Munir Skaf | Universidade Estadual de Campinas (original) (raw)

Papers by Munir Skaf

The Journal of Physical Chemistry B, 2015

The peroxisome proliferator-activated receptor γ (PPARγ) is an important transcription factor tha... more The peroxisome proliferator-activated receptor γ (PPARγ) is an important transcription factor that plays a major role in the regulation of glucose and lipid metabolisms and has, therefore, many implications in modern-life metabolic disorders such as diabetes, obesity, and cardiovascular diseases.

The Journal of chemical physics, Jan 14, 2014

Polarization effects on the structure and dynamics of ionic liquids are investigated using molecu... more Polarization effects on the structure and dynamics of ionic liquids are investigated using molecular dynamics simulations. Four different ionic liquids were simulated, formed by the anions Cl(-) and PF6(-), treated as single fixed charge sites, and the 1-n-alkyl-3-methylimidazolium cations (1-ethyl and 1-butyl-), which are polarizable. The partial charge fluctuation of the cations is provided by the electronegativity equalization model (EEM) and a complete parameter set for the cations electronegativity (χ) and hardness (J) is presented. Results obtained from a non-polarizable model for the cations are also reported for comparison. Relative to the fixed charged model, the equilibrium structure of the first solvation shell around the imidazolium cations shows that inclusion of EEM polarization forces brings cations closer to each other and that anions are preferentially distributed above and below the plane of the imidazolium ring. The polarizable model yields faster translational an...

Surface and Colloid Science, 2004

ABSTRACT We report a molecular dynamics computer simulation study of the liquid/liquid interface ... more ABSTRACT We report a molecular dynamics computer simulation study of the liquid/liquid interface formed by water and carbon tetrachloride (H2O/CCl4) at 298 K. The primary focus of the work is the characterization of the structural features of the interface at a molecular level. The computed density profiles for the aqueous and organic phases and the distribution of surface widths indicate a fairly smooth interface approximately 5-Å thick. Analyses of the water structure near and far from the interface show a significant depletion in the average number of hydrogen bonds in the vicinity of the organic phase with respect to the bulk. The average orientation of the water molecules reveals that close to the interface the dipole moments tend to align parallel to the interfacial plane, while the vector joining the hydrogen atoms points slightly away from this plane. These results are discussed in the light of recently reported nonlinear spectroscopy measurements. KeywordsLiquid interfaces–Molecular dynamics simulations–Water/CCl4 microstructure

The Plant journal : for cell and molecular biology, 2014

The interaction between xylan and cellulose microfibrils is important for secondary cell wall pro... more The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β-(1,4)-linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one-half of the xylosyl residues are O-acetylated at C-2 or C-3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecul...

The Journal of Physical Chemistry C, 2014

The Journal of Physical Chemistry B, 2009

Molecular dynamics simulations have been carried out to investigate the dynamics of fructose aque... more Molecular dynamics simulations have been carried out to investigate the dynamics of fructose aqueous solutions up to 70 wt % concentration. We find that the hydrogen (H)-bonded network of fructose molecules extends with increasing sugar content and forms a structurally heterogeneous system around and above 45 wt % concentration, characterized as a percolated-like solute domain permeated by patchy regions of solvent. The presence of such aggregates in concentrated solutions promotes the slowing down of water translational, reorientational, and H-bonding dynamics, typical of many biomolecular environments. Analysis of the effects of the topological and energetic disorder of the sugar aggregates on vicinal water dynamics, similar to that recently carried out for the hydration layer of proteins by Pizzitutti et al. (J. Phys. Chem. B 2007, 111, 7584), reveals many similarities between the dynamical anomaly of the hydration layers of both systems. Like a protein surface, topological and energetic disorders of the sugar aggregates both contribute to the translational diffusion anomaly. However, unlike in the vicinity of a protein surface, the rotational relaxation is also hindered by the topological disorder created by the intertwined, percolating sugar clusters in concentrated solutions.

