Analyses of circular dichroism spectra of membrane proteins

Circular dichroism (CD) spectroscopy is a valuable technique for the determination of protein secondary structures. Many linear and nonlinear algorithms have been developed for the empirical analysis of CD data, using reference databases derived from proteins of known structures. To date, the reference databases used by the various algorithms have all been derived from the spectra of soluble proteins. When applied to the analysis of soluble protein spectra, these methods generally produce calculated secondary structures that correspond well with crystallographic structures. In this study, however, it was shown that when applied to membrane protein spectra, the resulting calculations produce considerably poorer results. One source of this discrepancy may be the altered spectral peak positions (wavelength shifts) of membrane proteins due to the different dielectric of the membrane environment relative to that of water. These results have important consequences for studies that seek to use the existing soluble protein reference databases for the analyses of membrane proteins.

[1]  M. Cascio,et al.  Effects of local environment on the circular dichroism spectra of polypeptides. , 1995, Analytical biochemistry.

[2]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[3]  J. Thornton,et al.  PROMOTIF—A program to identify and analyze structural motifs in proteins , 1996, Protein science : a publication of the Protein Society.

[4]  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.

[5]  T L Blundell,et al.  Structural genomics: an overview. , 2000, Progress in biophysics and molecular biology.

[6]  S M King,et al.  Assigning secondary structure from protein coordinate data , 1999, Proteins.

[7]  W C Johnson,et al.  Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures. , 1992, Analytical biochemistry.

[8]  B. Wallace,et al.  A theoretical analysis of the effects of sonication on differential absorption flattening in suspensions of membrane sheets. , 1987, Biophysical journal.

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

[10]  B. Wallace,et al.  Differential light scattering and absorption flattening optical effects are minimal in the circular dichroism spectra of small unilamellar vesicles. , 1984, Biochemistry.

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

[12]  T. Keiderling,et al.  Relationships between secondary structure fractions for globular proteins. Neural network analyses of crystallographic data sets. , 1992, Biochemistry.

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

[14]  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.

[15]  B. Wallace,et al.  Synchrotron radiation circular-dichroism spectroscopy as a tool for investigating protein structures. , 2000, Journal of synchrotron radiation.

[16]  J. Deisenhofer,et al.  Crystal structure of the outer membrane active transporter FepA from Escherichia coli , 1999, Nature Structural Biology.

[17]  R. W. Janes,et al.  Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition and structural genomics. , 2001, Current opinion in chemical biology.

[18]  A. Savitzky,et al.  Smoothing and Differentiation of Data by Simplified Least Squares Procedures. , 1964 .

[19]  R. Dutzler,et al.  Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. , 1997, Journal of molecular biology.

[20]  B. Wallace,et al.  Circular dichroism analyses of membrane proteins: an examination of differential light scattering and absorption flattening effects in large membrane vesicles and membrane sheets. , 1984, Analytical biochemistry.

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

[22]  B. Wallace,et al.  Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments. , 1987, Biochemistry.

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

[24]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[25]  K. Diederichs,et al.  Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. , 1998, Science.

[26]  B. Wallace,et al.  Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles. , 1982, Biochemistry.

[27]  I. V. van Stokkum,et al.  Estimation of protein secondary structure and error analysis from circular dichroism spectra. , 1990, Analytical biochemistry.

[28]  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.

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

[30]  Lee Whitmore,et al.  DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra , 2002, Bioinform..

[31]  R. Woody,et al.  Circular dichroism. , 1995, Methods in enzymology.

[32]  Synchrotron radiation circular dichroism and conventional circular dichroism spectroscopy: A comparison , 2002 .

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

[34]  B. Wallace,et al.  Crambin in phospholipid vesicles: Circular dichroism analysis of crystal structure relevance. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

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

[36]  D C Rees,et al.  Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. , 1998, Science.

[37]  T. A. Link,et al.  Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. , 1998, Science.

[38]  H. Michel,et al.  Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.