Femtosecond IR pump-probe spectroscopy of nonlinear energy localization in protein models and model proteins

Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy

The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.

Interpretations of High-Order Transient Absorption Spectroscopies

Transient absorption (TA) spectroscopy is an invaluable tool for determining the energetics and dynamics of excited states. When pump intensities are sufficiently high, TA spectra include both the generally desired third-order response and responses that are higher in order in the field amplitudes. Recent work demonstrated that pump-intensity-dependent TA measurements allow separating the orders of response, but the information content in those higher orders has not been described. We give a general framework for understanding high-order TA spectra. We extend to higher order the fundamental processes of standard TA: ground-state bleach (GSB), stimulated emission (SE), and excited-state absorption (ESA). Each order introduces two new processes: SE and ESA from previously inaccessible highly excited states and negations of lower-order processes. We show the new spectral and dynamical information at each order and show how the relative signs of the signals in different orders can be used to identify which processes dominate.

Ultrafast vibrational coupling between C H and C O band of cyclic amide 2-Pyrrolidinone revealed by 2DIR spectroscopy

Coupling between C H and C O vibrational modes play an essential role on determination of biological structure and dynamics. However, due to the weakness of the C H absorption and strong absorption of the C O vibrational band make such experiments less straightforward than those with transitions of nearly the same strength. In this communication the characteristics of the C H and C O coupling has been studied using dual frequency two dimensional infrared spectroscopy. 2-Pyrrolidinone has been used as a model molecule of biological system. The coherent and incoherent couplings between C H and C O vibrational bands have been observed. The cross peaks dynamics have been discussed and time constant of the cross peak intensity has been calculated.

Coherent two-dimensional electronic and infrared crystallography

The two-dimensional electronic and infrared spectroscopy of oriented single crystals is sensitive to structure and point group symmetry. The third order response of crystals is generally different from measurements of isotropic solutions because each coherence path that contributes to the measured field scales to the ensemble average of the four-point correlation functions of the four field-dipole interactions involved in the respective Feynman paths. An analytical evaluation of 2D optical crystallography which depends on the crystal symmetry, laboratory orientation, and the orientation in the crystallographic frame is presented. Applying a symmetry operator in the basis of the allowed polarised radiation modes provides a method for evaluation of non-zero fourth rank tensor elements alternative to direct inspection methods. Uniaxial and biaxial systems are distinguished and the contributions to the rephasing and non-rephasing directions are evaluated for isolated and coupled oscillators. By exploiting coordinate analysis, the extension of non-linear electronic and infrared crystallography for coupled oscillators demonstrates the structural, directional, and symmetry dependent selection of coherences to the four-wave mixing signal.

Linear and non-linear infrared response of one-dimensional vibrational Holstein polarons in the anti-adiabatic limit: Optical and acoustical phonon models

The theory of linear and non-linear infrared response of vibrational Holstein polarons in one-dimensional lattices is presented in order to identify the spectral signatures of self-trapping phenomena. Using a canonical transformation, the optical response is computed from the small polaron point of view which is valid in the anti-adiabatic limit. Two types of phonon baths are considered: optical phonons and acoustical phonons, and simple expressions are derived for the infrared response. It is shown that for the case of optical phonons, the linear response can directly probe the polaron density of states. The model is used to interpret the experimental spectrum of crystalline acetanilide in the C=O range. For the case of acoustical phonons, it is shown that two bound states can be observed in the two-dimensional infrared spectrum at low temperature. At high temperature, analysis of the time-dependence of the two-dimensional infrared spectrum indicates that bath mediated correlations slow down spectral diffusion. The model is used to interpret the experimental linear-spectroscopy of model α-helix and β-sheet polypeptides. This work shows that the Davydov Hamiltonian cannot explain the observations in the NH stretching range.

Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH3CN, CHCl3, and CCl4), were examined using the N-H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics of NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N-H stretching mode was observed.

