Determining β‐sheet stability by Fourier transform infrared difference spectra

We describe here a new method for determining the conformational stability of antiparallel β‐sheets. Due to coupling between the transition dipoles, β‐sheet conformations typically exhibit a characteristic high‐frequency amide I component centered at ∼ 1680 cm−1. Using one β‐sheet protein and two small β‐hairpins, we demonstrate that this high‐frequency component, which is fairly narrow (∼ 8–10 cm−1), can be quantitatively resolved and used in thermal stability determination. Compared with the commonly used CD and fluorescence techniques, this ir method offers advantages. Since the area of this high‐frequency component is only proportional to the folded population, it eliminates the need for a priori information of the folded and unfolded baselines encountered in other methods. Thus, it is applicable to a variety of β‐sheet systems. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004

[1]  S. Mukamel,et al.  The origin of vibrational mode couplings in various secondary structural motifs of polypeptides. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  E. Powers,et al.  Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded beta-sheets. , 2001, Journal of the American Chemical Society.

[3]  R. Wade,et al.  Stability of the β-Sheet of the WW Domain: A Molecular Dynamics Simulation Study , 1999 .

[4]  F. Gai,et al.  Infrared study of the stability and folding kinetics of a 15-residue beta-hairpin. , 2003, Journal of the American Chemical Society.

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

[6]  L Serrano,et al.  Role of beta-turn residues in beta-hairpin formation and stability in designed peptides. , 1997, Journal of molecular biology.

[7]  Jason C. Crane,et al.  The folding mechanism of a -sheet: the WW domain1 , 2001 .

[8]  A. Barth,et al.  What vibrations tell about proteins , 2002, Quarterly Reviews of Biophysics.

[9]  T. Keiderling,et al.  Spectroscopic studies of structural changes in two beta-sheet-forming peptides show an ensemble of structures that unfold noncooperatively. , 2003, Biochemistry.

[10]  M. Sudol,et al.  The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Eftink.  The use of fluorescence methods to monitor unfolding transitions in proteins. , 1994, Biophysical journal.

[12]  P. Bork,et al.  The WW domain: a signalling site in dystrophin? , 1994, Trends in biochemical sciences.

[13]  R. Dyer,et al.  Fast events in protein folding: relaxation dynamics and structure of the I form of apomyoglobin. , 1997, Biochemistry.

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

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

[16]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[17]  Tanja Kortemme,et al.  Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein , 1998 .

[18]  V. Daggett,et al.  The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR , 2003, Protein science : a publication of the Protein Society.

[19]  M. Jiménez,et al.  Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution. , 1996, Folding & design.

[20]  H. Mantsch,et al.  Two-dimensional IR correlation spectroscopy: sequential events in the unfolding process of the lambda cro-V55C repressor protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  W. DeGrado,et al.  Helix formation via conformation diffusion search , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Gruebele,et al.  Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. , 2004, Journal of molecular biology.

[23]  W. DeGrado,et al.  Time-resolved infrared study of the helix-coil transition using (13)C-labeled helical peptides. , 2001, Journal of the American Chemical Society.

[24]  D. Naumann,et al.  Secondary structure and temperature-induced unfolding and refolding of ribonuclease T1 in aqueous solution. A Fourier transform infrared spectroscopic study. , 1993, Journal of molecular biology.

[25]  S. Venyaminov,et al.  The Effects of Chain Length and Thermal Denaturation on Helix-Forming Peptides: A Mode-Specific Analysis Using 2D FT-IR , 1997 .

[26]  W. C. Johnson,et al.  Experimental errors and their effect on analyzing circular dichroism spectra of proteins. , 1982, Analytical biochemistry.

[27]  M. Jiménez,et al.  Thermodynamic Analysis of β-Hairpin-Forming Peptides from the Thermal Dependence of 1H NMR Chemical Shifts , 2002 .

[28]  F. Goñi,et al.  Structure and dynamics of membrane proteins as studied by infrared spectroscopy. , 1999, Progress in biophysics and molecular biology.

[29]  H. Susi,et al.  Fourier Transform Infrared Study of Proteins with Parallel β-Chains. , 1987, Archives of biochemistry and biophysics.

[30]  J. Kelly,et al.  Progress towards understanding β-sheet structure , 1996 .

[31]  M. Gruebele,et al.  Mapping the transition state of the WW domain β-sheet , 2000 .

[32]  J. Bandekar,et al.  Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. , 1986, Advances in protein chemistry.

[33]  N. Skelton,et al.  Tryptophan zippers: Stable, monomeric β-hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  J. Olinger,et al.  Fourier transform infrared studies of ribonuclease in H2O and 2H2O solutions. , 1986, Biochimica et biophysica acta.

[35]  H. Susi,et al.  Examination of the secondary structure of proteins by deconvolved FTIR spectra , 1986, Biopolymers.

[36]  V. Sieber,et al.  Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide. , 1996, Biochemistry.

[37]  R. Woody,et al.  Theory of Circular Dichroism of Proteins , 1996 .

[38]  R. Winter,et al.  Temperature- and pressure-induced unfolding and refolding of ubiquitin: a static and kinetic Fourier transform infrared spectroscopy study. , 2002, Biochemistry.

[39]  M. Sudol,et al.  WW: An isolated three‐stranded antiparallel β‐sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state , 2008, Protein science : a publication of the Protein Society.

[40]  H. Torii.  Model calculations on the amide‐I infrared bands of globular proteins , 1992 .

[41]  M. Karplus,et al.  Understanding beta-hairpin formation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Douglas J. Moffatt,et al.  Fourier Self-Deconvolution: A Method for Resolving Intrinsically Overlapped Bands , 1981 .

[43]  O. Fedorov,et al.  Estimation of amino acid residue side‐chain absorption in the infrared spectra of protein solutions in heavy water , 1975, Biopolymers.