Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides

Abstract Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides

[1]  R. Hochstrasser,et al.  Two-dimensional spectroscopy at infrared and optical frequencies , 2007, Proceedings of the National Academy of Sciences.

[2]  S. Decatur.  Elucidation of residue-level structure and dynamics of polypeptides via isotope-edited infrared spectroscopy. , 2006, Accounts of chemical research.

[3]  S. Ham,et al.  Local Amide I Mode Frequencies and Coupling Constants in Polypeptides , 2003 .

[4]  R. Schweitzer‐Stenner.  Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure A critical review , 2006 .

[5]  S. Mukamel,et al.  Electrostatic DFT map for the complete vibrational amide band of NMA. , 2005, The journal of physical chemistry. A.

[6]  T. Keiderling,et al.  Vibrational Circular Dichroism of Proteins in H2O Solution , 1993 .

[7]  P. Bouř,et al.  Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the Trpzip model hairpin. , 2005, The journal of physical chemistry. B.

[8]  R. Hochstrasser,et al.  STRUCTURE OF THE AMIDE I BAND OF PEPTIDES MEASURED BY FEMTOSECOND NONLINEAR-INFRARED SPECTROSCOPY , 1998 .

[9]  H. Mantsch,et al.  Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment. , 1993, Biochemistry.

[10]  V. P. Gupta,et al.  Vibrational CD of the amide II band in some model polypeptides and proteins , 1992, Biopolymers.

[11]  Sanford A. Asher,et al.  Uncoupled Adjacent Amide Vibrations in Small Peptides , 2000 .

[12]  R. Mendelsohn,et al.  13C Isotope Labeling of Hydrophobic Peptides. Origin of the Anomalous Intensity Distribution in the Infrared Amide I Spectral Region of β-Sheet Structures , 2000 .

[13]  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.

[14]  N. Kallenbach,et al.  Vibrational Raman optical activity characterization of poly(l-proline) II helix in alanine oligopeptides. , 2004, Journal of the American Chemical Society.

[15]  K. Griebenow,et al.  Structure Analysis of Dipeptides in Water by Exploring and Utilizing the Structural Sensitivity of Amide III by Polarized Visible Raman, FTIR−Spectroscopy and DFT Based Normal Coordinate Analysis , 2002 .

[16]  S. Asher,et al.  Dihedral psi angle dependence of the amide III vibration: a uniquely sensitive UV resonance Raman secondary structural probe. , 2001, Journal of the American Chemical Society.

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

[18]  P. Mukherjee,et al.  Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles. , 2009, The journal of physical chemistry. B.

[19]  R. Mendelsohn,et al.  A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Globular Proteins: From Structure to Spectrum , 2005 .

[20]  Sihyun Ham,et al.  Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects , 2003 .

[21]  P. Bouř,et al.  Gauge-Origin Independent Density-Functional Theory Calculations of Vibrational Raman Optical Activity , 2002 .

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

[23]  T. Miyazawa.  Perturbation Treatment of the Characteristic Vibrations of Polypeptide Chains in Various Configurations , 1960 .

[24]  C. Toniolo,et al.  Different spectral signatures of octapeptide 3(10)- and alpha-helices revealed by two-dimensional infrared spectroscopy. , 2006, The journal of physical chemistry. B.

[25]  S. Krimm,et al.  General treatment of vibrations of helical molecules and application to transition dipole coupling in amide I and amide II modes of α-helical poly(l-alanine) , 1998 .

[26]  P. Nguyen,et al.  Quantum-classical description of the amide I vibrational spectrum of trialanine. , 2007, The Journal of chemical physics.

[27]  D. Raleigh,et al.  Two-dimensional infrared spectroscopy provides evidence of an intermediate in the membrane-catalyzed assembly of diabetic amyloid. , 2009, The journal of physical chemistry. B.

[28]  H. Havel.  Spectroscopic Methods for Determining Protein Structure in Solution , 1996 .

[29]  R. Hochstrasser,et al.  Two-dimensional infrared spectroscopy of isotopomers of an alanine rich α-helix , 2004 .

[30]  S. Ham,et al.  Inter-peptide interaction and delocalization of amide I vibrational excitons in myoglobin and flavodoxin , 2002 .

[31]  H. Gremlich,et al.  Infrared and Raman Spectroscopy of Biological Materials , 2000 .

[32]  R. Hochstrasser,et al.  Characteristics of the two-dimensional infrared spectroscopy of helices from approximate simulations and analytic models , 2004 .

[33]  S. Asher,et al.  Assignments and Conformational Dependencies of the Amide III Peptide Backbone UV Resonance Raman Bands , 2004 .

[34]  Seungsoo Hahn,et al.  Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: constrained MD simulation studies. , 2006, Biopolymers.

[35]  P. Hamm,et al.  Time-resolved two-dimensional vibrational spectroscopy of a short α-helix in water , 2001 .

[36]  C. Toniolo,et al.  Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. , 2002, Biopolymers.

[37]  S. Asher,et al.  Peptide bond vibrational coupling. , 2007, The journal of physical chemistry. B.

[38]  C. Toniolo,et al.  Onset of 3(10)-helical secondary structure in aib oligopeptides probed by coherent 2D IR spectroscopy. , 2008, Journal of the American Chemical Society.

