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ABSTRACT: The vibrational dynamics of liquid water, which result from a complex interplay between internal molecular vibrations and the fluctuating hydrogen bond network, are fundamental to many physicochemical and biological processes. Using a new ultrafast broadband mid-infrared light source with over 2000 cm(-1) of bandwidth, we performed ultrafast time-resolved infrared spectroscopy to study the vibrational couplings and relaxation dynamics of the stretching and bending vibrations of the mixed isotopologue, HOD, in D2O. Analysis of cross-peaks and induced absorptions in the two-dimensional infrared spectrum and transient absorption spectrum shows that the hydroxyl stretch of HOD is coupled to the HOD bending mode via Fermi resonance, with a 70° angle between their transition dipole moments. We see that HOD is also anharmonically coupled to the D2O solvent modes. From transient absorption spectra, we conclude that vibrational relaxation occurs through a number of paths. The strongly hydrogen bonded OH oscillators have the highest propensity to relax through the bending mode while the weakly hydrogen bonded oscillators relax through other modes.
The Journal of Physical Chemistry B 05/2013; · 3.70 Impact Factor
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ABSTRACT: The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm(-1) for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm(-1). These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.
The Journal of chemical physics 04/2013; 138(13):134116. · 3.09 Impact Factor
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ABSTRACT: Cold denaturation is a general property of globular proteins, but it is difficult to directly characterize since the transition temperature of protein cold denaturation, Tc, is often below the freezing point of water. As a result, studies of protein cold denaturation are often facilitated by addition of denaturants, or by using destabilizing pHs, or extremes of pressure, or by reverse micelle encapsulation, and there are few studies of cold induced unfolding under near native conditions. The thermal and denaturant induced unfolding of single domain proteins is usually cooperative, but the cooperativity of cold denaturation is controversial. The issue is of both fundamental and practical importance since cold unfolding may reveal information about otherwise inaccessible partially unfolded states and because many therapeutic proteins need to be stabilized against cold unfolding. It is thus desirable to obtain more information about the process under non-perturbing conditions. The ability to access cold denaturation in native buffer is also very useful for characterizing protein thermodynamics, especially when other methods are not applicable. In this work, we study a point mutant of the C-terminal domain of the ribosomal protein L9 (CTL9) which has a Tc above 0 C. The mutant was designed to enable the study of cold denaturation under near native conditions. The cold denaturation process of I98A CTL9 was characterized by NMR, CD, and FTIR. The results are consistent with apparently cooperative, two-state cold unfolding. SAXS studies show that the unfolded state expands as the temperature is lowered.
Biochemistry 03/2013; · 3.42 Impact Factor
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ABSTRACT: We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I' vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I' β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism.
Proceedings of the National Academy of Sciences 02/2013; · 9.68 Impact Factor
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ABSTRACT: Network layouts are introduced as a method to visualize couplings between local amide I vibrations in proteins. The method is used to identify groups of strongly-coupled oscillators in order to block-diagonalize the Hamiltonians, considerably reducing the expense associated with computing infrared spectra of large proteins. The quality of linear and nonlinear spectra generated from block-diagonal Hamiltonians is demonstrated by comparison with spectra generated from full Hamiltonian trajectories. A library of six proteins reveals that vibrational couplings within hydrogen-bonded residues in specific secondary structures give rise to the characteristic amide I lineshapes whereas other couplings play a minor role. Exciton delocalization analyses indicate that amide I vibrations in proteins remain largely localized to groups of less than ten residues.
The Journal of Physical Chemistry A 12/2012; · 2.95 Impact Factor
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ABSTRACT: The tautomerism of aromatic heterocycles is of great interest because it directly affects their chemical properties and biological function. The tautomerism of 2-pyridone, 6-chloro-2-pyridone, and 4-pyrimidinone have been examined in D(2)O using FTIR, two-dimensional IR (2D IR) spectroscopy and density functional theory (DFT) calculations. Using the 2D IR cross-peak patterns, the lactim tautomer of 6-chloro-2-pyridone was separated from the lactam tautomer, and its population was observed to increase with temperature. The equilibrium constant of [lac-tam]/[lactim] was determined to be 2.1 at room temperature for 6-chloro-2-pyridone. Similarly, the N1H and N3H lactam tautomers of 4-pyrimidinone were identified with 2D IR. To assign the vibrational modes of different tautomers, DFT calculations of these chemical species were performed with explicit water molecules, and the hydration effects on the vibrational frequencies and intensities were established.
