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1.
Article in English | MEDLINE | ID: mdl-38606934

ABSTRACT

BACKGROUND: Whether testosterone replacement therapy (TRT) conveys additional cardiometabolic benefit to an intensive lifestyle therapy (LT) in older men with obesity and hypogonadism remains unclear. OBJECTIVE: To determine whether TRT augments the effect of LT on metabolic outcomes in older men with obesity and hypogonadism. DESIGN: Secondary analysis of a randomized, double-blind, placebo-controlled trial. SETTING: Veterans Affairs Medical Center. PARTICIPANTS: 83 older (age ≥ 65 years) men with obesity (BMI ≥ 30 kg/m2) and persistently low AM testosterone (< 10.4 nmol/L) associated with frailty. INTERVENTIONS: LT (weight management and exercise training) plus either testosterone (LT+TRT) or placebo (LT+Pbo) for six months. OUTCOME MEASURES: Primary outcome was change in glycated hemoglobin (HbA1c). Secondary outcomes included changes in other glucometabolic and lipid profile components, liver enzymes, inflammatory markers, adipokines; subcutaneous, visceral, intramuscular, and hepatic fat; blood pressure, and metabolic syndrome score. RESULTS: HbA1c decreased similarly in LT+TRT and LT+Pbo groups (-0.5% vs. -0.6%, respectively; p= 0.35). While TRT showed no synergistic effect with LT on ameliorating secondary outcomes, it eliminated the augmentative effect of LT on high-density lipoprotein cholesterol concentration (5.4 ± 1.0 mg/dL in LT+Pbo group vs. 0.2 ± 1.1 mg/dL in LT+TRT group, p= 0.01) and adiponectin levels (-408 ± 489 ng/mL in TRT+LT group vs 1832 ± 468 ng/mL in LT+Pbo group, p= 0.02). CONCLUSION: In older men with obesity and hypogonadism, adding TRT for six months to LT does not result in further improved cardiometabolic profiles, and could potentially blunt some of the metabolic benefits induced by LT.

2.
Curr Med Chem ; 2023 Mar 21.
Article in English | MEDLINE | ID: mdl-36944627

ABSTRACT

BACKGROUND: The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE: Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHOD: We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS: The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION: The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.

3.
ACS Omega ; 7(2): 1988-2001, 2022 Jan 18.
Article in English | MEDLINE | ID: mdl-35071887

ABSTRACT

The RDL receptor is one of the most relevant protein targets for insecticide molecules. It belongs to the pentameric ligand-gated ion channel (pLGIC) family. Given that the experimental structures of pLGICs are difficult to obtain, homology modeling has been extensively used for these proteins, particularly for the RDL receptor. However, no detailed assessments of the usefulness of homology models for virtual screening (VS) have been carried out for pLGICs. The aim of this study was to evaluate which are the determinant factors for a good VS performance using RDL homology models, specially analyzing the impact of the template conformational state. Fifteen RDL homology models were obtained based on different pLGIC templates representing the closed, open, and desensitized states. A retrospective VS process was performed on each model, and their performance in the prioritization of active ligands was assessed. In addition, the three best-performing models among each of the conformations were subjected to molecular dynamics simulations (MDS) in complex with a representative active ligand. The models showed variations in their VS performance parameters that were related to the structural properties of the binding site. VS performance tended to improve in more constricted binding cavities. The best performance was obtained with a model based on a template in the closed conformation. MDS confirmed that the closed model was the one that best represented the interactions with an active ligand. These results imply that different templates should be evaluated and the structural variations between their channel conformational states should be specially examined, providing guidelines for the application of homology modeling for VS in other proteins of the pLGIC family.

