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Andrei Tokmakoff

Publications and source records attributed to Andrei Tokmakoff.

17 recordsLinked to original sources
PubMed2006

Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange two-dimensional infrared spectroscopy.

Two-dimensional infrared spectroscopy in conjunction with hydrogen-deuterium exchange experiments provides detailed information about solvent penetration into protein structure. Correlating the secondary-structure sensitivity of the amide I vibration and the solvent-exposure sensitivity of amide II provides a direct probe of solvent-inaccessible residues of proteins embedded in the hydrophobic core or those involved in strong hydrogen bonds in secondary structures. Distinct spectral signatures of the cross-peak region arising from the coupling of the amide I and II modes imply a significant degree of structural stability of hydrogen-bonded contacts in alpha-helices and beta-sheets in a series of proteins. Ubiquitin, an alpha/beta-protein, exhibits strong alpha-helical signatures and lacks those of the beta-sheet in the cross-peak region, demonstrating that ubiquitin's beta-sheet exchanges protons with the surrounding solvent and is conformationally unstable.

Amides↗
PubMed2006

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes.

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.

Journal Article↗
PubMed2006

Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics.

We use multidimensional infrared spectroscopy of the OH stretch of HOD in D2O to measure the interconversion of different hydrogen bonding environments. The OH stretching frequency distinguishes hydrogen bonded (HB) and non-hydrogen-bonded (NHB) configurations by their absorption on the low (red) and high (blue) sides of the line shape. Measured asymmetries in the two dimensional infrared OH line shapes are manifestations of the fundamentally different spectral relaxations of HB and NHB. HB oscillators exhibit coherent oscillations within the hydrogen-bonded free energy well before undergoing activated barrier crossing, resulting in the exchange of hydrogen bonded partners. Conversely, NHB oscillators rapidly return to HB frequencies within 150 fs. These results support a picture where NHB configurations are only visited transiently during large fluctuations about a hydrogen bond or during the switching of hydrogen bonding partners. The results are not consistent with the presence of entropically stabilized dangling hydrogen bonds or a conceptual picture of water as a mixture of environments with varying hydrogen bond strength separated by barriers >kT.

Journal Article↗
PubMed2006

The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide.

We investigate the influence of isotopic substitution and solvation of N-methylacetamide (NMA) on anharmonic vibrational coupling and vibrational relaxation of the amide I and amide II modes. Differences in the anharmonic potential of isotopic derivatives of NMA in D2O and DMSO-d6 are quantified by extraction of the anharmonic parameters and the transition dipole moment angles from cross-peaks in the two-dimensional infrared (2D-IR) spectra. To interpret the effects of isotopic substitution and solvent interaction on the anharmonic potential, density functional theory and potential energy distribution calculations are performed. It is shown that the origin of anharmonic variation arises from differing local mode contributions to the normal modes of the NMA isotopologues, particularly in amide II. The time domain manifestation of the coupling is the coherent exchange of excitation between amide modes seen as the quantum beats in femtosecond pump-probes. The biphasic behavior of population relaxation of the pump-probe and 2D-IR experiments can be understood by the rapid exchange of strongly coupled modes within the peptide backbone, followed by picosecond dissipation into weakly coupled modes of the bath.

Acetamides↗
PubMed2006

Characterization of spectral diffusion from two-dimensional line shapes.

The analysis of line shapes in two-dimensional optical and infrared spectroscopies is a powerful approach to characterizing the dynamics of molecules in the condensed phase. Changes in line shape from diagonally elongated to symmetric as a function of waiting time arise from evolution of the transition frequency. We describe a number of quantitative measures of frequency fluctuations and spectral diffusion through the analysis of two-dimensional (2D) line shapes. These metrics are identical to the system's frequency correlation function and independent of population relaxation in the limit of a short time approximation for the 2D response. We also test the broader applicability of these expressions for analyzing three-level vibrational systems and experiments with finite pulses.

Journal Article↗
PubMed2006

Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra.

