Two-Dimensional Heterospectral Correlation Analysis of the Redox-Induced Conformational Transition in Cytochrome c Using Surface-Enhanced Raman and Infrared Absorption Spectroscopies on a Two-Layer Gold Surface

The heme protein cytochrome c adsorbed to a two-layer gold surface modified with a self-assembled monolayer of 2-mercaptoethanol was analyzed using a two-dimensional (2D) heterospectral correlation analysis that combined surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise increasing electric potentials were applied to alter the redox state of the protein and to induce conformational changes within the protein backbone. We demonstrate herein that 2D heterospectral correlation analysis is a particularly suitable and useful technique for the study of heme-containing proteins as the two spectroscopies address different portions of the protein. Thus, by correlating SERS and SEIRAS data in a 2D plot, we can obtain a deeper understanding of the conformational changes occurring at the redox center and in the supporting protein backbone during the electron transfer process. The correlation analyses are complemented by molecular dynamics calculations to explore the intramolecular interactions.

[1]  G. Brayer,et al.  High-resolution three-dimensional structure of horse heart cytochrome c. , 1990, Journal of molecular biology.

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

[3]  F. Meersman,et al.  A principal component analysis and two-dimensional correlation infrared spectroscopy study on the thermal unfolding of ribonuclease A under reducing conditions , 2008 .

[4]  Yukihiro Ozaki,et al.  Two-Dimensional Infrared, Two-Dimensional Raman, and Two-Dimensional Infrared and Raman Heterospectral Correlation Studies of Secondary Structure of β-Lactoglobulin in Buffer Solutions , 2000 .

[5]  P. Karplus,et al.  (φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. , 2012, Journal of molecular biology.

[6]  E. Margoliash,et al.  Coupling to Lysine-13 Promotes Electron Tunneling through Carboxylate-Terminated Alkanethiol Self-Assembled Monolayers to Cytochrome c , 2003 .

[7]  Tim N. Heinz,et al.  Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations , 2001 .

[8]  R. Dickerson,et al.  Conformation change of cytochrome c. I. Ferrocytochrome c structure refined at 1.5 A resolution. , 1981, Journal of molecular biology.

[9]  Wilfred F van Gunsteren,et al.  GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. , 2011, Journal of chemical theory and computation.

[10]  L. G. Lopes,et al.  Electrochemistry, surface plasmon resonance, and quartz crystal microbalance: an associative study on cytochrome c adsorption on pyridine tail-group monolayers on gold. , 2013, The journal of physical chemistry. B.

[11]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[12]  A. E. Dowrey,et al.  Generalized Two-Dimensional Correlation Spectroscopy , 2000 .

[13]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[14]  Isao Noda,et al.  Two-dimensional correlation spectroscopy — Biannual survey 2007–2009 , 2010 .

[15]  W. Knoll,et al.  Electron Transfer Kinetics of Cytochrome C in the Submillisecond Time Regime Using Time-Resolved Surface-Enhanced Infrared Absorption Spectroscopy , 2009 .

[16]  J. Heberle,et al.  Functional vibrational spectroscopy of a cytochrome c monolayer: SEIDAS probes the interaction with different surface-modified electrodes. , 2004, Journal of the American Chemical Society.

[17]  Redox reactions of heme-containing metalloproteins: dynamic effects of self-assembled monolayers on thermodynamics and kinetics of cytochrome c electron-transfer reactions , 2000 .

[18]  Markus Christen,et al.  Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation , 2012, Comput. Phys. Commun..

[19]  Steven S Saavedra,et al.  Molecular orientation distributions in protein films. 1. Cytochrome c adsorbed to substrates of variable surface chemistry , 1997 .

[20]  I. Noda Generalized Two-Dimensional Correlation Method Applicable to Infrared, Raman, and other Types of Spectroscopy , 1993 .

[21]  Henry H. Mantsch,et al.  Two Dimensional Infrared Spectroscopy , 1993 .

[22]  Yukihiro Ozaki,et al.  Two-Dimensional Correlation Spectroscopy: Applications in Vibrational and Optical Spectroscopy , 2002 .

[23]  Isao Noda,et al.  Two-dimensional correlation spectroscopy , 2002 .

[24]  H. Roder,et al.  Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c. , 1990, Biochemistry.

[25]  R. Dickerson,et al.  Conformation change of cytochrome c. II. Ferricytochrome c refinement at 1.8 A and comparison with the ferrocytochrome structure. , 1981, Journal of molecular biology.

[26]  S. Saavedra,et al.  Molecular Orientation Distributions in Protein Films. V. Cytochrome c Adsorbed to a Sulfonate-Terminated, Self-Assembled Monolayer† , 2003 .

[27]  W. Knoll,et al.  A Two-Layer Gold Surface with Improved Surface Enhancement for Spectro-Electrochemistry Using Surface-Enhanced Infrared Absorption Spectroscopy , 2009, Applied spectroscopy.

[28]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[29]  Andreas P. Eichenberger,et al.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7 , 2011, European Biophysics Journal.

[30]  Christopher C. Moser,et al.  Natural engineering principles of electron tunnelling in biological oxidation–reduction , 1999, Nature.

[31]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[32]  K. Eisenthal,et al.  Protein Adsorption at Interfaces Detected by Second Harmonic Generation , 2000 .

[33]  M. Marchi,et al.  Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: The first steps , 2009, The European physical journal. E, Soft matter.

[34]  Yukihiro Ozaki,et al.  Two-Dimensional Correlation Spectroscopy - Applications in Vibrational and Optical Spectroscopy: Noda/Two-Dimensional Correlation Spectroscopy - Applications in Vibrational and Optical Spectroscopy , 2005 .

[35]  Thomas G. Spiro,et al.  Complete assignment of cytochrome c resonance Raman spectra via enzymic reconstitution with isotopically labeled hemes , 1993 .

[36]  Y. Ozaki,et al.  Two-Dimensional Correlation Spectroscopy Study of Temperature-Dependent Spectral Variations of N-Methylacetamide in the Pure Liquid State. 2. Two-Dimensional Raman and Infrared−Raman Heterospectral Analysis , 1996 .

[37]  H. Gray,et al.  Solution structure of oxidized horse heart cytochrome c. , 1997, Biochemistry.

[38]  Y. Ozaki,et al.  Raman imaging analysis of pharmaceutical tablets by two-dimensional (2D) correlation spectroscopy , 2009 .

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

[40]  R. Gennis,et al.  2D-SEIRA spectroscopy to highlight conformational changes of the cytochrome c oxidase induced by direct electron transfer. , 2011, Metallomics : integrated biometal science.

[41]  Isao Noda,et al.  Two-Dimensional Infrared (2D IR) Spectroscopy: Theory and Applications , 1990 .

[42]  Katz,et al.  Integration of Layered Redox Proteins and Conductive Supports for Bioelectronic Applications. , 2000, Angewandte Chemie.

[43]  K. Niki,et al.  Long-range electron-transfer reaction rates to cytochromec across long- and short-chain alkanethiol self-assembledmonolayers: Electroreflectancestudies , 1997 .

[44]  W. Caughey,et al.  Redox-dependent changes in beta-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra. , 1992, Biochemistry.

[45]  T. Cotton,et al.  An electrochemical approach to investigate gated electron transfer using a physiological model system: Cytochrome c immobilized on carboxylic acid-terminated alkanethiol self-assembled monolayers on gold electrodes , 2000 .

[46]  W. Mäntele,et al.  Redox-linked conformational changes in proteins detected by a combination of infrared spectroscopy and protein electrochemistry. Evaluation of the technique with cytochrome c. , 1990, European journal of biochemistry.