4.
J Comput Aided Mol Des ; 36(1): 25-37, 2022 01.
Article in English | MEDLINE | ID: mdl-34825285

ABSTRACT

Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput repurposing screens have already identified several existing drugs with potential to combat SARS-CoV-2. However, moving these hits forward for possible development into drugs specifically against this pathogen requires unambiguous identification of their corresponding targets, something the high-throughput screens are not typically designed to reveal. We present here a new computational inverse-docking protocol that uses all-atom protein structures and a combination of docking methods to rank-order targets for each of several existing drugs for which a plurality of recent high-throughput screens detected anti-SARS-CoV-2 activity. We demonstrate validation of this method with known drug-target pairs, including both non-antiviral and antiviral compounds. We subjected 152 distinct drugs potentially suitable for repurposing to the inverse docking procedure. The most common preferential targets were the human enzymes TMPRSS2 and PIKfyve, followed by the viral enzymes Helicase and PLpro. All compounds that selected TMPRSS2 are known serine protease inhibitors, and those that selected PIKfyve are known tyrosine kinase inhibitors. Detailed structural analysis of the docking poses revealed important insights into why these selections arose, and could potentially lead to more rational design of new drugs against these targets.


Subject(s)
Antiviral Agents/pharmacology , COVID-19 Drug Treatment , Drug Repositioning/methods , Pharmaceutical Preparations/administration & dosage , Protease Inhibitors/pharmacology , SARS-CoV-2/drug effects , Serine Endopeptidases/chemistry , COVID-19/virology , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation
5.
PLoS One ; 14(6): e0218042, 2019.
Article in English | MEDLINE | ID: mdl-31237897

ABSTRACT

γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the vertebrate and invertebrate nervous system. GABAA receptors are activated by GABA and their agonists, and modulated by a wide variety of recognized drugs, including barbiturates, anesthetics, and benzodiazepines. The phenols propofol, thymol, chlorothymol, carvacrol and eugenol act as positive allosteric modulators on GABAA-R receptor. These GABAergic phenols interact with the lipid membrane, therefore, their anesthetic activity could be the combined result of their specific activity (with receptor proteins) as well as nonspecific interactions (with surrounding lipid molecules) modulating the supramolecular organization of the receptor environment. Therefore, we aimed to contribute to a description of the molecular events that occur at the membrane level as part of the mechanism of general anesthesia, using a molecular dynamic simulation approach. Equilibrium molecular dynamics simulations indicate that the presence of GABAergic phenols in a DPPC bilayer orders lipid acyl chains for carbons near the interface and their effect is not significant at the bilayer center. Phenols interacts with the polar interface of phospholipid bilayer, particularly forming hydrogen bonds with the glycerol and phosphate group. Also, potential of mean force calculations using umbrella sampling show that propofol partition is mainly enthalpic driven at the polar region and entropic driven at the hydrocarbon chains. Finally, potential of mean force indicates that propofol partition into a gel DPPC phase is not favorable. Our in silico results were positively contrasted with previous experimental data.


Subject(s)
Lipid Bilayers/chemistry , Molecular Dynamics Simulation , Phenols/pharmacology , gamma-Aminobutyric Acid/chemistry , 1,2-Dipalmitoylphosphatidylcholine/chemistry , Entropy , Hydrogen Bonding , Propofol/pharmacology , Thermodynamics , Time Factors
6.
Rehabil Nurs ; 44(1): 29-34, 2019.
Article in English | MEDLINE | ID: mdl-30601431

ABSTRACT

PURPOSE: The aim of the study was to determine if listening to music may reduce anxiety experienced by stroke patients during acute rehabilitation. DESIGN: A prospective, nonblinded, randomized study in an inpatient rehabilitation setting. METHODS: Fifty participants were randomized into two groups: (1) 1 hour of music (intervention) or (2) no music (control). All participants completed pretest anxiety and depression screening and 44 completed the posttest anxiety screening. Differences between groups were determined using chi-square and t tests. FINDINGS: After listening to music for 1 hour, participants who completed the posttest (n = 44) reported significantly less anxiety (p < .0001) compared to before the intervention. The control group showed no difference in their pre- and posttest anxiety scores (p = .84). No differences were determined among age, gender, or diagnostic groups. CONCLUSIONS: These findings demonstrate that music intervention may help lessen anxiety in rehabilitation patients poststroke. CLINICAL RELEVANCE: Offering musical intervention to stroke patients in rehabilitation may lessen symptoms of anxiety.


