Analysis of Circular Dichroism Data

Publisher Summary This chapter focuses on the analysis of circular dichroism (CD) data to determine thermodynamic parameters of folding, binding constants, and estimates of secondary structure. Proteins and polypeptides have CD bands in the far ultraviolet region that arise mainly from the amides of the protein backbone and are sensitive to their conformations. Proteins have CD bands in the near ultraviolet and visible regions, which arise from aromatic amino acids and prosthetic groups. CD can be used to determine the enthalpy, entropy and midpoints, and values of unfolding/refolding transitions of a protein if they are reversible as a function of temperature or denaturant. The change in CD as a function of ligand concentration has been used to study numerous systems. It is found that if two proteins bind to each other only when they are folded and the protein complex unfolds cooperatively and reversibly to give two unfolded monomers, it is easy to determine the binding constant by determining the thermodynamics of folding of the complex compared with the thermodynamics of folding of the monomers.

[1]  G. Montelione,et al.  The structure of the N-terminus of striated muscle alpha-tropomyosin in a chimeric peptide: nuclear magnetic resonance structure and circular dichroism studies. , 1998, Biochemistry.

[2]  C. Pace,et al.  Substrate stabilization of lysozyme to thermal and guanidine hydrochloride denaturation. , 1980, Journal of Biological Chemistry.

[3]  C. Kay,et al.  Hydrodynamic and optical properties of troponin A. Demonstration of a conformational change upon binding calcium ion. , 1972, Biochemistry.

[4]  N. Greenfield.  Circular dichroism studies of dihydrofolate reductase from a methotrexate-resistant strain of Escherichia coli B, MB 1428: ternary complexes. , 1975, Biochimica et biophysica acta.

[5]  E. Freire,et al.  Thermal denaturation methods in the study of protein folding. , 1995, Methods in enzymology.

[6]  N. Sreerama,et al.  A self-consistent method for the analysis of protein secondary structure from circular dichroism. , 1993, Analytical biochemistry.

[7]  N. Greenfield.  Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. , 1996, Analytical biochemistry.

[8]  G. Montelione,et al.  Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein. , 2001, Journal of molecular biology.

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

[10]  W C Johnson,et al.  Protein secondary structure and circular dichroism: A practical guide , 1990, Proteins.

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

[12]  D. Marquardt.  An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[13]  R. L. Baldwin,et al.  Parameters of helix–coil transition theory for alanine‐based peptides of varying chain lengths in water , 1991, Biopolymers.

[14]  T. Schleich,et al.  Resolution of independently titrating spectral components in the ultraviolet circular dichroism of subtilisin enzymes by matrix rank analysis. , 1977, Biochimica et biophysica acta.

[15]  I. Kuo,et al.  Purification and characterization of a troponin C-like phosphodiesterase activator from bovine thyroid. , 1979, Metabolism: clinical and experimental.

[16]  C. Cantor,et al.  Biophysical chemistry. Part III, The behavior of biologicalmacromolecules , 1980 .

[17]  S. Provencher,et al.  Estimation of globular protein secondary structure from circular dichroism. , 1981, Biochemistry.

[18]  W C Johnson,et al.  Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. , 1987, Analytical biochemistry.

[19]  D. Muccio,et al.  Determination of RNase A/2'-cytidine monophosphate binding affinity and enthalpy by a global fit of thermal unfolding curves. , 2002, Analytical biochemistry.

[20]  R I Shrager,et al.  Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners. , 1994, Journal of biochemical and biophysical methods.

[21]  J. H. Collins,et al.  Dansylaziridine-labeled troponin C. A fluorescent probe of Ca2+ binding to the Ca2+-specific regulatory sites. , 1978, The Journal of biological chemistry.

[22]  A. Doig,et al.  Addition of side chain interactions to modified Lifson‐Roig helix‐coil theory: Application to energetics of Phenylalanine‐Methionine interactions , 1995, Protein science : a publication of the Protein Society.

[23]  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.

[24]  N J Greenfield,et al.  Circular dichroism and optical rotatory dispersion of proteins and polypeptides. , 1973, Methods in Enzymology.

[25]  I. Epstein,et al.  Extracting Experimental Information from Large Matrixes. 1. A New Algorithm for the Application of Matrix Rank Analysis , 1997 .

[26]  J. Schellman.  The effect of binding on the melting temperature of biopolymers , 1976 .

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

[28]  W. C. Johnson.  Circular dichroism and its empirical application to biopolymers. , 1985, Methods of biochemical analysis.

[29]  W. C. Johnson,et al.  Secondary structure of proteins through circular dichroism spectroscopy. , 1988, Annual review of biophysics and biophysical chemistry.

[30]  N. Sreerama,et al.  Poly(pro)II helices in globular proteins: identification and circular dichroic analysis. , 1994, Biochemistry.

[31]  D. W. Bolen,et al.  Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. , 1988, Biochemistry.

