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1.  Translocation Thermodynamics of Linear and Cyclic Nonaarginine into Model DPPC Bilayer via Coarse-Grained Molecular Dynamics Simulation: Implications of Pore Formation and Nonadditivity 
The Journal of Physical Chemistry. B  2014;118(10):2670-2682.
Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg9) into a model DPPC bilayer. In the case of the Arg9 cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg9) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg9 [Huang, K.; et al. Biophys. J., 2013, 104, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg9 translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg9 translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths systematically predict lower free-energy barriers (ca. 90 kJ/mol lower) than the non pore-forming paths, again consistent with all-atom force field simulations. The current force field suggests no preference for the more compact or covalently cyclic structures upon entering the bilayer. Decomposition of the PMF into the system’s components indicates that the dominant stabilizing contribution along the pore-forming path originates from the membrane as both layers of it deformed due to the formation of pore. Furthermore, our analysis revealed that although there is significant entropic stabilization arising from the enhanced configurational entropy exposing more states as the peptide moves through the bilayer, the enthalpic loss (as predicted by the interactions of this coarse-grained model) far outweighs any former stabilization, thus leading to significant barrier to translocation. Finally, we observe reduction in the translocation free-energy barrier for a second Arg9 entering the bilayer in the presence of an initial peptide restrained at the center, again, in qualitative agreement with all-atom force fields.
doi:10.1021/jp412600e
PMCID: PMC3983342  PMID: 24506488
2.  Coronary Artery Aneurysms in a 15-Year-Old Boy 
Texas Heart Institute Journal  2014;41(6):675-676.
doi:10.14503/THIJ-13-3789
PMCID: PMC4251349  PMID: 25593542
3.  Free Energetics of Arginine Permeation into Model DMPC Lipid Bilayers: Coupling of Effective Counterion Concentration and Lateral Bilayer Dimensions 
The journal of physical chemistry. B  2013;117(39):11641-11653.
Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely-held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a mono-arginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged mono-arginine peptide unit from water to the center of a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations, and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value.
doi:10.1021/jp404829y
PMCID: PMC4219256  PMID: 23888915
molecular dynamics; biological membranes; thermodynamic stability; charged amino acids
4.  Charge Equilibration Force Fields for Molecular Dynamics Simulations of Lipids, Bilayers, and Integral Membrane Protein Systems 
Biochimica et biophysica acta  2011;1818(2):318-329.
With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogues across the water-bilayer interface.
doi:10.1016/j.bbamem.2011.09.016
PMCID: PMC4216680  PMID: 21967961
5.  Liquid-Vapor Interfacial Properties of Aqueous Solutions of Guanidinium and Methyl Guanidinium Chloride: Influence of Molecular Orientation on Interface Fluctuations 
The journal of physical chemistry. B  2013;117(39):11719-11731.
The guanidinium cation (C(NH2)3+) is a highly stable cation in aqueous solution due to its efficient solvation by water molecules and resonance stabilization of the charge. Its salts increase the solubility of nonpolar molecules (”salting-in”) and decrease the ordering of water. It is one of the strongest denaturants used in biophysical studies of protein folding. We investigate the behavior of guanidinium and its derivative, methyl guanidinium (an amino acid analogue) at the air-water surface, using atomistic molecular dynamics (MD) simulations and calculation of potentials of mean force. Methyl guanidinium cation is less excluded from the air-water surface than guanidinium cation, but both cations show orientational dependence of surface affinity. Parallel orientations of the guanidinium ring (relative to the Gibbs dividing surface) show pronounced free energy minima in the interfacial region, while ring orientations perpendicular to the GDS exhibit no discernible surface stability. Calculations of surface fluctuations demonstrate that near the air-water surface, the parallel-oriented cations generate significantly greater interfacial fluctuations compared to other orientations, which induces more long-ranged perturbations and solvent density redistribution. Our results suggest a strong correlation with induced interfacial fluctuations and ion surface stability. These results have implications for interpreting molecular-level, mechanistic action of this osmolyte’s interaction with hydrophobic interfaces as they impact protein denaturation (solubilization).
doi:10.1021/jp405862p
PMCID: PMC4216681  PMID: 23937431
molecular dynamics; guanidinium; interface; fluctuations
6.  Dynamics and Energetics of Hydrophobically Confined Water 
PMCID: PMC4214077  PMID: 23004766
HYDROPHOBIC EFFECT; POLARIZABILITY; HYDROPHOBIC CONFINEMENT; DIFFUSION; WETTING; DEWETTING; DYNAMICS
7.  Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Non-Polarizable Ion Models 
The journal of physical chemistry. B  2008;112(37):11679-11693.
