Molecular dynamics and functional studies suggest brachyNH2 by binding to argininosuccinate synthase, induces relaxation in rat small mesenteric arteries.

Edição dos Abstracts do European Society for Microcirculation Conference, Aarhus, Dinamarca, 2023

Molecular Dynamics Studies on the Buffalo Prion Protein

It was reported that buffalo is a low susceptibility species resisting to prion diseases, which are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species. In molecular structures, TSE neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to reveal the reason why buffalo are resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonance structure of bovine and cattle PrP(124-227); immediately we found for buffalo PrPC(124-227) there are 5 hydrogen bonds at Asn143, but at this position bovine/cattle do not have such hydrogen bonds. Same as that of rabbits, dogs or horses, our molecular dynamics studies also confirmed there is a strong salt bridge ASP178-ARG164 (O-N) keeping the beta2-alpha2 loop linked in buffalo. We also found there is a very strong hydrogen bond SER170-TYR218 linking this loop with the C-terminal end of alpha-helix H3. Other information such as (i) there is a very strong salt bridge HIS187-ARG156 (N-O) linking alpha-helices H2 and H1 (if mutation H187R is made at position 187 then the hydrophobic core of PrPC will be exposed), (ii) at D178, there is a hydrogen bond Y169-D178 and a polar contact R164-D178 for BufPrPC instead of a polar contact Q168-D178 for bovine PrPC, (iii) BufPrPC owns 3-10 helices at 125-127, 152-156 and in the beta2-alpha2 loop respectively, and (iv) in beta2-alpha2 loop there are strong pi-contacts, etc, has been discovered

High-Resolution Photoelectron Spectroscopy of Molecules

Rotationally resolved photoelectron spectra can provide significant insight into the underlying dynamics of molecular photoionization. Here, we discuss and compare results of recent theoretical studies of rotationally resolved photoelectron spectra with measurements for molecules such as HBr, OH, NO, N_2, CO, H_2O, H_2CO, and CH_3. These studies reveal the rich dynamics of quantum-state-specific studies of molecular photoionization and provide a robust description of key spectral features resulting from Cooper minima, autoionization, alignment, partial-wave mixing, and interference in related experimental studies

Phase behaviour and dynamics in primitive models of molecular ionic liquids

The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and cation-shape anisotropy, which are all prominent features of important materials such as room-temperature ionic liquids. The vapour-liquid phase diagrams are determined using high-precision Monte Carlo simulations, setting the scene for in-depth studies of ion dynamics in the liquid state. Molecular dynamics simulations are used to explore the structure, single-particle translational and rotational autocorrelation functions, cation orientational autocorrelations, self diffusion, viscosity, and frequency-dependent conductivity. The results reveal some of the molecular-scale mechanisms for charge transport, involving molecular translation, rotation, and association.Comment: 15 pages, 7 figure

Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations

Molecular dynamics studies of anomalous transport in rarefied gas flows

We investigate the thermodynamically non-equilibrium gas dynamics by measuring molecular free path distribution functions, inter-molecular collision rates and wall dependent mean free path (MFP) profiles using the molecular dynamics (MD) method. The simulations cover a wide range of fluid densities for single-wall case, parallel walls cases and a cube with all periodic walls. The simulations are validated by deducing the theoretical unconfined MFP values at standardpressure and temperature conditions. The free path MD measurements of individual molecules convey that conventional exponential distribution function is not valid under rarefied conditions and molecules follow L´evy type flights, irrespective of the presence of a wall. MFP profile measurements for confined planar surfaces in the transition flow regime show sharp gradients close to the wall, while theoretical models predict shallower gradients. As gas transport properties can be related to the MFP through kinetic theory, our MD data may help to modify the constitutive relationships, which may then be fed into the Navier-Stokes equations for better effective modeling of micro gas flows in the transition flow regime

Friction anisotropy at Ni(100)/(100) interfaces: Molecular dynamics studies

The friction of surfaces moving relative to each other must derive from the atomic interaction at interfaces. However, recent experiments bring into question the fundamental understanding of this phenomenon. The analytic theories predict that most perfect clean incommensurate interfaces would produce no static friction, whereas commensurate aligned surfaces would have very high friction. In contrast recent experiments show that the static friction coefficient between clean but 45° misoriented Ni(001) surfaces is only a factor of 4 smaller than for the aligned surfaces (θ∼0°) and clearly does not vanish (θ is defined as the rotation angle between the relative crystallographic orientations of two parallel surfaces). To understand this friction anisotropy and the difference between analytic theory and experiment, we carried out a series of nonequilibrium molecular dynamics simulations at 300 K for sliding of Ni(001)/Ni(001) interfaces under a constant shear force. Our molecular dynamics calculations on interfaces with the top layer roughed (and rms roughness of 0.8 Å) lead to the static frictional coefficients in good agreement with the corresponding experimental data. On the other hand, perfect smooth surfaces (rms roughness of 0 Å) lead to a factor of 34–330 decreasing of static friction coefficients for misaligned surfaces, a result more consistent with the analytic theories. This shows that the major source of the discrepancy is that small amounts of roughness dramatically increase the friction on incommensurate surfaces, so that misaligned directions are comparable to aligned directions

Hair keratin molecular dynamics studies

EJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional EstruturalThe keratin is a key element of the hair, nails and skin in vertebrates. Understand the keratin features such as its assembling in the mentioned structures, its interaction with some compounds or mechanical properties is of great interest in the fight against some diseases or in the development and optimization of cosmetic products. Although molecular dynamics simulations provides unique information at molecular level there are only a few studies using this technique on the study of keratin. This is likely the result of the non-existence of full length keratin crystallographic model. In the few works published about keratin using molecular dynamics simulations the authors had to design and build the computational keratin model, to make the simulations of interest. This work addresses some molecular dynamics studies about hair keratin, from the physicochemical properties of the molecular models to the correlation of the simulations results with experimental data. Our work on this field, with recently developed computational models of hair fibers, is also discussed. We built molecular dynamics models able to reproduce in simulations some phenomena observed in experimental assays, providing important information at molecular level about the mechanisms that lead to the experimental results.info:eu-repo/semantics/publishedVersio

Hair keratin molecular dynamics studies

Book of Abstracts of CEB Annual Meeting 2017[Excerpt] The keratin is a key element of the hair, nails and skin in vertebrates. Understand the keratin features such its assembling in the mentioned structures, its interactions with some compounds or mechanical properties is of great interest in the fight against some diseases or in the development and optimization of cosmetic products. Although molecular dynamics (MD) simulations provides unique information at molecular level in a dynamic way, there are only a few studies using this technique on the study of keratin. This is likely the result of the nonexistence of full length keratin crystallographic model. In the few published works the authors had to design and build the computational keratin model to perform the simulations of interest. [...]info:eu-repo/semantics/publishedVersio