Journal of Physical Chemistry Letters 10/2012; 3(22):3302-3306. · 6.21 Impact Factor
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ABSTRACT: We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.
The Journal of chemical physics 04/2012; 136(13):134507. · 3.09 Impact Factor
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ABSTRACT: We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550-1720 cm(-1)). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.
The Analyst 03/2012; 137(8):1793-9. · 4.23 Impact Factor
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ABSTRACT: The peptide amide-I vibration of a proline turn encodes information on the turn structure. In this study, FTIR, two-dimensional IR spectroscopy and molecular dynamics simulations were employed to characterize the varying turn conformations that exist in the GVGX(L)PGVG family of disordered peptides. This analysis revealed that changing the size of the side chain at the X amino acid site from Gly to Ala to Val substantially alters the conformation of the peptide. To quantify this effect, proline peak shifts and intensity changes were compared to a structure-based spectroscopic model. These simulated spectra were used to assign the population of type-II β turns, bulged turns, and irregular β turns for each peptide. Of particular interest was the Val variant commonly found in the protein elastin, which contained a 25% population of irregular β turns containing two peptide hydrogen bonds to the proline C═O.
Journal of the American Chemical Society 03/2012; 134(11):5032-5. · 9.91 Impact Factor
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ABSTRACT: We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.
The Journal of chemical physics 12/2011; 135(23):234507. · 3.09 Impact Factor
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ABSTRACT: Despite a large body of work, the exact molecular details underlying
ion-selectivity and transport in the potassium channel have not been fully laid
to rest. One major reason has been the lack of experimental methods that can
probe these mechanisms dynamically on their biologically relevant time scales.
Recently it was suggested that quantum coherence and its interplay with thermal
vibration might be involved in mediating ion-selectivity and transport. In this
work we present an experimental strategy for using time resolved infrared
spectroscopy to investigate these effects. We show the feasibility by
demonstrating the IR absorption and Raman spectroscopic signatures of potassium
binding model molecules that mimic the transient interactions of potassium with
binding sites of the selectivity filter during ion conduction. In addition to
guide our experiments on the real system we have performed molecular
dynamic-based simulations of the FTIR and 2DIR spectra of the entire KcsA
complex, which is the largest complex for which such modeling has been
performed. We found that by combing isotope labeling with 2D IR spectroscopy,
the signatures of potassium interaction with individual binding sites would be
experimentally observable and identified specific labeling combinations that
would maximize our expected experimental signatures.
10/2011;
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ABSTRACT: Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.
Journal of the American Chemical Society 08/2011; 133(39):15650-60. · 9.91 Impact Factor
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ABSTRACT: Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.
The Journal of chemical physics 08/2011; 135(5):054509. · 3.09 Impact Factor
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ABSTRACT: We use temperature-dependent ultrafast infrared spectroscopy of dilute HOD in H(2)O to study the picosecond reorganization of the hydrogen bond network of liquid water. Temperature-dependent two-dimensional infrared (2D IR), pump-probe, and linear absorption measurements are self-consistently analyzed with a response function formalism that includes the effects of spectral diffusion, population lifetime, reorientational motion, and nonequilibrium heating of the local environment upon vibrational relaxation. Over the range 278-345 K, we find the time scales of spectral diffusion and reorientational relaxation decrease from approximately 2.4 to 0.7 ps and 4.6 to 1.2 ps, respectively, which corresponds to barrier heights of 3.4 and 3.7 kcal/mol, respectively. We compare the temperature dependence of the time scales to a number of measures of structural relaxation and find similar effective activation barrier heights and slightly non-Arrhenius behavior, which suggests that the reaction coordinate for the hydrogen bond rearrangement in water is collective. Frequency and orientational correlation functions computed from molecular dynamics (MD) simulations over the same temperature range support our interpretations. Finally, we find the lifetime of the OD stretch is nearly the same from 278 K to room temperature and then increases as the temperature is increased to 345 K.