The effects of ion force field polarizability on the interfacial electrostatic properties of ~1 M aqueous solutions of NaCl, CsCl and NaI are investigated using molecular dynamics simulations employing both non-polarizable and Drude-polarizable ion sets. Differences in computed depth-dependent orientational distributions, “permanent” and induced dipole and quadrupole moment profiles, and interfacial potentials are obtained for both ion sets to further elucidate how ion polarizability affects interfacial electrostatic properties among the various salts relative to pure water. We observe that the orientations and induced dipoles of water molecules are more strongly perturbed in the presence of polarizable ions via a stronger ionic double layer effect arising from greater charge separation. Both anions and cations exhibit enhanced induced dipole moments and strong z alignment in the vicinity of the Gibbs dividing surface (GDS) with the magnitude of the anion induced dipoles being nearly an order of magnitude larger than those of the cations and directed into the vapor phase. Depth-dependent profiles for the trace and zz components of the water molecular quadrupole moment tensors reveal 40% larger quadrupole moments in the bulk phase relative to the vapor mimicking a similar observed 40% increase in the average water dipole moment. Across the GDS, the water molecular quadrupole moments increase non-monotonically (in contrast to the water dipoles) and exhibit a locally reduced contribution just below the surface due to both orientational and polarization effects. Computed interfacial potentials for the non-polarizable salts yield values 20 to 60 mV more positive than pure water and increase by an additional 30 to 100 mV when ion polarizability is included. A rigorous decomposition of the total interfacial potential into ion monopole, water and ion dipole, and water quadrupole components reveals that a very strong, positive ion monopole contribution is offset by negative contributions from all other potential sources. Water quadrupole components modulated by the water density contribute significantly to the observed interfacial potential increments and almost entirely explain observed differences in the interfacial potentials for the two chloride salts. By lumping all remaining non-quadrupole interfacial potential contributions into a single “effective” dipole potential, we observe that the ratio of quadrupole to “effective” dipole contributions range from 2:1 in CsCl to 1:1.5 in NaI suggesting that both contributions are comparably important in determining the interfacial potential increments. We also find that oscillations in the quadrupole potential in the double layer region are opposite in sign and partially cancel those of the “effective” dipole potential.
doi:10.1021/jp8038835
PMCID: PMC4214153  PMID: 18712908
AIR/WATER INTERFACE; SURFACE; SALTS; SIMULATIONS; MOLECULAR DYNAMICS; ELECTROLYTE SOLUTIONS; SODIUM CHLORIDE; SODIUM IODIDE; CESIUM CHLORIDE; SURFACE POTENTIAL; INTERFACIAL POTENTIAL; QUADRUPOLE MOMENT
8.  Binding Structures of tri-N-acetyl-β-glucosamine in Hen Egg White Lysozyme using Molecular Dynamics with a Polarizable Force Field 
Lysozyme is a well-studied enzyme that hydrolyzes the β-(1,4)-glycosidic linkage of N-acetyl-β-glucosamine (NAG)n oligomers. The active site of hen egg-white lysozyme (HEWL) is believed to consist of six subsites, A-F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all-atom molecular dynamics simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)3. Molecular dynamics trajectories are applied to analyze structures and conformation of the complex as well as protein-ligand interactions, including the hydrogen-bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)3 are investigated independently based on a fixed-charge model and a polarizable model. We also apply MM-GBSA methods based on molecular dynamics using both non-polarizable and polarizable force fields in order to compute binding free energies. We also study the correlation between RMSD and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed-charge models.
doi:10.1002/jcc.23109
PMCID: PMC4214157  PMID: 23109228
9.  Interfacial Structure, Thermodynamics, and Electrostatics of Aqueous Methanol Solutions via Molecular Dynamics Simulations Using Charge Equilibration Models 
The journal of physical chemistry. B  2009;113(27):9241-9254.