Subject(s)
Anxiety/therapy , Music Therapy/standards , Stroke Rehabilitation/standards , Aged , Anxiety/psychology , Chi-Square Distribution , Female , Humans , Male , Middle Aged , Music Therapy/methods , Prospective Studies , Stress, Psychological/etiology , Stress, Psychological/prevention & control , Stress, Psychological/therapy , Stroke/complications , Stroke/psychology , Stroke Rehabilitation/methods
7.
Endocr Relat Cancer ; 25(10): 837-852, 2018 10.
Article in English | MEDLINE | ID: mdl-29875136

ABSTRACT

In pituitary adenomas, early recurrences and resistance to conventional pharmacotherapies are common, but the mechanisms involved are still not understood. The high expression of epidermal growth factor receptor 2 (HER2)/extracellular signal-regulated kinase (ERK1/2) signal observed in human pituitary adenomas, together with the low levels of the antimitogenic transforming growth factor beta receptor 2 (TBR2), encouraged us to evaluate the effect of the specific HER2 inhibition with trastuzumab on experimental pituitary tumor cell growth and its effect on the antiproliferative response to TGFB1. Trastuzumab decreased the pituitary tumor growth as well as the expression of ERK1/2 and the cell cycle regulators CCND1 and CDK4. The HER2/ERK1/2 pathway is an attractive therapeutic target, but its intricate relations with other signaling modulators still need to be unraveled. Thus, we investigated possible cross-talk with TGFB signaling, which has not yet been studied in pituitary tumors. In tumoral GH3 cells, co-incubation with trastuzumab and TGFB1 significantly decreased cell proliferation, an effect accompanied by a reduction in ERK1/2 phosphorylation, an increase of SMAD2/3 activation. In addition, through immunoprecipitation assays, a diminution of SMAD2/3-ERK1/2 and an increase SMAD2/3-TGFBR1 interactions were observed when cells were co-incubated with trastuzumab and TGFB1. These findings indicate that blocking HER2 by trastuzumab inhibited pituitary tumor growth and modulated HER2/ERK1/2 signaling and consequently the anti-mitogenic TGFB1/TBRs/SMADs cascade. The imbalance between HER2 and TGFBRs expression observed in human adenomas and the response to trastuzumab on experimental tumor growth may make the HER2/ERK1/2 pathway an attractive target for future pituitary adenoma therapy.


Subject(s)
Adenoma/metabolism , Cell Proliferation/drug effects , Pituitary Neoplasms/metabolism , Signal Transduction/drug effects , Smad Proteins/metabolism , Transforming Growth Factor beta/metabolism , Trastuzumab/pharmacology , Adenoma/pathology , Adult , Cell Cycle/drug effects , Female , Humans , Male , Middle Aged , Phosphorylation , Pituitary Neoplasms/pathology , Young Adult
8.
PLoS One ; 13(3): e0194154, 2018.
Article in English | MEDLINE | ID: mdl-29518146

ABSTRACT

The fatty acid-binding proteins L-BABP and Rep1-NCXSQ bind to anionic lipid membranes by electrostatic interactions. According to Molecular Dynamics (MD) simulations, the interaction of the protein macrodipole with the membrane electric field is a driving force for protein binding and orientation in the interface. To further explore this hypothesis, we studied the interactions of these proteins with cationic lipid membranes. As in the case of anionic lipid membranes, we found that both proteins, carrying a negative as well as a positive net charge, were bound to the positively charged membrane. Their major axis, those connecting the bottom of the ß-barrel with the α-helix portal domain, were rotated about 180 degrees as compared with their orientations in the anionic lipid membranes. Fourier transform infrared (FTIR) spectroscopy of the proteins showed that the positively charged membranes were also able to induce conformational changes with a reduction of the ß-strand proportion and an increase in α-helix secondary structure. Fatty acid-binding proteins (FABPs) are involved in several cell processes, such as maintaining lipid homeostasis in cells. They transport hydrophobic molecules in aqueous medium and deliver them into lipid membranes. Therefore, the interfacial orientation and conformation, both shown herein to be electrostatically determined, have a strong correlation with the specific mechanism by which each particular FABP exerts its biological function.