The Journal of Physical Chemistry B, 2005

Through the use of molecular dynamics techniques, we analyze equilibrium and dynamical aspects of... more Through the use of molecular dynamics techniques, we analyze equilibrium and dynamical aspects of the solvation of Coumarin 314 adsorbed at water/air interfaces in the presence of sodium dodecyl sulfate surfactant molecules. Three different coverages in the submonolayer regime were considered, 500, 250, and 100 Å 2 / SDS molecule. The surfactant promotes two well-differentiated solvation environments, which can be clearly distinguished in terms of their structures for the largest surfactant coverage considered. The first one is characterized by the probe lying adjacent or exterior to two-dimensional spatial domains formed by clustered surfactant molecules. A second type of solvation environment is found in which the coumarin appears embedded within compact surfactant domains. Equilibrium and dynamical aspects of the interfacial orientation of the probe are investigated. Our results show a gradual transition from parallel to perpendicular dipolar alignment of the probe with respect to the interface as the concentration of surfactant F s increases. The presence of the surfactant leads to an increase in the roughness and in the characteristic width of the water/air interface. These modifications are also manifested by the decorrelation times for the probe reorientational dynamics, which become progressively slower with F s in both solvation states, although much more pronounced for the embedded ones. The dynamical characteristics of the solvation responses of the charged interfaces are also analyzed, and the implications of our findings to the interpretation of available experimental measurements are discussed.

The Journal of Physical Chemistry B, 2007

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous s... more We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.

Physical Review Letters, 2005

We present molecular dynamics simulations of the optical Kerr effect in liquid and supercooled wa... more 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.

Physical Chemistry Chemical Physics, 2005

A molecular dynamics simulation study is presented for the dynamics of the polarizability anisotr... more A molecular dynamics simulation study is presented for the dynamics of the polarizability anisotropy of liquid water using the SPC/E model and a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors obtained from ab initio quantum chemical calculations at the MP2/6-311++G(d,p) level. The time-correlation functions for the collective polarizability anisotropy, the optical Kerr effect response, and the frequency spectra are analyzed in terms of the intrinsic and induced polarizability contributions. At short times, the simulated Kerr nuclear response exhibits maxima near 15, 50 and 180 fs, followed by a diffusive tail which has been fitted by a bi-exponential with time constants ca. 0.4 and 2.5 ps. The short time features are in good agreement with available simulation and experimental results. The agreement with experiments is less satisfactory for the diffusive components. The main features of the frequency spectrum include a rotational-diffusion peak centered around 3 cm(-1), a collision-induced (hindered translations) band near 200 cm(-1), and a broad librational band at 450 cm(-1). The simulation results are in good agreement with experimental frequency spectra obtained from Kerr effect and related spectroscopies, but fail to reproduce the experimental band near 60 cm(-1).

Molecular Endocrinology, 2008

Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-depend... more Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17beta-estradiol (E(2)) and the selective ER modulator raloxifene (RAL)] from the human ERalpha ligand-binding domain in monomeric and dimeric forms. E(2) dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II'). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I'). Remarkably, ER dimerization strongly suppresses Paths II and II' for E(2) dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

Journal of Molecular Biology, 2013

Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear trans... more Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.

Journal of Computational Chemistry, 2012

Journal of Biological Chemistry, 2013

Background: ␤-Glucosidase completes cellulose enzymatic hydrolysis by releasing glucose from cell... more Background: ␤-Glucosidase completes cellulose enzymatic hydrolysis by releasing glucose from cellobiose. Results: SAXS experiments revealed that Aspergillus niger ␤-glucosidase has a cellulase-like tadpole molecular shape, uncommon to enzymes that act on the soluble substrates. Conclusion: We show that AnBgl1 N-and C-terminal domains are linked by a long extended linker. Significance: Understanding AnBgl1 architecture is useful for comprehension of the enzyme-cell wall interaction and the process of biomass saccharification.

International Journal of Quantum Chemistry, 2011

We develop a CHARMM-based interaction potential for rosiglitazone, a well-known selective ligand ... more We develop a CHARMM-based interaction potential for rosiglitazone, a well-known selective ligand to the c isoform of the peroxisome proliferator-activated receptor (PPARc) 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-PPARc 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.

Molecular pharmacology, 2012

Peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabete... more Peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabetes and other conditions. PPARγ full agonists, like thiazolidinediones (TZDs), are effective insulin sensitizers and anti-inflammatories but their use is limited by adverse side effects. Luteolin is flavonoid with anti-inflammatory actions that binds PPARγ but, unlike TZDs, does not promote adipocyte differentiation. However, previous reports variously suggested that luteolin is a PPARγ agonist or an antagonist. We show that luteolin exhibits weak partial agonist/antagonist activity in transfections, inhibits several PPARγ target genes in 3T3-L1 cells (LPL, ORL1 and CBPα) and PPARγ-dependent adipogenesis but activates GLUT4 similarly to rosiglitazone implying gene-specific partial agonism. The crystal structure of the PPARγ ligand binding domain (LBD) reveals that luteolin occupies buried ligand binding pocket (LBP) but binds an inactive PPARγ LBD conformer and occupies a space near the β-...

Brazilian Journal of Physics, 2004

We present a review on the intermolecular dynamics of liquid aqueous systems focusing mainly on M... more 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.