A model for the calculation of amide I FTIR and 2DIR spectra taking into account fluctuations in hydrogen bonding and structure from molecular dynamics (MD) simulations is tested on three systems. It is found that although the homogeneous lineshape approximation yields satisfactory FTIR spectra, 2DIR spectra are sensitive to the inhomogeneity naturally present in any solvated protein and the common approximations of a static structure and averaged-effect solvent are invalid. By building on the local amide Hamiltonian and incorporating site energy variation with electrostatic-based models and disorder from MD trajectories, good agreement is obtained between calculated and measured 2DIR spectra. The largest contribution to the observed inhomogeneity is found to be the fluctuating site energies, which in turn are most sensitive to the water solvent. With the ability to accurately predict 2DIR spectra from atomistic simulations, new opportunities to test force fields and mechanistic predictions from MD are revealed.

Computer Simulation↗
PubMed2006

Visualization and characterization of the infrared active amide I vibrations of proteins.

To facilitate the analysis of frequency-structure correlations in the amide I vibrational spectroscopy of proteins, we investigate visualization methods and spatial correlation functions that describe delocalized vibrations of proteins and protein secondary structures. To study those vibrational modes revealed in infrared spectroscopy, we characterize frequency-dependent bright states obtained from doorway mode analysis. Our visualization methods pictorially color code amplitude and phase of each oscillator within the structure to reveal spatially varying patterns characteristic of excitations within sheets and helices. Spatial correlation functions in the amplitude and phase of amide I oscillators quantitatively address the extent of delocalization and the alpha helical and beta sheet character of these modes. Specifically, we investigate the vibrations of idealized antiparallel beta sheets and alpha helices and perform case studies on three proteins: concanavalin A, myoglobin, and ubiquitin.

Amides↗
PubMed2006

Single-shot two-dimensional spectrometer.

A two-dimensional optical spectrometer is demonstrated using simple optical components. This spectrometer is based on ultrafast two-dimensional (2D) frequency-dispersed pump-probe spectroscopy and can be used for single-shot correlation spectroscopy. To demonstrate functionality of this device, we measure the 2D correlation spectrum of atomic rubidium.

Journal Article↗
PubMed2005

Electric field fluctuations drive vibrational dephasing in water.

We present a microscopic description of the vibrational spectroscopy of the OH stretch of HOD in liquid D(2)O. Our model predicts that OH frequency correlations decay with a sharp and rapid ( approximately 35 fs) decrease, followed by a beat at approximately 125 fs from intermolecular oxygen vibrations. On a short time scale ( approximately 200 fs), ultrafast infrared spectroscopy of the OH stretch is sensitive to localized intermolecular motions. For times longer than approximately 200 fs, cooperative molecular rearrangements drive dephasing. The interplay of electric field fluctuations, both local and cooperative, dictate vibrational frequency shifts and destroy vibrational coherence in water.

Computer Simulation↗
PubMed2005

Residual native structure in a thermally denatured beta-hairpin.

We investigate the thermal denaturation of trpzip2 between 15 and 82 degrees C using two-dimensional infrared (2D IR) vibrational spectroscopy, dispersed vibrational echo (DVE) spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. The FTIR and DVE spectra of trpzip2 show in the amide I region of the spectrum two resonances, which arise primarily from the interstrand coupling between local amide I oscillators along the peptide backbone. The coupling is seen directly in the 2D IR spectra as the formation of cross-peak ridges. Although small shifts of these frequencies occur on heating the sample, the existence of cross-peak ridges at all temperatures indicates that stable hydrogen bond interactions persist between the two beta-strands. These observations indicate a significant amount of native structure in the thermally denatured state of trpzip2.

Hot Temperature↗
PubMed2005

Polarizable molecules in the vibrational spectroscopy of water.