Subject(s)
Cell Membrane/chemistry , Fatty Acid-Binding Proteins/chemistry , Membrane Lipids/chemistry , Molecular Dynamics Simulation , Cell Membrane/metabolism , Fatty Acid-Binding Proteins/metabolism , Humans , Membrane Lipids/metabolism , Protein Structure, Secondary , Static Electricity
9.
J Chem Theory Comput ; 13(8): 3874-3880, 2017 Aug 08.
Article in English | MEDLINE | ID: mdl-28657750

ABSTRACT

The coalescence process of two nanoparticles to yield a core-shell structure is analyzed by a well-tempered metadynamics procedure. This methodology has been shown to be useful in understanding the present phenomenon in terms of two collective variables: the distance between the center of mass of the coalescing particles and the gyration radius of the resulting core element. The free-energy contour plots clearly show that the coalescence process involves the deformation of the core material, which is manifested in the residence of the system in regions with a larger gyration radius. Results from molecular dynamics for the same system were found helpful to reach the definition of this second collective variable. The advantages and limitations of the latter approach are discussed.

10.
Inj Prev ; 23(5): 321-327, 2017 10.
Article in English | MEDLINE | ID: mdl-27923800

ABSTRACT

BACKGROUND: Data on the factors associated with school shootings in the USA are limited. The public conversation has often suggested several factors that may be linked to these events, however with little empirical support. Aiming to fill this gap, we describe the characteristics of school shooting incidents in the USA between 2013 and 2015 and explore whether four factors that represent domains of firearm policy, educational policy and epidemiological risk factors for intentional firearm injuries-background check (BC) policies, per capita mental health expenditures (MHE), K-12 education expenditure (KEE) and urbanicity-were associated with school shootings during this period. METHODS: We searched LexisNexis, a newspaper and broadcast media databases for school shooting incidents from 1 January 2013 to 31 December 2015. Presence of BC laws was extracted from legal information in LexisNexis. State-level covariates of per capita MHE (2013), KEE (2013) and urbanicity (2010) rates were obtained from publicly available data sources. We used negative binomial regression models accounting for clustering by state to explore unadjusted associations between the BC laws, state-level covariates and school shootings to report IRR and 95% CI. RESULTS: We documented 154 school shootings (35, 55 and 64 each year). In unadjusted models, BC for firearm purchase (IRR=0.55, 95% CI 0.39 to 0.76), ammunition purchase (IRR=0.11, 95% CI 0.05 to 0.27), log per capita MHE (IRR=0.58, 95% CI 0.37 to 0.90), log per-capita KEE (IRR=0.09, 9% CI 0.02 to 0.29) and urbanicity (IRR=0.97, 95% CI 0.96 to 0.99) were associated with school shooting. CONCLUSIONS: School shootings are less likely in states with BC laws, higher MHE and KEE, and with greater per cent urban population.


Subject(s)
Firearms , Homicide/statistics & numerical data , Mass Casualty Incidents/statistics & numerical data , Ownership/legislation & jurisprudence , Public Policy , Schools , Suicide/statistics & numerical data , Wounds, Gunshot/epidemiology , Adolescent , Adult , Age Factors , Child , Female , Firearms/legislation & jurisprudence , Humans , Incidence , Male , Rural Population , Schools/legislation & jurisprudence , Sex Factors , United States/epidemiology , Urban Population , Young Adult
11.
Biochim Biophys Acta ; 1858(11): 2903-2910, 2016 11.
Article in English | MEDLINE | ID: mdl-27591685

ABSTRACT

Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the Lα phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.