[32]  C. Kay,et al.  Physicochemical and biological studies on the metal-induced conformational change in troponin A. Implication of carboxyl groups in the binding of calcium ion. , 1973, Biochemistry.

[33]  A. Baici,et al.  Very rapid, ionic strength-dependent association and folding of a heterodimeric leucine zipper. , 1997, Biochemistry.

[34]  R. L. Baldwin,et al.  Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions , 1994, Protein science : a publication of the Protein Society.

[35]  J F Brandts,et al.  Study of strong to ultratight protein interactions using differential scanning calorimetry. , 1990, Biochemistry.

[36]  G. Engel.  Estimation of binding parameters of enzyme-ligand complex from fluorometric data by a curve fitting procedure: seryl-tRNA synthetase-tRNA Ser complex. , 1974, Analytical biochemistry.

[37]  C. Hayes,et al.  Equilibrium and Kinetic Binding Interactions between DNA and a Group of Novel, Nonspecific DNA-binding Proteins from Spores ofBacillus and Clostridium Species* , 2000, The Journal of Biological Chemistry.

[38]  R. Woody,et al.  The effect of conformation on the CD of interacting helices: A theoretical study of tropomyosin , 1990, Biopolymers.

[39]  B. Gyurcsik,et al.  CD spectroscopic study on the speciation and solution structure of copper(II) complexes of some tripeptides in combination with potentiometric and spectrophotometric results. , 2001, Journal of inorganic biochemistry.

[40]  W. J. Becktel,et al.  Protein stability curves , 1987, Biopolymers.

[41]  G. Böhm,et al.  Quantitative analysis of protein far UV circular dichroism spectra by neural networks. , 1992, Protein engineering.

[42]  T. Oas,et al.  Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein. , 2001, Biochemistry.

[43]  T. Konno.  Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra , 1998, Protein science : a publication of the Protein Society.

[44]  M. Eftink.  Use of multiple spectroscopic methods to monitor equilibrium unfolding of proteins. , 1995, Methods in enzymology.

[45]  P. V. von Hippel,et al.  Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. , 1974, Journal of molecular biology.

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

[47]  N. C. Price,et al.  The use of circular dichroism in the investigation of protein structure and function. , 2000, Current protein & peptide science.

[48]  A. Labhardt.  [7]Folding intermediates studied by circular dichroism , 1986 .

[49]  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.

[50]  E. Stellwagen,et al.  Incorporation of pairwise interactions into the Lifson‐Roig model for helix prediction , 1995, Protein science : a publication of the Protein Society.

[51]  C. Klee,et al.  Positive cooperative binding of calcium to bovine brain calmodulin. , 1980, Biochemistry.

[52]  R. L. Baldwin,et al.  Urea unfolding of peptide helices as a model for interpreting protein unfolding. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[53]  N. Greenfield.  Applications of circular dichroism in protein and peptide analysis , 1999 .

[54]  A. Doig.  Recent advances in helix-coil theory. , 2002, Biophysical chemistry.

[55]  A. Holtzer,et al.  Alpha-helix to random coil transitions: interpretation of the CD in the region of linear temperature dependence. , 1992, Biopolymers.

[56]  Charles R. Cantor,et al.  The behavior of biological macromolecules , 1980 .

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

[58]  R. L. Baldwin,et al.  Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N- and C-capping. , 1994, Biochemistry.

[59]  N. Greenfield,et al.  Conformational intermediates in the folding of a coiled‐coil model peptide of the N‐terminus of tropomyosin and αα‐tropomyosin , 1993 .

[60]  Robert W Woody,et al.  Is polyproline II a major backbone conformation in unfolded proteins? , 2002, Advances in protein chemistry.

[61]  G. Fasman,et al.  Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. , 1991, Protein engineering.

[62]  Michael L. Johnson,et al.  [16] Nonlinear least-squares analysis , 1985 .

[63]  J. M. Sanchez-Ruiz,et al.  A model-independent, nonlinear extrapolation procedure for the characterization of protein folding energetics from solvent-denaturation data. , 1996, Biochemistry.

[64]  G. Fasman,et al.  Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: a practical guide. , 1992, Analytical biochemistry.

[65]  K. P. Murphy,et al.  Van't Hoff and calorimetric enthalpies from isothermal titration calorimetry: are there significant discrepancies? , 2001, Biochemistry.

[66]  L. Mueller,et al.  Characterization of a new four‐chain coiled‐coil: Influence of chain length on stability , 1995, Protein science : a publication of the Protein Society.

[67]  C. Kay,et al.  Circular dichroism and fluorescence studies on troponin—tropomyosin interactions , 1975, FEBS letters.

[68]  N. Greenfield,et al.  Enzyme ligand complexes: spectroscopic studies. , 1975, CRC critical reviews in biochemistry.

[69]  S. Lifson,et al.  On the Theory of Helix—Coil Transition in Polypeptides , 1961 .

[70]  T. Creamer,et al.  Determinants of the polyproline II helix from modeling studies. , 2002, Advances in protein chemistry.