The Journal of Physical Chemistry B 03/2011; 115(18):5604-16. · 3.70 Impact Factor
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ABSTRACT: While it is generally recognized that the hydroxide ion can rapidly diffuse through aqueous solution due to its ability to accept a proton from a neighboring water molecule, a description of the OH(-) solvation structure and mechanism of proton transfer to the ion remains controversial. In this report, we present the results of femtosecond infrared spectroscopy measurements of the O-H stretching transition of dilute HOD dissolved in NaOD/D(2)O. Pump-probe, photon echo peak shift, and two-dimensional infrared spectroscopy experiments performed as a function of deuteroxide concentration are used to assign spectral signatures that arise from the OH(-) ion and its solvation shell. A spectral feature that decays on a ∼110 fs time scale is assigned to the relaxation of transiently formed configurations wherein a proton is equally shared between a HOD molecule and an OD(-) ion. Over picosecond waiting times, features appear in 2D IR spectra that are indicative of the exchange of population between OH(-) ions and HOD molecules due to deuteron transfer. The construction of a spectral model that includes spectral relaxation, chemical exchange, and thermalization processes, and self-consistently treats all of our data, allows us to qualitatively explain the results of our experiments and gives a lower bound of 3 ps for the deuteron transfer kinetics.
The Journal of Physical Chemistry A 02/2011; 115(16):3957-72. · 2.95 Impact Factor
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ABSTRACT: Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides.
The Journal of Physical Chemistry B 09/2010; 114(34):10913-24. · 3.70 Impact Factor
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ABSTRACT: Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the β-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the β-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I′ β-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 °C, the fraction of population with a type I′ turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides.
08/2010;
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ABSTRACT: A compact and stable method for generating high-intensity linearly polarized continuum mid-IR and terahertz light using ultrafast femtosecond (fs) laser pulses is demonstrated. Continuous light generation from <400 cm(-1) (12 THz, 25 microm) to >3300 cm(-1) (100 THz, 3 microm) in a sub-100 fs laser pulse is facilitated by nonlinear mixing of the fundamental, second harmonic, and third harmonic of an ultrafast amplified laser source through filamentation in air. Including the third harmonic in the mixing scheme leads to a tenfold increase in the generated IR power. The compact optical configuration utilizing a delay plate in a collinear geometry serves to simplify alignment and increase stability, making it a practical source for transient IR spectroscopy.
Optics Letters 06/2010; 35(12):1962-4. · 3.40 Impact Factor
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ABSTRACT: The monomer-dimer transition of insulin has been probed with two-dimensional infrared spectroscopy and related infrared spectroscopies to isolate spectral signatures of the conformational changes concomitant with dissociation. These experiments were atomistically interpreted using 2D IR spectra calculated from an ensemble of monomer and dimer structures including the effects of disorder, which provided a complement and a point of comparison to NMR and X-ray crystallography models. The amide I nu(perpendicular) mode, which is delocalized over both monomer units through an intermolecular antiparallel beta sheet, was lost upon dimer dissociation and shifts were observed in the nu(parallel)beta-sheet and alpha-helix bands. These spectral changes provided a structurally sensitive probe of dimer dissociation, which was used to measure the binding constant, K(D), and to parameterize a thermodynamic model for the dimer fraction. The solvent conditions surveyed the effects of ethanol and salt addition on the dimer fraction in acidic, deuterated water as a function of temperature. It was found that addition of ethanol had a significant destabilizing effect on the dimer state, and shifted K(D) from 70 microM in D(2)O to 7.0 mM in 20% EtOD at 22 degrees C. Simulation of the monomer 2D IR spectra indicates that the B-chain C terminus is partially disordered, although not fully solvated by water.
Physical Chemistry Chemical Physics 04/2010; 12(14):3579-88. · 3.57 Impact Factor
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ABSTRACT: We use temperature-dependent two-dimensional infrared spectroscopy (2D IR) of dilute HOD in H2O to investigate hydrogen bond rearrangements in water. The OD stretching frequency is sensitive to its environment, and loss of frequency correlation provides a picture of local and collective hydrogen bond dynamics. The time scales for hydrogen bond rearrangements decrease from roughly 2 ps at 278 K to 0.5 ps at 345 K. We find the barrier to dephasing and hydrogen bond switching to be Ea = 3.4 ± 0.5 kcal/mol, although the trend is slightly non-Arrhenius. The value is in good agreement with the reported barrier height for OD reorientation observed in pump−probe anisotropy measurements. This provides evidence for the proposal that hydrogen bond switching occurs through concerted large angular jump reorientation. MD simulations of temperature-dependent OD vibrational dephasing and orientational correlation functions are used to support our conclusions.Keywords (keywords): water; hydrogen bond dynamics; temperature dependence; ultrafast spectroscopy; molecular dynamics; pump−probe geometry
03/2010;