We present results from molecular dynamics simulations of methanol-water solutions using charge equilibration force fields to explicitly account for non-additive electronic interaction contributions to the potential energy. We study solutions across the concentration range from 0.1 to 0.9 methanol mole fraction. At dilute concentrations, methanol density is enhanced at the liquid-vapor interface, consistent with previous molecular dynamics and experimental studies. Interfacial thickness exhibits a monotonic increase with increasing methanol mole fraction, while surface tensions display monotonic decrease with methanol concentration, in qualitative agreement with experimental data and previous molecular dynamics predictions using polarizable force fields. In terms of interfacial structure, in keeping with predictions of traditional force fields, there is a unique preferential orientation of methanol molecules at the interface. Moreover, there is a free energetic preference for methanol molecules at the interface as evidenced by potential of mean force calculations. The pmf calculations suggest an interfacial state with 0.8 kcal/mole stability relative to the bulk, again, in qualitative agreement with previous simulation and experimental studies. Interfacial potentials based on double integration of total charge density range from −610 mV to −330 mV over the dilute to concentrated regimes, respectively. The preponderance of methanol at the interface at all mole fractions gives rise to a dominant methanol contribution to the total interfacial potential. Interestingly, there is a transition of the water surface potential contribution from negative to positive upon the transition from methanol mole fraction of 0.1 to 0.2. The dipole and quadrupole contributions to the water component of the total interfacial potential are effectively of equal magnitude and opposite sign, thus canceling one another. We compute the in-plane component of the dielectric permittivity along the interface normal. We observe a non-monotonic behavior of the methanol in-plane dielectric permittivity that tracks the methanol density profiles at low methanol mole fractions. At higher methanol mole fractions, the total in-plane permittivity is dominated by methanol, and displays a monotonic decrease from bulk to vapor. We finally probe the nature of hydration of water in the bulk versus interfacial regions for methanol mole fractions of 0.1 and 0.2. In the bulk, methanol perturbs water structure so as to give rise to water hydrogen bond excesses. Moreover, we observe negative hydrogen bond excess in the vicinity of the alkyl group, as reported by Zhong et al for bulk ethanol-water solutions using charge equilibration force fields, and positive excess in regions hydrogen bonding to nearest-neighbor methanol molecules. Within the interfacial region, water and methanol density reduction lead to concomitant water hydrogen bond deficiencies (negative hydrogen-bond excess).
doi:10.1021/jp900446f
PMCID: PMC4214159  PMID: 19569724
10.  Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models 
Journal of computational chemistry  2008;29(7):1142-1152.
We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure.
doi:10.1002/jcc.20877
PMCID: PMC4212651  PMID: 18074339
methanol; water; aqueous solutions; polarizable force field; fluctuating charge; non-additive interactions
11.  Spherical Monovalent Ions at Aqueous Liquid-Vapor Interfaces: Interfacial Stability and Induced Interface Fluctuations 
The journal of physical chemistry. B  2013;117(39):11732-11742.
Ion-specific interfacial behaviors of monovalent halides impact processes such as protein denaturation, interfacial stability, surface tension modulation, and as such, their molecular and thermodynamic underpinnings garner much attention. We use molecular dynamics simulations of monovalent anions in water to explore effects on distant interfaces. We observe long-ranged ion-induced perturbations of the aqueous environment as suggested by experiment and theory. Surface stable ions, characterized as such by minima in potentials of mean force computed using umbrella sampling MD simulations, induce larger interfacial fluctuations compared to non-surface active species, conferring more entropy approaching the interface. Smaller anions and cations show no interfacial potential of mean force minima. The difference is traced to hydration shell properties of the anions, and the coupling of these shells with distant solvent. The effects correlate with the positions of the anions in the Hofmeister series (acknowledging variations in force field ability to recapitulate essential underlying physics), suggesting how differences in induced, non-local perturbations of interfaces may be related to different specific-ion effects in dilute biophysical and nanomaterial systems.
doi:10.1021/jp406001b
PMCID: PMC4210775  PMID: 24032752
ions; liquid-vapor interface; surface-stability; Hofmeister; fluctuations
12.  Temperature Dependence and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface 
The journal of physical chemistry. B  2013;117(21):6512-6523.