Subject(s)
1,2-Dipalmitoylphosphatidylcholine/chemistry , Lipid Bilayers/chemistry , Molecular Dynamics Simulation , Phosphatidylcholines/chemistry , Phase Transition , Surface Tension , Temperature , Thermodynamics , Water/chemistry
12.
PLoS One ; 11(5): e0155183, 2016.
Article in English | MEDLINE | ID: mdl-27171006

ABSTRACT

Autodock Vina is a very popular, and highly cited, open source docking program. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. We show that the traditional approach to train empirical scoring functions, using linear regression to optimize the correlation of predicted and experimental binding affinities, does not result in a function with optimal docking capabilities. On the other hand, a combination of scoring, minimization, and re-docking on carefully curated training datasets allowed us to develop a simplified scoring function with optimum docking performance. This article provides an overview of the development of the Vinardo scoring function, highlights its differences with Vina, and compares the performance of the two scoring functions in scoring, docking and virtual screening applications. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. The Vinardo scoring function is available as an option within Smina, a fork of Vina, which is freely available under the GNU Public License v2.0 from http://smina.sf.net. Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address.


Subject(s)
Drug Evaluation, Preclinical , Molecular Docking Simulation , Software , Databases as Topic , Ligands , Thermodynamics
13.
Ann Epidemiol ; 26(1): 1-6.e1-2, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26596958

ABSTRACT

PURPOSE: To better understand the effects of race and/or ethnicity and neighborhood poverty on pediatric firearm injuries in the United States, we compared overall and intent-specific firearm hospitalizations (FH) with those of pedestrian motor vehicle crash hospitalizations (PMVH). METHODS: We used Nationwide Inpatient Sample data (1998-2011) among 0-15 year-olds in a 1:1 case-case study; 4725 FH and 4725 PMVH matched by age, year, and region. RESULTS: Risk of FH versus PMVH was 64% higher among black children, Odds ratio (OR) = 1.64, 95% confidence interval (95% CI) = 1.44-1.87, as compared to white children (P < .0001); this risk did not vary by neighborhood poverty (P interaction = .52). Risk of homicide FH versus PMVH was 842% higher among black (OR = 8.42, 95% CI = 6.27-11.3), 452% higher among Hispanics (OR = 4.52, 95% CI = 3.33-6.13) and 233% higher among other race (OR = 2.33, 95% CI = 1.52-3.59) compared to white children. There was a lower risk for unintentional FH among black OR = 0.73, 95% CI = 0.62-0.87, Hispanics (OR = 0.60, 95% CI = 0.49-0.74), and other (OR = 0.63, 95% CI = 0.47-0.83) compared to whites. These intent-specific risks attributed to race did not vary by neighborhood affluence. CONCLUSIONS: Black children were at greater likelihood of FH compared to white children regardless of neighborhood economic status. Minority children had an increased likelihood of intentional FH and a decreased likelihood of unintentional FH as compared to white children irrespective of neighborhood income.


Subject(s)
Ethnicity , Hospitalization/statistics & numerical data , Poverty Areas , White People , Wounds, Gunshot/economics , Wounds, Gunshot/ethnology , Accidents, Traffic/statistics & numerical data , Adolescent , Child , Child, Preschool , Databases, Factual , Female , Humans , Infant , Infant, Newborn , Logistic Models , Male , Odds Ratio , Risk Factors , United States/epidemiology
14.
Psychoneuroendocrinology ; 63: 178-90, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26454419

