Optical Kerr Effect In Supercooled Water.

We present molecular dynamics simulations of the optical Kerr effect in liquid and supercooled water and compare with recent time-resolved Kerr spectroscopy measurements [R. Torre, Nature (London) 428, 296 (2004)]. The short time features of the Kerr response, characterized by peaks near 15, 60, and 160 fs, are weakly temperature dependent. The long-time decay is well described by a stretched exponential with a nearly constant stretch parameter and relaxation times that follow a power law approximately (T-T(S))(-gamma), with T(S)=198.3 K and gamma=2.35. Our findings are discussed in the light of the spectroscopy data and previous simulation analyzes of the structural relaxation in supercooled water.9413780

Collision-Induced Effects on the Dielectric Properties of Liquid Dimethylsulfoxide

We present a molecular dynamics (MD) simulation study of the dielectric properties of liquid dimethyl sulfoxide that includes interaction-induced effects due to molecular polarizability using a perturbative scheme in which the induced dipoles are computed a posteriori from the MD trajectories generated without explicit inductive forces. Static and dynamical quantities of relevance to the dielectric characterization of the liquid are reported for both polarizable and nonpolarizable versions of the system's collective dipolar densities. Our analysis within this scheme indicates that the role of the interaction induced contributions is predominantly to renormalize the magnitude of the permanent dipole fluctuations, with marginal effects upon the system's dielectric relaxation in the rotational-diffusion, microwave region of the spectrum. At higher frequencies, however, where the dielectric absorption is dominated by fast intermolecular librational motions, the dynamical effects of the molecular polarizability are more pronounced. In the presence of interaction induced contributions, the location of the peak in the MD far infrared absorption coefficient is in much better agreement with recent spectroscopic measurements of the intermolecular dynamics of this liquid.É apresentado um estudo por simulação de dinâmica molecular das propriedades dielétricas do dimetil sulfóxido líquido, onde são incluídos efeitos de indução devido à polarizabilidade molecular através de perturbação em primeira ordem. Neste formalismo, os dipolos induzidos são computados a partir de trajetórias geradas pelos potenciais intermoleculares isentos de forças indutivas. Propriedades dielétricas estáticas e dinâmicas são computadas para as versões polarizável e não-polarizável da densidade dipolar. As análises indicam que o principal papel das componentes de indução nesta abordagem é o de renormalizar o valor das flutuações estáticas dos dipolos permanentes, sendo apenas marginal a influência sobre as propriedades de relaxação no regime de difusão rotacional que caracteriza o espectro na região de micro-ondas. Entretanto, para maiores frequências, onde a absorção dielétrica é predominantemente determinada por movimentos intermoleculares libracionais, os efeitos dinâmicos da polarizabilidade molecular são mais aparentes. Na presença de contribuições indutivas, o máximo do espectro infravermelho obtido das simulações está em melhor concordância com recentes medidas espectroscópicas da dinâmica intermolecular deste líquido.583591Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOThe natural ligand 17β-estradiol (E2) is so far believed to induce a unique agonist-bound active conformation in the ligand binding domain (LBD) of the estrogen receptors (ERs). Both subtypes, ERα and ERβ, are transcriptionally activated in the presence o7FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2014/22007-02013/08293-72012/24750-6301981/2011-6This work was supported by the São Paulo Research Foundation FAPESP (grants 2014/22007-0, 2013/08293-7, 2012/24750-6) and by CNPq (grant 301981/2011-6

CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands

The peroxisome proliferator-activated receptor γ (PPARγ) ligands are important therapeutic drugs for the treatment of type 2 diabetes, obesity and cardiovascular diseases. In particular, partial agonists and non-agonists are interesting targets to reduce glucose levels, presenting few side effects in comparison to full agonists. In this work, we present a set of CHARMM-based parameters of a molecular mechanics force field for two PPARγ ligands, GQ16 and SR1664. GQ16 belongs to the thiazolidinedione class of drugs and it is a PPARγ partial agonist that has been shown to promote the “browning” of white adipose tissue. SR1664 is the precursor of the PPARγ non-agonist class of ligands that activates PPARγ in a non-classical manner. Here, we use quantum chemical calculations consistent with the CHARMM protocol to obtain bonded and non-bonded parameters, including partial atomic charges and effective torsion potentials for both molecules. The newly parameterized models were evaluated by examining the behavior of GQ16 and SR1664 free in water and bound to the ligand binding pocket of PPARγ using molecular dynamics simulations. The potential parameters derived here are readily transferable to a variety of pharmaceutical compounds and similar PPARγ ligands