We investigate temperature-dependence of free energetics with two single halide anions, I− and Cl−, crossing the aqueous liquid-vapor interface through molecular dynamics simulations. The result shows that I− has a modest surface stability of 0.5 kcal/mol at 300 K and the stability decreases as the temperature increases, indicating the surface adsorption process for the anion is entropically disfavored. In contrast, Cl− shows no such surface state at all temperatures. Decomposition of free energetics reveals that water-water interactions provide a favorable enthalpic contribution, while the desolvation of ion induces an increase in free energy. Calculations of surface fluctuations demonstrate that I− generates significantly greater interfacial fluctuations compared to Cl−. The fluctuation is attributed to the malleability of the solvation shells, which allows for more long-ranged perturbations and solvent density redistribution induced by I− as the anion approaches the liquid-vapor interface. The increase in temperature of the solvent enhances the inherent thermally-excited fluctuations and consequently reduces the relative contribution from anion to surface fluctuations, which is consistent with the decrease in surface-stability of I−. Our results indicate a strong correlation with induced interfacial fluctuations and anion surface stability; moreover, resulting temperature dependent behavior of induced fluctuations suggests the possibility of a critical level of induced fluctuations associated with surface stability.
doi:10.1021/jp401243m
PMCID: PMC4210776  PMID: 23537166
ions; liquid-vapor interface; surface-stability; Hofmeister; fluctuations
13.  Role of Spatial Ionic Distribution on the Energetics of Hydrophobic Assembly and Properties of the Water/Hydrophobe Interface† 
We present results from all-atom molecular dynamics simulations of large-scale hydrophobic plates solvated in NaCl and NaI salt solutions. As observed in studies of ions at the air-water interface, the density of iodide near the water-plate interface is significantly enhanced relative to chloride and in the bulk. This allows for the partial hydration of iodide while chloride remains more fully hydrated. In 1M solutions, iodide directly pushes the hydrophobes together (contributing −2.51 kcal/mol) to the PMF. Chloride, however, strengthens the water-induced contribution to the PMF by ~ −2.84 kcal/mol. These observations are enhanced in 3M solutions, consistent with the increased ion density in the vicinity of the hydrophobes. The different salt solutions influence changes in the critical hydrophobe separation distance and characteristic wetting/dewetting transitions. These differences are largely influenced by the ion-specific expulsion of iodide from bulk water. Results of this study are of general interest to the study of ions at interfaces and may lend insight to the mechanisms underlying the Hofmeister series.
doi:10.1039/c1cp20839j
PMCID: PMC4211274  PMID: 22231014
14.  Diffuse pulmonary lymphangiomatosis 
Diffuse pulmonary lymphangiomatosis (DPL) is a rare disease characterized by infiltration of the lung, pleura and mediastinum with thin-walled lymphangiomas. DPL can result in mass effect from infiltrative disease, restrictive and obstructive pulmonary physiology, chylous effusions and respiratory failure. The present article discusses clinical, radiographic and pathological features, and treatment options for DPL.
PMCID: PMC3628648  PMID: 23457676
Chylous effusions; Diffuse pulmonary lymphangiomatosis; Interstitial lung disease; Lymphangiomatosis
15.  Orthobiologics and platelet rich plasma 
Orthobiologics have evolved to the extent that they significantly influence modern orthopedic surgical practice. A better understanding of the role of various growth factors and cells in the process of tendon healing, ligament repair, cartilage regeneration and bone formation has stimulated focused research in many chronic musculoskeletal ailments. Investigators have published results of laboratory as well as clinical studies, using orthobiologics like platelet rich plasma, stem cells, autologous conditioned serum etc., with variable results. However, a clear consensus over the best orthobiologic substance and the method of preparation and usage of these substances is lacking. Much of the confusion is due to the fact that studies ranging from RCTs to case reports present variable results, and the interpretations are wide-ranging. We have reviewed the available orthobiologics related data with a focus on platelet rich plasma in orthopedic conditions.
doi:10.4103/0019-5413.125477
PMCID: PMC3931137  PMID: 24600055
Platelet rich plasma; orthobiologics; tendon healing; ligament repair
16.  Left Atrial Appendage Dysfunction in a Patient with Premature Ventricular Contractions - A Risk Factor for Stroke? 
A 16-year-old female with ventricular dysfunction and frequent ventricular arrhythmia presented with a cardioembolic stroke. Prior electrophysiology study and ablation was performed for ventricular tachycardia (VT). For remaining ventricular ectopy, the patient was maintained on carvedilol and mexiletine. After one year on this regimen, she presented with an acute stroke. Transesophageal echocardiography revealed no evidence of an intracardiac or ventricular thrombus but demonstrated markedly decreased left atrial appendage (LAA) flow velocity worsened during frequent premature ventricular contractions (PVC). In the absence of atrial fibrillation (AF), the LAA dysfunction was considered secondary to the frequent PVCs and was thought to be the underlying cause for the stroke. We present this case to highlight a potential under recognized association between LAA dysfunction and ventricular arrhythmia, similar to that observed with atrioventricular dyssynchronous pacing.