[39]  S. Krimm.  Infrared spectra and chain conformation of proteins. , 1962, Journal of molecular biology.

[40]  Chewook Lee,et al.  Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel beta-sheet polypeptides: simulation studies. , 2005, The Journal of chemical physics.

[41]  M. Diem,et al.  Solution-phase Raman studies of alanyl dipeptides and various isotopomers: a reevaluation of the amide III vibrational assignment , 1984 .

[42]  Ewan W Blanch,et al.  A new perspective on beta-sheet structures using vibrational Raman optical activity: from poly(L-lysine) to the prion protein. , 2003, Journal of the American Chemical Society.

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

[44]  R. Schweitzer‐Stenner.  Secondary structure analysis of polypeptides based on an excitonic coupling model to describe the band profile of amide I' of IR, raman, and vibrational circular dichroism spectra , 2004 .

[45]  Andrei Tokmakoff,et al.  Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Prabuddha Mukherjee,et al.  Picosecond dynamics of a membrane protein revealed by 2D IR. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[47]  N. Berova,et al.  Circular Dichroism: Principles and Applications , 1994 .

[48]  Joong-Soo Kim,et al.  Amide I vibrational circular dichroism of polypeptides: generalized fragmentation approximation method. , 2005, The Journal of chemical physics.

[49]  A. Tokmakoff,et al.  The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide. , 2006, The journal of physical chemistry. B.

[50]  Leo Radom,et al.  Harmonic Vibrational Frequencies: An Evaluation of Hartree−Fock, Møller−Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors , 1996 .

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

[52]  Chewook Lee,et al.  Vibrational dynamics of DNA. I. Vibrational basis modes and couplings. , 2006, The Journal of chemical physics.

[53]  H. Susi,et al.  Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. , 1986, Methods in enzymology.

[54]  J. Knoester,et al.  A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy. , 2006, The Journal of chemical physics.

[55]  A. Tokmakoff,et al.  Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity. , 2009, Journal of the American Chemical Society.

[56]  Timothy A. Keiderling,et al.  Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra , 1997 .

[57]  A. Tokmakoff,et al.  Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy. , 2004, The Journal of chemical physics.

[58]  Andrei Tokmakoff,et al.  Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure. , 2004, Journal of the American Chemical Society.

[59]  S. Mukamel,et al.  Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides. , 2007, The journal of physical chemistry. B.

[60]  M. Tasumi,et al.  Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di‐ and tripeptides and considerations on the conformation of the extended helix , 1998 .

[61]  Minhaeng Cho,et al.  Coherent two-dimensional optical spectroscopy. , 2008, Chemical reviews.

[62]  S. Mukamel,et al.  Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map. , 2006, The Journal of chemical physics.

[63]  S. Mukamel,et al.  Linear and nonlinear infrared signatures of local α- and 310-helical structures in alanine polypeptides , 2003 .

[64]  T. Jansen,et al.  Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide. , 2006, The journal of physical chemistry. B.

[65]  I. Chabay,et al.  Optical Activity of Vibrational Transitions: A Coupled Oscillator Model , 1972 .

[66]  J. Choi,et al.  Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis. , 2004, The Journal of chemical physics.

[67]  T. Keiderling,et al.  Protein and peptide secondary structure and conformational determination with vibrational circular dichroism. , 2002, Current opinion in chemical biology.

[68]  A. Tokmakoff,et al.  Amide I two-dimensional infrared spectroscopy of proteins. , 2008, Accounts of chemical research.

[69]  R. Hochstrasser,et al.  Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide. , 2008, The journal of physical chemistry. B.

[70]  S. Ham,et al.  Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water. , 2005, The journal of physical chemistry. B.

[71]  T. Keiderling,et al.  Discrimination between Peptide 310- and α-Helices. Theoretical Analysis of the Impact of α-Methyl Substitution on Experimental Spectra , 2002 .

[72]  T. Keiderling,et al.  Characterization of alanine-rich peptides, Ac-(AAKAA)n-GY-NH2 (n = 1-4), using vibrational circular dichroism and Fourier transform infrared. Conformational determination and thermal unfolding. , 1997, Biochemistry.

[73]  T. Keiderling,et al.  Differentiation of β-Sheet-Forming Structures: Ab Initio-Based Simulations of IR Absorption and Vibrational CD for Model Peptide and Protein β-Sheets , 2001 .

[74]  J. Skinner,et al.  Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches. , 2004, The Journal of chemical physics.

[75]  M. Zanni,et al.  Tracking fiber formation in human islet amyloid polypeptide with automated 2D-IR spectroscopy. , 2008, Journal of the American Chemical Society.

[76]  J. Choi,et al.  Computational spectroscopy of ubiquitin: comparison between theory and experiments. , 2007, The Journal of chemical physics.

[77]  S. Krimm,et al.  Ab initio-based vibrational analysis of α-poly( L -alanine) , 1998 .

[78]  S. Bykov,et al.  Peptide secondary structure folding reaction coordinate: correlation between uv raman amide III frequency, Psi Ramachandran angle, and hydrogen bonding. , 2006, The journal of physical chemistry. B.

[79]  R. Hochstrasser,et al.  Local Structure of β-Hairpin Isotopomers by FTIR, 2D IR, and Ab Initio Theory , 2006 .