ABSTRACT

Anxiety and affective disorders are often associated with hypercortisolism and dysfunctional serotonergic systems, including increased expression of TPH2, the gene encoding the rate-limiting enzyme of neuronal serotonin synthesis. We previously reported that chronic glucocorticoid exposure is anxiogenic and increases rat Tph2 mRNA expression, but it was still unclear if this also translates to increased TPH2 protein levels and in vivo activity of the enzyme. Here, we found that adult male rats treated with corticosterone (CORT, 100 µg/ml) via the drinking water for 21 days indeed show increased TPH2 protein expression in the dorsal and ventral part of the dorsal raphe nucleus (DRD, DRV) during the light phase, abolishing the enzyme's diurnal rhythm. In a second study, we systemically blocked the conversion of 5-hydroxytryptophan (5-HTP) to serotonin immediately before rats treated with CORT or vehicle were either exposed to 30 min acoustic startle stress or home cage control conditions. This allowed us to measure 5-HTP accumulation as a direct readout of basal versus stress-induced in vivo TPH2 activity. As expected, basal TPH2 activity was elevated in the DRD, DRV and MnR of CORT-treated rats. In response to stress, a multitude of serotonergic systems reacted with increased TPH2 activity, but the stress-, anxiety-, and learned helplessness-related dorsal and caudal DR (DRD/DRC) displayed stress-induced increases in TPH2 activity only after chronic CORT-treatment. To address the mechanisms underlying this region-specific CORT-dependent sensitization, we stereotaxically implanted CORT-treated rats with cannulae targeting the DR, and pharmacologically blocked either corticotropin-releasing hormone receptor type 1 (CRHR1) or type 2 (CRHR2) 10 min prior to acoustic startle stress. CRHR2 blockade prevented stress-induced increases of TPH2 activity within the DRD/DRC, while blockade of CRHR1 potentiated stress-induced TPH2 activity in the entire DR. Stress-induced TPH2 activity in the DRD/DRC furthermore predicted TPH2 activity in the amygdala and in the caudal pontine reticular nucleus (PnC), while serotonin synthesis in the PnC was strongly correlated with the maximum startle response. Our data demonstrate that chronically elevated glucocorticoids sensitize stress- and anxiety-related serotonergic systems, and for the first time reveal competing roles of CRHR1 and CRHR2 on stress-induced in vivo serotonin synthesis.


Subject(s)
Receptors, Corticotropin-Releasing Hormone/physiology , Serotonin/metabolism , Stress, Psychological/metabolism , Amygdala/drug effects , Amygdala/metabolism , Animals , Anxiety/genetics , Anxiety/metabolism , Corticosterone/pharmacology , Dorsal Raphe Nucleus/drug effects , Dorsal Raphe Nucleus/metabolism , Homeostasis/drug effects , Homeostasis/genetics , Male , Metabolic Networks and Pathways/drug effects , Metabolic Networks and Pathways/genetics , Rats , Rats, Sprague-Dawley , Stress, Psychological/genetics , Tryptophan Hydroxylase/genetics , Tryptophan Hydroxylase/metabolism
15.
Colloids Surf B Biointerfaces ; 139: 25-32, 2016 Mar 01.
Article in English | MEDLINE | ID: mdl-26700230

ABSTRACT

The protein's primary structure has all the information for specific protein/peptide folding and, in many cases, can define specific amphiphilic regions along molecules that are important for interaction with membranes. In order to shed light on how peptide sequence is important for the surface properties of amphiphilic peptides, we designed three pairs of peptides with the following characteristics: (1) all molecules have the same hydrophobic residues; (2) the couples differ from each other in their hydrophilic amino acids: positively, negatively and non-charged; (3) each pair has the same residues (same global molecular hydrophobicity) but the primary structure is reversed in comparison to its partner (retro-isomer), giving a molecule with a hydrophilic N or C-terminus and a hydrophobic C or N-terminus. Using the Langmuir monolayer approach, we observed that sequence reversal has a central role in the lateral stability of peptide monolayers, in the ability of the molecules to partition into the air-water interface and in the rheological properties of peptide films, whereas the peptide's secondary structure, determined by ATR-FTIR, was the same for all peptides. Reversing the sequence also gives a differential way of peptide/lipid interaction when peptides are in the presence of POPC lipid bilayers. Our results show how sequence inversion confers a distinctive peptide surface behaviour and lipid interaction for molecules with a similar structure.


