Nature of vibrational frequency modulations and the related one- and two-dimensional vibrational spectral features analysed for the amide I mode of tetraalanine in aqueous solution

A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures

Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.

Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.

Theoretical Sum Frequency Generation Spectroscopy of Peptides

Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called "chiral" SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore's orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.

Modeling the vibrational dynamics and nonlinear infrared spectra of coupled amide I and II modes in peptides

The amide vibrational modes play an important role in energy transport and relaxation in polypeptides and proteins and provide us with spectral markers for structure and structural dynamics of these macromolecules. Here, we present a detailed model to describe the dynamic properties of the amide I and amide II modes and the resulting linear and nonlinear spectra. These two modes have large oscillator strengths, and their mutual coupling plays an important role in their relaxation. Using first-principles calculations of NMA-d(7) and a dipeptide in a fluctuating bath described by molecular dynamics simulations, we model the frequencies of the local vibrations as well as the coupling between them. Both the coherent couplings and the fluctuations induced by contact with their environment are taken into account. We apply the resulting model of interacting fluctuating oscillators to study the collective vibrations and the partially coherent transport of vibrational energy through a model α-helix. We find that the instantaneous vibrations are delocalized over a few (up to four) amide units, while the coherences in the helix survive for 0.5-1 ps, leading to coherent transport on a similar time scale.

Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase

Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.