BMC Structural Biology, 2008

Background: Thyroid receptors, TRα and TRβ, are involved in important physiological functions suc... more Background: Thyroid receptors, TRα and TRβ, are involved in important physiological functions such as metabolism, cholesterol level and heart activities. Whereas metabolism increase and cholesterol level lowering could be achieved by TRβ isoform activation, TRα activation affects heart rates. Therefore, β-selective thyromimetics have been developed as promising drugcandidates for treatment of obesity and elevated cholesterol level. GC-1 [3,5-dimethyl-4-(4'hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid] has ability to lower LDL cholesterol with 600-to 1400-fold more potency and approximately two-to threefold more efficacy than atorvastatin (Lipitor © ) in studies in rats, mice and monkeys.

Biophysical Journal, 2005

Nuclear receptor (NR) ligands occupy a pocket that lies within the core of the NR ligand-binding ... more Nuclear receptor (NR) ligands occupy a pocket that lies within the core of the NR ligand-binding domain (LBD), and most NR LBDs lack obvious entry/exit routes upon the protein surface. Thus, significant NR conformational rearrangements must accompany ligand binding and release. The precise nature of these processes, however, remains poorly understood. Here, we utilize locally enhanced sampling (LES) molecular dynamics computer simulations to predict molecular motions of x-ray structures of thyroid hormone receptor (TR) LBDs and determine events that permit ligand escape. We find that the natural ligand 3,5,39-triiodo-L-thyronine (T 3 ) dissociates from the TRa1 LBD along three competing pathways generated through i), opening of helix (H) 12; ii), separation of H8 and H11 and the V-loop between H2 and H3; and iii), opening of H2 and H3, and the intervening b-strand. Similar pathways are involved in dissociation of T 3 and the TRb-selective ligand GC24 from TRb; the TR agonist IH5 from the a-and b-TR forms; and Triac from two natural human TRb mutants, A317T and A234T, but are detected with different frequencies in simulations performed with the different structures. Path I was previously suggested to represent a major pathway for NR ligand dissociation. We propose here that Paths II and III are also likely ligand escape routes for TRs and other NRs. We also propose that different escape paths are preferred in different situations, implying that it will be possible to design NR ligands that only associate stably with their cognate receptors in specific cellular contexts.

The Journal of Physical Chemistry B, 2011

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and... more Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 Å resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting β-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of chargeÀcharge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

The Journal of Physical Chemistry B, 2015

The peroxisome proliferator-activated receptor γ (PPARγ) is an important transcription factor tha... more The peroxisome proliferator-activated receptor γ (PPARγ) is an important transcription factor that plays a major role in the regulation of glucose and lipid metabolisms and has, therefore, many implications in modern-life metabolic disorders such as diabetes, obesity, and cardiovascular diseases.

The Journal of chemical physics, Jan 14, 2014

Polarization effects on the structure and dynamics of ionic liquids are investigated using molecu... more Polarization effects on the structure and dynamics of ionic liquids are investigated using molecular dynamics simulations. Four different ionic liquids were simulated, formed by the anions Cl(-) and PF6(-), treated as single fixed charge sites, and the 1-n-alkyl-3-methylimidazolium cations (1-ethyl and 1-butyl-), which are polarizable. The partial charge fluctuation of the cations is provided by the electronegativity equalization model (EEM) and a complete parameter set for the cations electronegativity (χ) and hardness (J) is presented. Results obtained from a non-polarizable model for the cations are also reported for comparison. Relative to the fixed charged model, the equilibrium structure of the first solvation shell around the imidazolium cations shows that inclusion of EEM polarization forces brings cations closer to each other and that anions are preferentially distributed above and below the plane of the imidazolium ring. The polarizable model yields faster translational an...

Surface and Colloid Science, 2004

ABSTRACT We report a molecular dynamics computer simulation study of the liquid/liquid interface ... more ABSTRACT We report a molecular dynamics computer simulation study of the liquid/liquid interface formed by water and carbon tetrachloride (H2O/CCl4) at 298 K. The primary focus of the work is the characterization of the structural features of the interface at a molecular level. The computed density profiles for the aqueous and organic phases and the distribution of surface widths indicate a fairly smooth interface approximately 5-Å thick. Analyses of the water structure near and far from the interface show a significant depletion in the average number of hydrogen bonds in the vicinity of the organic phase with respect to the bulk. The average orientation of the water molecules reveals that close to the interface the dipole moments tend to align parallel to the interfacial plane, while the vector joining the hydrogen atoms points slightly away from this plane. These results are discussed in the light of recently reported nonlinear spectroscopy measurements. KeywordsLiquid interfaces–Molecular dynamics simulations–Water/CCl4 microstructure

The Plant journal : for cell and molecular biology, 2014

The interaction between xylan and cellulose microfibrils is important for secondary cell wall pro... more The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β-(1,4)-linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one-half of the xylosyl residues are O-acetylated at C-2 or C-3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecul...