The patterned structure of galactoglucomannan suggests it may bind to cellulose in seed mucilage

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOThe interaction between mannan polysaccharides and cellulose microfibrils contributes to cell wall properties in some vascular plants, but the molecular arrangement of mannan in the cell wall and the nature of the molecular bonding between mannan and cell178310111026FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO2013/08293-7The authors would like to acknowledge Prof. George Lomonossoff (John Innes Centre, UK), who developed the pEAQ-HyperTrans expression system used in this study. Plant Bioscience Limited supplied the pEAQ-HT vector that was used in this wor

Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose.

The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls.This work was supported by the Leverhulme Trust Centre for Natural Material Innovation (MBW, PD), The Low Carbon Energy University Alliance (AL), BBSRC Grant: BB/G016240/1 BBSRC Sustainable Bioenergy Centre cell wall sugars (TT, PD) and the Sao Paulo Research Foundation (RLS, CSP, MSS, TCFG) (Grants 2013/08293-7, 2014/10448-1 and 2015/25031-1)

A review on the dynamics of water

We present a review on the intermolecular dynamics of liquid aqueous systems focusing mainly on Molecular Dynamics simulation work that has been carried out at the State University of Campinas in recent years. Emphasis is given on simulation results that are more directly related to modern experimental spectroscopic measurements.316Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

X-ray Structure And Molecular Dynamics Simulations Of Endoglucanase 3 From Trichoderma Harzianum: Structural Organization And Substrate Recognition By Endoglucanases That Lack Cellulose Binding Module.

Plant biomass holds a promise for the production of second-generation ethanol via enzymatic hydrolysis, but its utilization as a biofuel resource is currently limited to a large extent by the cost and low efficiency of the cellulolytic enzymes. Considerable efforts have been dedicated to elucidate the mechanisms of the enzymatic process. It is well known that most cellulases possess a catalytic core domain and a carbohydrate binding module (CBM), without which the enzymatic activity can be drastically reduced. However, Cel12A members of the glycosyl hydrolases family 12 (GHF12) do not bear a CBM and yet are able to hydrolyze amorphous cellulose quite efficiently. Here, we use X-ray crystallography and molecular dynamics simulations to unravel the molecular basis underlying the catalytic capability of endoglucanase 3 from Trichoderma harzianum (ThEG3), a member of the GHF12 enzymes that lacks a CBM. A comparative analysis with the Cellulomonas fimi CBM identifies important residues mediating interactions of EG3s with amorphous regions of the cellulose. For instance, three aromatic residues constitute a harboring wall of hydrophobic contacts with the substrate in both ThEG3 and CfCBM structures. Moreover, residues at the entrance of the active site cleft of ThEG3 are identified, which might hydrogen bond to the substrate. We advocate that the ThEG3 residues Asn152 and Glu201 interact with the substrate similarly to the corresponding CfCBM residues Asn81 and Arg75. Altogether, these results show that CBM motifs are incorporated within the ThEG3 catalytic domain and suggest that the enzymatic efficiency is associated with the length and position of the substrate chain, being higher when the substrate interact with the aromatic residues at the entrance of the cleft and the catalytic triad. Our results provide guidelines for rational protein engineering aiming to improve interactions of GHF12 enzymes with cellulosic substrates.8e5906

CHARMM force field parameterization of rosiglitazone

We develop a CHARMM-based interaction potential for rosiglitazone, a well-known selective ligand to the γ isoform of the peroxisome proliferator-activated receptor (PPARγ) and widely marketed antidiabetic drug of the thiazolidinedione (TZD) class. We derive partial atomic charges and dihedral torsion potentials for seven rotations in the molecule, for which there are no analogs available in CHARMM. The potential model is validated by performing a series of molecular dynamics simulations of rosiglitazone in neat water and of a fully solvated rosiglitazone-PPARγ complex. The structural and dynamical behavior of the complex is analyzed in comparison with available experimental data. The potential parameters derived here are readily transferable to a variety of pharmaceutically important TZD compounds.FAPESPCNP