PMCID: PMC3775302  PMID: 24086095
PVC; left atrial appendage; stroke; risk; noncompaction cardiomyopathy
17.  Free Energetics of Carbon Nanotube Association in Pure and Aqueous Ionic Solutions 
The journal of physical chemistry. B  2012;116(28):8154-8168.
Carbon nanotubes are a promising platform across a broad spectrum of applications ranging from separations technology, drug delivery, to bio(electronic) sensors. Proper dispersion of carbon nanotube materials is important to retaining the electronic properties of nanotubes. Experimentally it has been shown that salts can regulate the dispersing properties of CNTs in aqueous system with surfactants (J. Am. Chem. Soc., 2009, 131:1144–1153); details of the physico-chemical mechanisms underlying such effects continue to be explored. We address the effects of inorganic monovalent salts (NaCl and NaI) on dispersion stability of carbon nanotubes. We perform all-atom molecular dynamics simulations using non-polarizable interaction models to compute the potential of mean force between two (10,10) single-walled carbon nanotubes (SWNTs) in the presence of NaCl/NaI and compare to the potential of mean force between SWNTs in pure water. Addition of salts enhances stability of the contact state between two SWNT’s on the order of 4 kcal/mole. The ion-specific spatial distribution of different halide anions gives rise to starkly different contributions to the free energy stability of nanotubes in the contact state. Iodide anion directly stabilizes the contact state to a much greater extent than chloride anion. The enhanced stability arises from the locally repulsive forces imposed on nanotubes by the surface-segregated iodide anion. Within the timescale of our simulations, both NaI and NaCl solutions stabilize the contact state by equivalent amounts. The marginally higher stability for contact state in salt solutions recapitulates results for small hydrophobic solutes in NaCl solutions (Athawale et al, J. Phys. Chem. B., 112, 5661. 2008) as well as single walled carbon nanotubes in NaCl and CaCl2 aqueous solutions.
doi:10.1021/jp3025717
PMCID: PMC3562760  PMID: 22780909
single-walled nanotubes; hydrophobic effect; specific-ion effects; molecular dynamics simulation
18.  Pulmonary alveolar proteinosis 
Pulmonary alveolar proteinosis (PAP) is a disease of alveolar accumulation of phospholipoproteinaceous material that results in gas exchange impairment leading to dyspnea and alveolar infiltrates. There are three forms of PAP: congenital, acquired and idiopathic; of which the latter two are predominant in the adult population. Previous case studies have found that the acquired form can be secondary to various autoimmune, infectious, malignant and environmental etiologies. Recent advances in the understanding of the pathophysiology of PAP demonstrate that the idiopathic form is due to antigranulocyte macrophage-colony stimulating factor antibodies. Therapeutic targets that replace granulocyte macrophage colony stimulating factor or remove these antibodies are being actively developed. The current standard of care is to perform whole lung lavage on these patients to clear the alveolar space to help improve respiratory physiology. A case of PAP is reported, followed by a literature review on the diagnosis and management of this rare condition with the aim of increasing awareness among physicians when treating patients who present with alveolar infiltrates.
PMCID: PMC3411387  PMID: 22891182
Alveolar infiltrates; Crazy paving; GM-CSF; Pulmonary alveolar proteinosis
19.  Impaired coronary microvascular reactivity in women with apical ballooning syndrome (Takotsubo/stress cardiomyopathy) 
Aims:
The pathophysiology of apical ballooning syndrome (ABS) remains to be elucidated. The aim of this study was to evaluate the coronary vascular reactivity of patients who were previously diagnosed with ABS.
