Miyahara T, Nakatsuji H, Sugiyama H (2016) Similarities and differences between RNA and DNA double-helical structures in circular dichroism spectroscopy: a SAC–CI study. J Phys Chem A 120(45):9008–9018. https://doi.org/10.1021/acs.jpca.6b08023
Nagy G, Igaev M, Jones NC, Hoffmann SV, Grubmüller H (2019) SESCA: predicting circular dichroism spectra from protein molecular structures. J Chem Theory Comput 15(9):5087–5102. https://doi.org/10.1021/acs.jctc.9b00203
Sreerama N, Woody RW (1993) A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal Biochem 209(1):32–44. https://doi.org/10.1006/abio.1993.1079
Toniolo C, Formaggio F, Woody RW (2012) Electronic Circular dichroism of peptides. In: Berova N, Polavarapu PL, Nakanishi K, Woody RW (eds) Comprehensive chiroptical spectroscopy, vol 2. Wiley, New Jersey, pp 499–574
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(1):110–118. https://doi.org/10.1016/0003-2697(90)90396-q
Wallace BA (2009) Protein characterization by synchrotron radiation circular dichroism spectroscopy. Q Rev Biophys 42(04):317–370. https://doi.org/10.1017/S003358351000003X
Wallace BA, Lees JG, Orry AJ, Lobley A, Janes RW (2003) Analyses of circular dichroism spectra of membrane proteins. Protein Sci 12(4):875–884. https://doi.org/10.1110/ps.0229603
Whitmore L, Wallace BA (2004) DICHROWEB: an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res 32:W668–W673. https://doi.org/10.1093/nar/gkh371
Acknowledgements
Authors are grateful to Prof. Bonnie Wallace from Birkbeck College, UK for scientific discussions and her intellectual support. This work has been supported by FAPESP grants 19546-7 (to JLSL) and 19567-7 (to JAFP), CNPq-Brazil grant 300406-8 (to JLSL), and the International Mobility Program of AUCANI-USP/Santander (to JLSL).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Sousa, V.K., Pedro, J.A.F., Kumagai, P.S. et al. Effect of setting data collection parameters on the reliability of a circular dichroism spectrum. Eur Biophys J 50, 687–697 (2021). https://doi.org/10.1007/s00249-021-01499-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-021-01499-4