We examine the role of electronic polarizability in water on short (tens of femtoseconds), intermediate (hundreds of femtoseconds), and long (approximately 1 ps) time scales by comparing molecular dynamics results to experimental data for vibrational spectroscopy of HOD in liquid D2O. Because the OH absorption frequency is sensitive to the details of the atomic forces experienced in the liquid, our results provide important quantitative comparisons for several popular empirical water potentials. When compared with their fixed-charge counterparts, the polarizable models give similar slower long time constants for the decay of vibrational correlations and re-orientational motion that is in better agreement with experiments. Polarizable potentials yield qualitatively dissimilar predictions for frequency fluctuations and transition dipole moment fluctuations at equilibrium. Models that confine the polarizability to the plane of the molecule (i.e., TIP4P-FQ) overestimate the width of the distribution describing frequency fluctuations by more than a factor of two. These models also underestimate the amplitude of the hydrogen-bond stretch at 170 cm(-1). A potential that has both an out-of-plane polarization and fluctuating charges, POL5-TZ, compares best with experiments. We interpret our findings in terms of microscopic dynamics and make suggestions that may improve the quality of emerging polarizable force fields for water.

Journal Article↗
PubMed2005

Upconversion multichannel infrared spectrometer.

A multichannel IR spectrometer using a standard silicon CCD array is demonstrated. Sum frequency generation between an ultrafast optical pulse and a frequency-dispersed IR beam generates a spatially extended optical signal that is collected on a generic CCD video camera. This method provides an inexpensive and efficient alternative to conventional multichannel IR arrays.

Journal Article↗
PubMed2005

Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D(2)O.

We present an investigation into hydrogen bonding dynamics and kinetics in water using femtosecond infrared spectroscopy of the OH stretching vibration of HOD in D(2)O. Infrared vibrational echo peak shift and polarization-selective pump-probe experiments were performed with mid-IR pulses short enough to capture all relevant dynamical processes. The experiments are self-consistently analyzed with a nonlinear response function expressed in terms of three dynamical parameters for the OH stretching vibration: the frequency correlation function, the lifetime, and the second Legendre polynomial dipole reorientation correlation function. It also accounts for vibrational-relaxation-induced excitation of intermolecular motion that appears as heating. The long time, picosecond behavior is consistent with previous work, but new dynamics are revealed on the sub-200 fs time scale. The frequency correlation function is characterized by a 50 fs decay and 180 fs beat associated with underdamped intermolecular vibrations of hydrogen bonding partners prior to 1.4 ps exponential relaxation. The reorientational correlation function observes a 50 fs librational decay prior to 3 ps diffusive reorientation. Both of these correlation functions compare favorably with the predictions from classical molecular dynamics simulations. The time-dependent behavior can be separated into short and long time scales by the 340 fs correlation time for OH frequency shifts. The fast time scales arise from dynamics that are mainly local: fluctuations in hydrogen bond distances and angles within relatively fixed intermolecular configurations. On time scales longer than the correlation time, dephasing and reorientations reflect collective reorganization of the liquid structure. Since the OH transition frequency and dipole are only weakly sensitive to these collective coordinates, this is a kinetic regime which gives an effective rate for exchange of intermolecular structures.

Journal Article↗
PubMed2005

Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.

Steady-state and transient conformational changes upon the thermal unfolding of ubiquitin were investigated with nonlinear IR spectroscopy of the amide I vibrations. Equilibrium temperature-dependent 2D IR spectroscopy reveals the unfolding of the beta-sheet of ubiquitin through the loss of cross peaks formed between transitions arising from delocalized vibrations of the beta-sheet. Transient unfolding after a nanosecond temperature jump is monitored with dispersed vibrational echo spectroscopy, a projection of the 2D IR spectrum. Whereas the equilibrium study follows a simple two-state unfolding, the transient experiments observe complex relaxation behavior that differs for various spectral components and spans 6 decades in time. The transient behavior can be separated into fast and slow time scales. From 100 ns to 0.5 ms, the spectral features associated with beta-sheet unfolding relax in a sequential, nonexponential manner, with time constants of 3 micros and 80 micros. By modeling the amide I vibrations of ubiquitin, this observation is explained as unfolding of the less stable strands III-V of the beta-sheet before unfolding of the hairpin that forms part of the hydrophobic core. This downhill unfolding is followed by exponential barrier-crossing kinetics on a 3-ms time scale.

Kinetics↗
PubMed2004

Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure.

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel beta-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel beta-sheet. In the proteins with antiparallel beta-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic "Z"-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.

Amides↗
PubMed2004

Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy.

Using idealized models for parallel and antiparallel beta sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition-dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel beta sheets and between beta hairpins and extended beta sheets.

Amides↗