Methods and results:
A total of 228 cases of ABS were prospectively identified, and of these, 10 patients (median age 61 years (IQR 48–75); all females) who underwent coronary vasomotion testing were included in the study. Coronary epicardial and microvascular responses to intracoronary acetylcholine (ACH; % change in diameter and % change in blood flow at doses of 10−6–10−4 mol/l), nitroglycerin (200–300 mg), and adenosine (36–60 µg) were evaluated. The median change in diameter with ACH was –9.3% (IQR –36.4, 3.2) with six patients (60%) demonstrating epicardial coronary constriction. The median increase in peak coronary blood flow in response to ACH was 13.1% (IQR –18.6, 55.0). This was markedly lower than the blood flow response seen in a reference group of 211 women from our laboratory (mean age 60 years) with normal microvascular responses to ACH: 103% (IQR 75, 149). Seven (70%) patients had <50% increase in coronary blood flow indicating abnormal microvascular response to ACH. 70% had either abnormal epicardial or microvascular response to ACH. Median coronary flow reserve was abnormal at 2.2% (IQR 2.0, 3.4; normal >2.5), and 90% had at least one abnormal measure of microvascular vasomotion.
Conclusion:
The novel observation is that coronary microvascular dysfunction is highly prevalent in patients with ABS. Thus, chronically impaired coronary vascular reactivity, especially involving the microcirculation, may be a central feature of the pathophysiology of ABS.
doi:10.1177/2048872613475891
PMCID: PMC3821803  PMID: 24222824
Apical ballooning syndrome; endothelium; microcirculation; stress cardiomyopathy; Tako-Tsubo cardiomyopathy
20.  How do we manage post-OLT redundant bile duct? 
AIM: To address endoscopic outcomes of post-Orthotopic liver transplantation (OLT) patients diagnosed with a “redundant bile duct” (RBD).
METHODS: Medical records of patients who underwent OLT at the Liver Transplant Center, University Texas Health Science Center at San Antonio Texas were retrospectively analyzed. Patients with suspected biliary tract complications (BTC) underwent endoscopic retrograde cholangiopancreatography (ERCP). All ERCP were performed by experienced biliary endoscopist. RBD was defined as a looped, sigmoid-shaped bile duct on cholangiogram with associated cholestatic liver biomarkers. Patients with biliary T-tube placement, biliary anastomotic strictures, bile leaks, bile-duct stones-sludge and suspected sphincter of oddi dysfunction were excluded. Therapy included single or multiple biliary stents with or without sphincterotomy. The incidence of RBD, the number of ERCP corrective sessions, and the type of endoscopic interventions were recorded. Successful response to endoscopic therapy was defined as resolution of RBD with normalization of associated cholestasis. Laboratory data and pertinent radiographic imaging noted included the pre-ERCP period and a follow up period of 6-12 mo after the last ERCP intervention.
RESULTS: One thousand two hundred and eighty-two patient records who received OLT from 1992 through 2011 were reviewed. Two hundred and twenty-four patients underwent ERCP for suspected BTC. RBD was reported in each of the initial cholangiograms. Twenty-one out of 1282 (1.6%) were identified as having RBD. There were 12 men and 9 women, average age of 59.6 years. Primary indication for ERCP was cholestatic pattern of liver associated biomarkers. Nineteen out of 21 patients underwent endoscopic therapy and 2/21 required immediate surgical intervention. In the endoscopically managed group: 65 ERCP procedures were performed with an average of 3.4 per patient and 1.1 stent per session. Fifteen out of 19 (78.9%) patients were successfully managed with biliary stenting. All stents were plastic. Selection of stent size and length were based upon endoscopist preference. Stent size ranged from 7 to 11.5 Fr (average stent size 10 Fr); Stent length ranged from 6 to 15 cm (average length 9 cm). Concurrent biliary sphincterotomy was performed in 10/19 patients. Single ERCP session was sufficient in 6/15 (40.0%) patients, whereas 4/15 (26.7%) patients needed two ERCP sessions and 5/15 (33.3%) patients required more than two (average of 5.4 ERCP procedures). Single biliary stent was sufficient in 5 patients; the remaining patients required an average of 4.9 stents. Four out of 19 (21.1%) patients failed endotherapy (lack of resolution of RBD and recurrent cholestasis in the absence of biliary stent) and required either choledocojejunostomy (2/4) or percutaneous biliary drainage (2/4). Endoscopic complications included: 2/65 (3%) post-ERCP pancreatitis and 2/10 (20%) non-complicated post-sphincterotomy bleeding. No endoscopic related mortality was found. The medical records of the 15 successful endoscopically managed patients were reviewed for a period of one year after removal of all biliary stents. Eleven patients had continued resolution of cholestatic biomarkers (73%). One patient had recurrent hepatitis C, 2 patients suffered septic shock which was not associated with ERCP and 1 patient was transferred care to an outside provider and records were not available for our review.