The Journal of Physical Chemistry C, 2014

The Journal of Physical Chemistry B, 2009

Molecular dynamics simulations have been carried out to investigate the dynamics of fructose aque... more Molecular dynamics simulations have been carried out to investigate the dynamics of fructose aqueous solutions up to 70 wt % concentration. We find that the hydrogen (H)-bonded network of fructose molecules extends with increasing sugar content and forms a structurally heterogeneous system around and above 45 wt % concentration, characterized as a percolated-like solute domain permeated by patchy regions of solvent. The presence of such aggregates in concentrated solutions promotes the slowing down of water translational, reorientational, and H-bonding dynamics, typical of many biomolecular environments. Analysis of the effects of the topological and energetic disorder of the sugar aggregates on vicinal water dynamics, similar to that recently carried out for the hydration layer of proteins by Pizzitutti et al. (J. Phys. Chem. B 2007, 111, 7584), reveals many similarities between the dynamical anomaly of the hydration layers of both systems. Like a protein surface, topological and energetic disorders of the sugar aggregates both contribute to the translational diffusion anomaly. However, unlike in the vicinity of a protein surface, the rotational relaxation is also hindered by the topological disorder created by the intertwined, percolating sugar clusters in concentrated solutions.

The Journal of Physical Chemistry B, 2005

Through the use of molecular dynamics techniques, we analyze equilibrium and dynamical aspects of... more Through the use of molecular dynamics techniques, we analyze equilibrium and dynamical aspects of the solvation of Coumarin 314 adsorbed at water/air interfaces in the presence of sodium dodecyl sulfate surfactant molecules. Three different coverages in the submonolayer regime were considered, 500, 250, and 100 Å 2 / SDS molecule. The surfactant promotes two well-differentiated solvation environments, which can be clearly distinguished in terms of their structures for the largest surfactant coverage considered. The first one is characterized by the probe lying adjacent or exterior to two-dimensional spatial domains formed by clustered surfactant molecules. A second type of solvation environment is found in which the coumarin appears embedded within compact surfactant domains. Equilibrium and dynamical aspects of the interfacial orientation of the probe are investigated. Our results show a gradual transition from parallel to perpendicular dipolar alignment of the probe with respect to the interface as the concentration of surfactant F s increases. The presence of the surfactant leads to an increase in the roughness and in the characteristic width of the water/air interface. These modifications are also manifested by the decorrelation times for the probe reorientational dynamics, which become progressively slower with F s in both solvation states, although much more pronounced for the embedded ones. The dynamical characteristics of the solvation responses of the charged interfaces are also analyzed, and the implications of our findings to the interpretation of available experimental measurements are discussed.

The Journal of Physical Chemistry B, 2007

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous s... more We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.

Physical Review Letters, 2005

We present molecular dynamics simulations of the optical Kerr effect in liquid and supercooled wa... more 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.

Physical Chemistry Chemical Physics, 2005

A molecular dynamics simulation study is presented for the dynamics of the polarizability anisotr... more A molecular dynamics simulation study is presented for the dynamics of the polarizability anisotropy of liquid water using the SPC/E model and a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors obtained from ab initio quantum chemical calculations at the MP2/6-311++G(d,p) level. The time-correlation functions for the collective polarizability anisotropy, the optical Kerr effect response, and the frequency spectra are analyzed in terms of the intrinsic and induced polarizability contributions. At short times, the simulated Kerr nuclear response exhibits maxima near 15, 50 and 180 fs, followed by a diffusive tail which has been fitted by a bi-exponential with time constants ca. 0.4 and 2.5 ps. The short time features are in good agreement with available simulation and experimental results. The agreement with experiments is less satisfactory for the diffusive components. The main features of the frequency spectrum include a rotational-diffusion peak centered around 3 cm(-1), a collision-induced (hindered translations) band near 200 cm(-1), and a broad librational band at 450 cm(-1). The simulation results are in good agreement with experimental frequency spectra obtained from Kerr effect and related spectroscopies, but fail to reproduce the experimental band near 60 cm(-1).

Molecular Endocrinology, 2008

Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-depend... more Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17beta-estradiol (E(2)) and the selective ER modulator raloxifene (RAL)] from the human ERalpha ligand-binding domain in monomeric and dimeric forms. E(2) dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II'). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I'). Remarkably, ER dimerization strongly suppresses Paths II and II' for E(2) dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

Journal of Molecular Biology, 2013

Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear trans... more Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.

