Analysis of Velocity Autocorrelation Functions from Molecular Dynamics Simulations of a Small Peptide by the Generalized Langevin Equation with a Power-Law Kernel

Internal motions play an essential role in the biological functions of proteins and have been the subject of numerous theoretical and spectroscopic studies. Such complex environments are associated with anomalous diffusion where, in contrast to the classical Brownian motion, the relevant correlation functions have power law decays with time. In this work, we investigate the presence of long memory stochastic processes through the analysis of atomic velocity autocorrelation functions. Analytical expressions of the velocity autocorrelation function spectrum obtained through a Mori–Zwanzig projection approach were shown to be compatible with molecular dynamics simulations of a small helical peptide (8-polyalanine)

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We discuss in this work a new software tool, named E-SpiReS (Electron Spin Resonance Simulations), aimed at the interpretation of dynamical properties of molecules in fluids from electron spin resonance (ESR) measurements. The code implements an integrated computational approach (ICA) for the calculation of relevant molecular properties that are needed in order to obtain spectral lines. The protocol encompasses information from atomistic level (quantum mechanical) to coarse grained level (hyd... Title of program: E-SpiReS Catalogue Id: AEEM_v1_0 Nature of problem ab initio simulation of cw-ESR spectra of radicals in solution Versions of this program held in the CPC repository in Mendeley Data AEEM_v1_0; E-SpiReS; 10.1016/j.cpc.2009.06.01

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed

Charge Transfer in Model Bioinspired Carotene–Porphyrin Dyads

We present a computational study based on accurate DFT and TD-DFT methods on model bioinspired donor–acceptor dyads, formed by a carotenoid covalently linked to a tetraphenylporphyrin (TPP) at the ortho position of one of the TPP phenyl rings. Dyadic systems can be used in the construction of organic solar cells and development of efficient photocatalytic systems for the solar energy conversion, due to the unique advantages they offer in terms of synthetic feasibility. This study aims to describe the influence of chemical modifications on the absorption spectra, in particular on the lowest energy charge transfer bands. Effects of different metals of biological interest, i.e., Mg, Fe, Ni, and Zn, and of H₂O and histidine molecules coordinated to the metals in different axial positions are rationalized

Stochastic Modeling of CW-ESR Spectroscopy of [60]Fulleropyrrolidine Bisadducts with Nitroxide Probes

In this work, we address the interpretation of continuous wave electron spin resonance (CW-ESR) spectra of fulleropyrrolidine bisadducts with nitroxide addends. Our approach is based on a definition of the spin Hamiltonian which includes exchange and dipolar interactions and on a complete numerical solution of the resulting stochastic Liouville equation, with inclusion of diffusive rotational dynamics. CW-ESR spectra are simulated for a series of C60 bisadducts made up of four trans isomers and the equatorial isomer. A nonlinear least-squares fitting procedure allows extraction directly from the available experimental spectra of a wide range of parameters, namely interprobe relative distances, diffusion tensors, and values of the exchange parameter J. Results are in good agreement with previous, more phenomenological estimates, proving that the combination of sensitive ESR spectroscopy based on multiple spin labeling with nitroxide radicals and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems

Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. I. Internal Dynamics of Cyclodextrins: γ‑Cyclodextrin as a Case Study

In this work, we address the description of the dynamics of cyclodextrins in relation with nuclear magnetic resonance (NMR) relaxation data collected for hydroxymethyl groups. We define an integrated computational approach based on the definition and parametrization of a stochastic equation able to describe the relevant degrees of freedom affecting the NMR observables. The computational protocol merges molecular dynamics simulations and hydrodynamics approaches for the evaluation of most of the molecular parameters entering the stochastic description of the system. We apply the method to the interpretation of the 13C NMR relaxation of the −CH2OH group of cyclodextrins. We use γ-cyclodextrin as a case study. Results are in agreement with quantitative and qualitative analyses performed in the past with simpler models and molecular dynamics simulations. The element of novelty in our approach is in the treatment of the coupling of the relevant internal (glucopyranose ring twisting/tilting and hydroxymethyl group jumps) and global (molecular tumbling) degrees of freedom

Modelling of Ca²⁺-promoted structural effects in wild type and post-translationally modified Connexin26

Connexins (Cx) are a class of membrane proteins important for auditory function, intercellular signalling and skin biology. Although the presence of concentration of calcium ions is known to work as a trigger for the Cx functionality, the structural changes induced by calcium binding still need to be well elucidated. In this computational study, we have explored the structural effects promoted by Ca2+ on both the wild type (Cx26WT) and on two post-translationally modified Connexin 26 (Cx26): Cx26E42-47γ, which contains two glutamates (E42 and E47) that are γ-carboxylated and Cx26R75m, where a key arginine (R75) is N-monomethylated. These modified amino acids, whose forcefield parameters have been developed in this work, alter Cx26 structure around the Ca2+coordination site. Structural changes were assessed from the analysis of molecular dynamics (MD) simulations. We observed a strict relation between the chemical properties of the post-translational modifications and significantly different responses of Cx26 to Ca2+-binding, while charge-adding modifications have destabilising effects upon calcium coordination, the uncharged ones share the same structural properties of the wild-type counterpart. Overall, these findings suggest the critical role of the electrostatic network flanking the Ca2+ coordination site in maintaining the native tertiary and quaternary structures.</p

Development and Validation of an Integrated Computational Approach for the Modeling of cw-ESR Spectra of Free Radicals in Solution: <i>p</i>-(Methylthio)phenyl Nitronylnitroxide in Toluene as a Case Study

In this work we address the interpretation, via an ab initio integrated computational approach, of continuous wave electron spin resonance (cw-ESR) spectra of p-(methylthio)phenyl nitronylnitroxide (MTPNN) dissolved in toluene. Our approach is based on the determination of the spin Hamiltonian, averaged with respect to fast vibrational motions, with magnetic tensor parameters (Zeeman and hyperfine tensors) characterized by quantum mechanical density functional calculations. The system is then described by a stochastic Liouville equation, with inclusion of diffusive rotational dynamics. Parametrization of diffusion rotational tensor is provided by a hydrodynamic model. Cw-ESR spectra of MTPNN are simulated for a wide range of temperatures (155−292 K) with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems

Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear Oligosaccharides

A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters

Similarity and Specificity of Chlorophyll <i>b</i> Triplet State in Comparison to Chlorophyll <i>a</i> as Revealed by EPR/ENDOR and DFT Calculations

An investigation of the photoexcited triplet state of chlorophyll (Chl) b has been carried out by means of electron nuclear double resonance, both in a frozen organic solvent and in a protein environment provided by the water-soluble chlorophyll protein of Lepidium virginicum. Density functional theory calculations have allowed the complete assignment of the observed hyperfine couplings corresponding to the methine protons and the methyl groups, leading to a complete picture of the spin density distribution of the triplet state in the tetrapyrrole macrocycle. The triplet-state properties of Chl b are found to be similar, in many respects, to those previously reported for Chl a, although some specificities have been highlighted. Concerning the spin density distribution, the differences are mainly localized on the carbon atoms close to the formyl group which, in Chl b, replaces the methyl group of Chl a