Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis

Protein basis sets have been extensively used as reference data for the determination of protein structure with optical methods such as circular dichroism and infrared spectroscopies. We have taken a new approach to basis protein selection by utilizing three crystal structure classification databases: CATH, SCOP, and PDB_SELECT. Through the use of the information available in these and other online resources, we identified 115 commercially available proteins as potential basis set candidates. By carefully screening the quality of the crystal structures and commercial protein preparations, we obtained a final set of 50 rationally selected proteins (RaSP50) that has been optimized for use in spectroscopic protein structure determination studies. These proteins span the full range of known protein folds as well as α‐helix and β‐sheet contents, and they represent a more comprehensive variety of fold types than any previous reference set. This report includes a detailed presentation of the reasoning behind the rational protein selection process, a description of the properties of the RaSP50 set, and a discussion of the types of structural and spectral variations that are represented in the set.

[1]  E. Goormaghtigh,et al.  Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures. , 1994, Sub-cellular biochemistry.

[2]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998 , 1998, Nucleic Acids Res..

[3]  T. Keiderling,et al.  Statistical analyses of the vibrational circular dichroism of selected proteins and relationship to secondary structures. , 1991, Biochemistry.

[4]  D. Wetlaufer,et al.  A new basis for interpreting the circular dichroic spectra of proteins. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[5]  S. Venyaminov,et al.  Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands , 1990, Biopolymers.

[6]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[7]  G. Fasman,et al.  Computed circular dichroism spectra for the evaluation of protein conformation. , 1969, Biochemistry.

[8]  R. Jakobsen,et al.  An Algorithm for the Reproducible Spectral Subtraction of Water from the FT-IR Spectra of Proteins in Dilute Solutions and Adsorbed Monolayers , 1986 .

[9]  E Goormaghtigh,et al.  Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. I. Assignments and model compounds. , 1994, Sub-cellular biochemistry.

[10]  R. Woody,et al.  [4] Circular dichroism , 1995 .

[11]  S. Venyaminov,et al.  Determination of Protein Secondary Structure , 1996 .

[12]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank. , 1991, Nucleic acids research.

[13]  Tim J. P. Hubbard,et al.  SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..

[14]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments , 1993, Nucleic Acids Res..

[15]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[16]  G. Barton.  Scop: structural classification of proteins. , 1994, Trends in biochemical sciences.

[17]  A. Barth,et al.  The infrared absorption of amino acid side chains. , 2000, Progress in biophysics and molecular biology.

[18]  Johnson Wc,et al.  Information content in the circular dichroism of proteins. , 1981 .

[19]  R. Mitchell,et al.  Determination of protein secondary structure using factor analysis of infrared spectra. , 1990, Biochemistry.

[20]  T. Keiderling,et al.  Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: effect of Fourier self-deconvolution of the amide I and amide II bands. , 1998, Biospectroscopy.

[21]  T. P. Flores,et al.  Comparison of conformational characteristics in structurally similar protein pairs , 1993, Protein science : a publication of the Protein Society.

[22]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[23]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[24]  Y H Chen,et al.  Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. , 1972, Biochemistry.

[25]  J. Brahms,et al.  Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. , 1980, Journal of molecular biology.

[26]  N. Nevskaya,et al.  Infrared spectra and resonance interactions of amide‐I and II vibrations of α‐helix , 1976 .

[27]  Y H Chen,et al.  Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. , 1974, Biochemistry.

[28]  T. Keiderling,et al.  Empirical studies of protein secondary structure by vibrational circular dichroism and related techniques. Alpha-lactalbumin and lysozyme as examples. , 1994, Faraday discussions.

[29]  S. Venyaminov,et al.  Circular dichroic analysis of denatured proteins: inclusion of denatured proteins in the reference set. , 1993, Analytical biochemistry.

[30]  G. Böhm,et al.  Structural relationships of homologous proteins as a fundamental principle in homology modeling , 1993, Proteins.

[31]  P. V. von Hippel,et al.  Calculation of protein extinction coefficients from amino acid sequence data. , 1989, Analytical biochemistry.

[32]  S. Venyaminov,et al.  Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure , 1990, Biopolymers.

[33]  Venyaminov SYu,et al.  Determination of protein tertiary structure class from circular dichroism spectra. , 1994, Analytical biochemistry.

[34]  R. Woody.  Contributions of tryptophan side chains to the far-ultraviolet circular dichroism of proteins , 2004, European Biophysics Journal.

[35]  T. Keiderling,et al.  Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure , 1995, Protein science : a publication of the Protein Society.

[36]  Chris Sander,et al.  The HSSP data base of protein structure-sequence alignments , 1993, Nucleic Acids Res..

[37]  J. T. Yang,et al.  Circular dichroic analysis of protein conformation: inclusion of the beta-turns. , 1978, Analytical biochemistry.

[38]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[39]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[40]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[41]  T. Keiderling,et al.  Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example. , 1996, Biochemistry.

[42]  Y H Chen,et al.  A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism. , 1971, Biochemical and biophysical research communications.

[43]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments and family profiles , 1998, Nucleic Acids Res..

[44]  E. Goormaghtigh,et al.  Relevance of Protein Thin Films Prepared for Attenuated Total Reflection Fourier Transform Infrared Spectroscopy: Significance of the pH , 1996 .

[45]  W C Johnson,et al.  Information content in the circular dichroism of proteins. , 1981, Biochemistry.

[46]  T. Keiderling,et al.  Predictions of secondary structure using statistical analyses of electronic and vibrational circular dichroism and Fourier transform infrared spectra of proteins in H2O. , 1996, Journal of molecular biology.

[47]  R. Woody,et al.  Contributions of tryptophan side chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators. , 1994, Faraday discussions.

[48]  P. Haris,et al.  Protein secondary structure from Fourier transform infrared and/or circular dichroism spectra. , 1993, Analytical biochemistry.

[49]  W. C. Krueger,et al.  Protein secondary structure from Fourier transform infrared spectroscopy: a data base analysis. , 1991, Analytical biochemistry.

[50]  G. Fasman,et al.  Deconvolution of the circular dichroism spectra of proteins: The circular dichroism spectra of the antiparallel β‐sheet in proteins , 1992, Proteins.

[51]  A. Dunker,et al.  Aromatic and Cystine Side-Chain Circular Dichroism in Proteins , 1996 .

[52]  W. Krueger,et al.  An infrared and circular dichroism combined approach to the analysis of protein secondary structure. , 1991, Analytical biochemistry.

[53]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[54]  T. Keiderling,et al.  Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins. , 1991, Biochemistry.

[55]  M. Pézolet,et al.  Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods. , 1990, Biochemistry.

[56]  M. Levitt,et al.  Automatic identification of secondary structure in globular proteins. , 1977, Journal of molecular biology.

[57]  Narasimha Sreerama,et al.  Structural composition of βI‐ and βII‐proteins , 2003 .

[58]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.