Reaction Dynamics of ATP Hydrolysis in Actin Determined by ab Initio Molecular Dynamics Simulations

Energy released by the hydrolysis of the high-energy phosphate bond of nucleoside triphosphate (NTP) cofactors is the driving force behind most biological processes. To understand how this energy is used to induce differences in protein structure and function, we examine the transfer of vibrational energy into the nucleotide-bound actin active site immediately after reaction activation. To this end, we perform Born-Oppenheimer molecular dynamics simulations of the active site at the level of density functional theory (DFT) starting at the calculated transition state (TS) structure. Similarly to the mechanism determined in many nucleotide-bound protein systems, the Os-Pγ bond is first elongated. Then, nucleophilic attack of the lytic water on Pγ occurs. Subsequently, protons are transferred in a cycle formed by water molecules, a protein residue, Asp154, and the γ-phosphate group, resulting in the formation of H2PO4(-). To investigate the possible creation of excited vibrational states in the products, power spectra of bond-length autocorrelation functions for relevant bonds within the active site are compared for simulations that start at the TS, at reactants, and at reaction end products. The hydroxyl bond formed in the final proton transfer to the phosphate molecule is observed to exhibit relatively high kinetic energies and large oscillations during reaction. It is also likely that some of the energy released by the reaction is captured by the low-energy stretching vibrations of the phosphoryl bonds of orthophosphate, which oscillate with large amplitudes in nonequilibrium simulations of end products.

Infrared protein crystallography

We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO(2). Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Vibron-phonon coupling strength in a finite size lattice of H-bonded peptide units

An attempt is made to measure the vibron-phonon coupling strength in a finite size lattice of H-bonded peptide units. Within a finite temperature density matrix approach, we compare separately the influence of both the vibron-phonon coupling and the dipole-dipole interaction on the coherence between the ground state and a local one-vibron state. Due to the confinement, it is shown that the vibron-phonon coupling yields a series of dephasing-rephasing mechanisms that prevents the coherence to decay. Similarly, the dipole-dipole interaction gives rise to quantum recurrences for specific revival times. Nevertheless, intense recurrences are rather rare events so that the coherence behaves as a random variable whose most probable value vanishes. By comparing the degree of the coherence for each interaction, a critical coupling chi*(L) is defined to discriminate between the weak and the strong coupling limits. Its size dependence indicates that the smaller the lattice size is, the weaker the vibron-phonon coupling relative to the dipole-dipole interaction is.

Vibron phonon in a lattice of H-bonded peptide units: A criterion to discriminate between the weak and the strong coupling limit

Based on dynamical considerations, a simple and intuitive criterion is established to measure the strength of the vibron-phonon coupling in a lattice of H-bonded peptide units. The main idea is to compare separately the influence of both the vibron-phonon coupling and the dipole-dipole interaction on a specific element of the vibron reduced density matrix. This element, which refers to the coherence between the ground state and a local excited amide-I mode, generalizes the concept of survival amplitude at finite temperature. On the one hand, when the dipole-dipole interaction is neglected, it is shown that dephasing-limited coherent dynamics is induced by the vibron-phonon coupling. On the other hand, when the vibron-phonon coupling is disregarded, decoherence occurs due to dipole-dipole interactions since the local excited state couples with neighboring local excited states. Therefore, our criterion simply states that the strongest interaction is responsible for the fastest decoherence. It yields a critical coupling chi( *) approximately 25 pN at biological temperature.

The Davydov/Scott model for energy storage and transport in proteins

The current status of the Davydov/Scott model for energy transfer in proteins is reviewed. After a brief introduction to the theoretical framework and to the basic results, the problems of finite temperature dynamics and of the full quantum and mixed quantum-classical approximations are described, as well as recent results obtained within each of these approximations. A short survey of experimental evidence in support of the Davydov/Scott model is made and absorption spectra are calculated that show the same temperature dependence as that measured in crystalline acetanilide. Future applications of the Davydov/Scott model to protein folding and function and to misfolding diseases are outlined.