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Register a new userHyperpolarization of Amino Acid Derivatives in Water for Biological Applications
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Louis-Serge Bouchard
Publication date
2017
fields
Physics
and research's language is
English
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We report on the successful synthesis and hyperpolarization of N unprotected {alpha} amino acid ethyl acrylate esters and extensively, on an alanine derivative hyperpolarized by PHIP (4.4$pm$1% $^{13}$C-polarization), meeting required levels for in vivo detection. Using water as solvent increases biocompatibility and the absence of N-protection is expected to maintain biological activity.
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Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for $psi$ and $psi$ angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of $alpha$-helical and $beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the objective to capture some well-known experimental features of soft tissues. It was obtained the optimized geometry, binding and coupling energies and dipole moments. The results concerning the stability of the confined water clusters, the water-water and water-collagen interactions within the CLBM framework were successfully correlated to some important trends observed experimentally in inflammatory tissues.
We demonstrate that the coupling of excitonic and vibrational motion in biological complexes can provide mechanisms to explain the long-lived oscillations that have been obtained in non linear spectroscopic signals of different photosynthetic pigment protein complexes and we discuss the contributions of excitonic versus purely vibrational components to these oscillatory features. Considering a dimer model coupled to a structured spectral density we exemplify the fundamental aspects of the electron-phonon dynamics, and by analyzing separately the different contributions to the non linear signal, we show that for realistic parameter regimes purely electronic coherence is of the same order as purely vibrational coherence in the electronic ground state. Moreover, we demonstrate how the latter relies upon the excitonic interaction to manifest. These results link recently proposed microscopic, non-equilibrium mechanisms to support long lived coherence at ambient temperatures with actual experimental observations of oscillatory behaviour using 2D photon echo techniques to corroborate the fundamental importance of the interplay of electronic and vibrational degrees of freedom in the dynamics of light harvesting aggregates.
Recent literatures reported blue-green emission from amyloid fibril as exclusive signature of fibril formation. This unusual visible luminescence is regularly used to monitor fibril growth. Blue-green emission has also been observed in crystalline protein and in solution. However, the origin of this emission is not known exactly. Our spectroscopic study of serum proteins reveals that the blue-green emission is a property of protein monomer. Evidences suggest that semiconductor-like band structure of proteins with the optical band-gap in the visible region is possibly the origin of this phenomenon. We show here that the band structure of proteins is primarily the result of electron delocalization through the peptide chain, rather than through the hydrogen bond network in secondary structure.
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well studied unsolvated alanine based polypeptides, Ac-Alan-LysH+. By exploring extensively the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n=4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics), but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through emph{ab initio} molecular dynamics, and generalized by testing different terminations and considering larger helical peptide models.
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