[71]  R. L. Baldwin,et al.  N‐ and C‐capping preferences for all 20 amino acids in α‐helical peptides , 1995, Protein science : a publication of the Protein Society.

[72]  K. Breslauer.  Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. , 1995, Methods in enzymology.

[73]  A. Holtzer,et al.  The use of spectral decomposition via the convex constraint algorithm in interpreting the CD‐observed unfolding transitions of C coils , 1995 .

[74]  M. Eftink,et al.  Analysis of multidimensional spectroscopic data to monitor unfolding of proteins. , 1994, Methods in enzymology.

[75]  D. Livingston,et al.  Spectro-chemical probes for protein conformation and function. , 1972, Cold Spring Harbor symposia on quantitative biology.

[76]  A. Doig,et al.  Effect of the N1 residue on the stability of the α‐helix for all 20 amino acids , 2001, Protein science : a publication of the Protein Society.

[77]  M. A. Andrade,et al.  Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. , 1993, Protein engineering.

[78]  W C Johnson,et al.  Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. , 1986, Analytical biochemistry.

[79]  N. Greenfield,et al.  The effects of deletion of the amino-terminal helix on troponin C function and stability. , 1994, The Journal of biological chemistry.

[80]  N. Sreerama,et al.  Analysis of protein circular dichroism spectra based on the tertiary structure classification. , 2001, Analytical biochemistry.

[81]  R. Woody,et al.  Recent developments in the electronic spectroscopy of amides and α-helical polypeptides , 2002 .

[82]  R. Tauler,et al.  Multivariate curve resolution: a possible tool in the detection of intermediate structures in protein folding. , 1998, Biophysical journal.

[83]  X. Zhai,et al.  Phosphatidylserine binding alters the conformation and specifically enhances the cofactor activity of bovine factor Va. , 2002, Biochemistry.

[84]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[85]  T. Palm,et al.  Structure and interactions of the carboxyl terminus of striated muscle alpha-tropomyosin: it is important to be flexible. , 2002, Biophysical journal.

[86]  P. Privalov,et al.  Unfolding of a leucine zipper is not a simple two-state transition. , 2002, Journal of molecular biology.

[87]  R. Ionescu,et al.  Global analysis of the acid-induced and urea-induced unfolding of staphylococcal nuclease and two of its variants. , 1997, Biochemistry.

[88]  V. Fowler,et al.  Tropomyosin requires an intact N-terminal coiled coil to interact with tropomodulin. , 2002, Biophysical journal.

[89]  Romà Tauler,et al.  Detection and resolution of intermediate species in protein folding processes using fluorescence and circular dichroism spectroscopies and multivariate curve resolution. , 2002, Analytical chemistry.

[90]  N. Sreerama,et al.  Protein secondary structure from circular dichroism spectroscopy. Combining variable selection principle and cluster analysis with neural network, ridge regression and self-consistent methods. , 1994, Journal of molecular biology.

[91]  G. Scatchard,et al.  THE ATTRACTIONS OF PROTEINS FOR SMALL MOLECULES AND IONS , 1949 .

[92]  G. Fasman.  Circular dichroism analysis of chromatin and DNA--nuclear protein complexes. , 1978, Methods in cell biology.

[93]  P. Privalov,et al.  A calorimetric study of the folding-unfolding of an alpha-helix with covalently closed N and C-terminal loops. , 1999, Journal of molecular biology.

[94]  P. Privalov,et al.  A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. , 1974, Journal of molecular biology.

[95]  S. Beychok.  Circular Dichroism of Biological Macromolecules , 1966, Science.

[96]  C. Kay,et al.  Circular dichroism studies of native and chemically modified Ca2+-dependent protein modulator. , 1979, Canadian journal of biochemistry.

[97]  N. Sreerama,et al.  Estimation of the number of α‐helical and β‐strand segments in proteins using circular dichroism spectroscopy , 2008, Protein science : a publication of the Protein Society.

[98]  G. Fasman,et al.  The use of computed optical rotatory dispersion curves for the evaluation of protein conformation. , 1967, Biochemistry.

[99]  N. Sreerama,et al.  Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. , 2000, Analytical biochemistry.

[100]  N. Sreerama,et al.  Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis. , 2000, Analytical biochemistry.

[101]  Kevin L. Shaw,et al.  Tyrosine hydrogen bonds make a large contribution to protein stability. , 2001, Journal of molecular biology.

[102]  R. L. Baldwin,et al.  Helix propagation and N‐cap propensities of the amino acids measured in alanine‐based peptides in 40 volume percent trifluoroethanol , 1996, Protein science : a publication of the Protein Society.

[103]  K. Thompson,et al.  Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. , 1993, Biochemistry.

[104]  C. Arrowsmith,et al.  Thermodynamic analysis of the structural stability of the tetrameric oligomerization domain of p53 tumor suppressor. , 1995, Biochemistry.

[105]  G. Fasman.  Circular Dichroism and the Conformational Analysis of Biomolecules , 1996, Springer US.