CONCLUSION: Although surgical biliary reconstruction techniques have improved, RBD represents a post-OLT complication. This entity is rare however, endoscopic management of RBD represents a reasonable initial approach.
doi:10.3748/wjg.v19.i16.2501
PMCID: PMC3646140  PMID: 23674851
Redundant bile duct; Orthotopic liver transplantation; Biliary complications; Biliary stent; Endoscopic retrograde cholangiopancreatography
21.  Beta3-Adrenoreceptor Stimulation Ameliorates Myocardial Ischemia-Reperfusion Injury Via Endothelial Nitric Oxide Synthase and Neuronal Nitric Oxide Synthase Activation 
Objectives
This paper examined whether nebivolol protects the heart via nitric oxide (NO) synthase and NO-dependent signaling in an in vivo model of acute myocardial infarction.
Background
Beta3-adrenergic receptor (AR) activation promotes endothelial nitric oxide synthase (eNOS) activity and NO bioavailability. We hypothesized that specific beta3-AR agonists would attenuate myocardial ischemia-reperfusion (MI/R) injury via eNOS activation and increased NO bioavailability.
Methods
Mice were subjected to 45 min of myocardial ischemia in vivo followed by 24 h of reperfusion (R). Nebivolol (500 ng/kg), CL 316243 (1 μg/kg), BRL-37344 (1 μg/kg), or vehicle (VEH) was administered at the time of R. Myocardial area-at-risk (AAR) and infarct size (INF)/AAR was measured at 24 h of R. Cardiac tissue and plasma were collected to evaluate eNOS phosphorylation, neuronal nitric oxide synthase (nNOS), inducible nitric oxide synthase expression, and nitrite and nitrosothiol levels.
Results
Nebivolol (500 ng/kg) reduced INF/AAR by 37% (p < 0.001 vs. VEH) and serum troponin-I levels from 41 ± 4 ng/ml to 25 ± 4 ng/ml (p < 0.05 vs. VEH). CL 316243 and BRL-37344 reduced INF by 39% and 42%, respectively (p < 0.001 vs. VEH). Nebivolol and CL 316243 increased eNOS phosphorylation at Ser-1177 (p < 0.05 vs. VEH) and increased nitrite and total nitrosylated protein levels. Nebivolol and CL 316243 significantly increased myocardial nNOS expression. Nebivolol failed to reduce INF after MI/R in beta3-AR−/−, eNOS−/−, and in nNOS−/− mice.
Conclusions
Our results indicate that beta3-AR agonists protect against MI/R injury. Furthermore, the cardioprotective effects of beta3-AR agonists are mediated by rapid eNOS and nNOS activation and increased NO bioavailability.
doi:10.1016/j.jacc.2011.09.033
PMCID: PMC3586978  PMID: 22152956
beta3 adrenergic receptor; cardiac ischemia; endothelial nitric oxide synthase; neuronal nitric oxide synthase; nitric oxide
22.  Solvation Structure and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface 
Chemical physics letters  2012;527:22-26.
Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy.
doi:10.1016/j.cplett.2011.12.061
PMCID: PMC3488351  PMID: 23136448
Ions; Polarizable Force Fields; Molecular Dynamics; TIP4P-FQ; TIP4P-QDP; Potential of Mean Force; Solvation Structure
23.  Molecular Dynamics Simulation of Hydrated DPPC Monolayers Using Charge Equilibration Force Fields 
We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ± 1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ± 1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ± 0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. Since the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly-modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.
doi:10.1002/jcc.21927
PMCID: PMC3488352  PMID: 21997857
24.  Solvation Properties of N-acetyl-β-glucosamine: A Molecular Dynamics Study Incorporating Electrostatic Polarization 
Journal of computational chemistry  2011;32(16):3339-3353.
N-acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous non-polarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas-phase relative rotation energy of exocyclic hydroxymethyl side-chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.
doi:10.1002/jcc.21873
PMCID: PMC3193586  PMID: 21898464
25.  Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs) 
Journal of computational chemistry  2011;32(14):2958-2973.
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the Particle Mesh Ewald method (PME) for solution of Poisson’s Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17004, 68484 and 273936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (SCD), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.
doi:10.1002/jcc.21871
PMCID: PMC3188664  PMID: 21793003

Results 1-25 (55)