Amide modes and protein conformation.

Spectroscopic study of extracellular polymeric substances from Bacillus subtilis: aqueous chemistry and adsorption effects.

Identification of β-turn and random coil amide III infrared bands for secondary structure estimation of proteins

An empirical correction to amide group vacuum force fields is proposed in order to account for the influence of the aqueous environment on the C=O stretching vibration (amide I). The dependence of the vibrational absorption spectral intensities on the geometry is studied with density functional theory methods at the BPW91/6-31G** level for N-methyl acetamide interacting with a variety of of water molecule clusters hydrogen bonded to it. These cluster results are then generalized to form an empirical correction for the force field and dipole intensity of the amide I (C=O stretch) mode. As an example of its extension, the method is applied to a larger (β-turn model) peptide molecule and its IR spectrum is simulated. The method provides realistic bandwidths for the amide I bands if the spectra are generated from the ab initio force field corrected by perturbation from an ensemble of solvent geometries obtained using molecular dynamic simulations.

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Empirical modeling of the peptide amide I band IR intensity in water solution

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.

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

Heat denaturation of albumin aqueous solution enables us to control the α-helix content to a reasonable level, and denatured albumin, whose conformation is different, can be obtained. Fourier transform-infrared absorption spectra in the amide I, II, and III band regions of these albumins have been measured and compared with each other. As a result, the characteristic frequencies associated with each conformation of α-helix, β-sheet, and random structure have been observed; moreover it has been newly proved that the intensity ratio of the amide II band to the amide I band depends on the α-helix content in albumin. In this paper, we demonstrate that this intensity ratio is very useful for quantitative estimation of α-helix content in albumin and apply this method to analysis of ATR spectra of albumin adsorbed on polyethylene surface.

Tomoko Matsui

Papers

Quantitative Estimation of α-Helix Coil Content in Bovine Serum Albumin by Fourier Transform-Infrared Spectroscopy