Journal of Computational Chemistry, 2012

Journal of Biological Chemistry, 2013

Background: ␤-Glucosidase completes cellulose enzymatic hydrolysis by releasing glucose from cell... more Background: ␤-Glucosidase completes cellulose enzymatic hydrolysis by releasing glucose from cellobiose. Results: SAXS experiments revealed that Aspergillus niger ␤-glucosidase has a cellulase-like tadpole molecular shape, uncommon to enzymes that act on the soluble substrates. Conclusion: We show that AnBgl1 N-and C-terminal domains are linked by a long extended linker. Significance: Understanding AnBgl1 architecture is useful for comprehension of the enzyme-cell wall interaction and the process of biomass saccharification.

International Journal of Quantum Chemistry, 2011

We develop a CHARMM-based interaction potential for rosiglitazone, a well-known selective ligand ... more We develop a CHARMM-based interaction potential for rosiglitazone, a well-known selective ligand to the c isoform of the peroxisome proliferator-activated receptor (PPARc) 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-PPARc 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.

Molecular pharmacology, 2012

Peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabete... more Peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabetes and other conditions. PPARγ full agonists, like thiazolidinediones (TZDs), are effective insulin sensitizers and anti-inflammatories but their use is limited by adverse side effects. Luteolin is flavonoid with anti-inflammatory actions that binds PPARγ but, unlike TZDs, does not promote adipocyte differentiation. However, previous reports variously suggested that luteolin is a PPARγ agonist or an antagonist. We show that luteolin exhibits weak partial agonist/antagonist activity in transfections, inhibits several PPARγ target genes in 3T3-L1 cells (LPL, ORL1 and CBPα) and PPARγ-dependent adipogenesis but activates GLUT4 similarly to rosiglitazone implying gene-specific partial agonism. The crystal structure of the PPARγ ligand binding domain (LBD) reveals that luteolin occupies buried ligand binding pocket (LBP) but binds an inactive PPARγ LBD conformer and occupies a space near the β-...

Brazilian Journal of Physics, 2004

We present a review on the intermolecular dynamics of liquid aqueous systems focusing mainly on M... more 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.

BMC Structural Biology, 2008

Background: Thyroid receptors, TRα and TRβ, are involved in important physiological functions suc... more Background: Thyroid receptors, TRα and TRβ, are involved in important physiological functions such as metabolism, cholesterol level and heart activities. Whereas metabolism increase and cholesterol level lowering could be achieved by TRβ isoform activation, TRα activation affects heart rates. Therefore, β-selective thyromimetics have been developed as promising drugcandidates for treatment of obesity and elevated cholesterol level. GC-1 [3,5-dimethyl-4-(4'hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid] has ability to lower LDL cholesterol with 600-to 1400-fold more potency and approximately two-to threefold more efficacy than atorvastatin (Lipitor © ) in studies in rats, mice and monkeys.

Biophysical Journal, 2005

Nuclear receptor (NR) ligands occupy a pocket that lies within the core of the NR ligand-binding ... more Nuclear receptor (NR) ligands occupy a pocket that lies within the core of the NR ligand-binding domain (LBD), and most NR LBDs lack obvious entry/exit routes upon the protein surface. Thus, significant NR conformational rearrangements must accompany ligand binding and release. The precise nature of these processes, however, remains poorly understood. Here, we utilize locally enhanced sampling (LES) molecular dynamics computer simulations to predict molecular motions of x-ray structures of thyroid hormone receptor (TR) LBDs and determine events that permit ligand escape. We find that the natural ligand 3,5,39-triiodo-L-thyronine (T 3 ) dissociates from the TRa1 LBD along three competing pathways generated through i), opening of helix (H) 12; ii), separation of H8 and H11 and the V-loop between H2 and H3; and iii), opening of H2 and H3, and the intervening b-strand. Similar pathways are involved in dissociation of T 3 and the TRb-selective ligand GC24 from TRb; the TR agonist IH5 from the a-and b-TR forms; and Triac from two natural human TRb mutants, A317T and A234T, but are detected with different frequencies in simulations performed with the different structures. Path I was previously suggested to represent a major pathway for NR ligand dissociation. We propose here that Paths II and III are also likely ligand escape routes for TRs and other NRs. We also propose that different escape paths are preferred in different situations, implying that it will be possible to design NR ligands that only associate stably with their cognate receptors in specific cellular contexts.

The Journal of Physical Chemistry B, 2011

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and... more Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 Å resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting β-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of chargeÀcharge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.