Subject(s)
Peptides/chemistry , Phosphatidylcholines/chemistry , Unilamellar Liposomes/chemistry , Amino Acid Sequence , Biological Transport , Hydrophobic and Hydrophilic Interactions , Molecular Sequence Data , Permeability , Protein Structure, Secondary , Spectroscopy, Fourier Transform Infrared , Static Electricity , Structure-Activity Relationship
16.
Inj Prev ; 22(3): 216-20, 2016 06.
Article in English | MEDLINE | ID: mdl-26124073

ABSTRACT

We assessed gun ownership rates in 2013 across the USA and the association between exposure to a social gun culture and gun ownership. We used data from a nationally representative sample of 4000 US adults, from 50 states and District of Columbia, aged >18 years to assess gun ownership and social gun culture performed in October 2013. State-level firearm policy information was obtained from the Brady Law Center and Injury Prevention and Control Center. One-third of Americans reported owning a gun, ranging from 5.2% in Delaware to 61.7% in Alaska. Gun ownership was 2.25-times greater among those reporting social gun culture (PR=2.25, 95% CI 2.02 to 2.52) than those who did not. In conclusion, we found strong association between social gun culture and gun ownership. Gun cultures may need to be considered for public health strategies that aim to change gun ownership in the USA.


Subject(s)
Culture , Firearms/statistics & numerical data , Ownership/statistics & numerical data , Adult , Cross-Sectional Studies , Humans , Licensure , Policy Making , Social Desirability , Socioeconomic Factors , Symbolism , United States
17.
J Chem Theory Comput ; 11(12): 5929-38, 2015 Dec 08.
Article in English | MEDLINE | ID: mdl-26597989

ABSTRACT

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.


Subject(s)
Molecular Dynamics Simulation , Proteins/chemistry , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Hydrogen Bonding , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Interaction Domains and Motifs , Protein Structure, Quaternary , Protein Unfolding
18.
Breast Cancer Res Treat ; 152(2): 231-7, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26067931

ABSTRACT

Toxicity due to treatment causes a negative impact on quality of life in breast cancer survivors. Hot flash symptoms, described as intense sensations of heat, sweating and flushing occur in more than 50 % of breast cancer patients taking tamoxifen. We hypothesized that venlafaxine, a selective-norepinephrine reuptake inhibitor drug, was effective for reducing patient-reported hot flash scores among women treated for breast cancer compared to other non-hormonal treatments. We searched Medline, Scopus, and Cochrane Central Register of Controlled Trials from inception till May 2015 for venlafaxine (75 mg once daily or greater) with non-hormonal comparators for the treatment of hot flashes in female breast cancer patients. The primary outcome was hot flash score (derived from patient-reported hot flash severity and frequency) in randomized controlled trials. Standardized mean differences (SMD) were calculated for each study due to variation in the outcome measures. Heterogeneity was determined using I (2) statistics, and publication bias was assessed using a contour funnel plot and Egger's tests. Pooled analyses demonstrated that venlafaxine significantly reduced hot flash scores compared to the trial comparators (overall SMD 2.06; 95% confidence interval (CI) [0.40, 3.72]). There was significant heterogeneity among these studies (I (2) = 98.7%, P < 0.001). Asymmetry in the contour funnel plot suggests the presence of publication bias and a trend towards small study effects (Egger's test, P = 0.096). Venlafaxine is efficacious in managing hot flashes among women with breast cancer. This review highlights methodological issues that arise from eligible trials and recommends a collaborative approach in survivorship studies.


Subject(s)
Breast Neoplasms/complications , Hot Flashes/drug therapy , Hot Flashes/etiology , Serotonin and Noradrenaline Reuptake Inhibitors/therapeutic use , Venlafaxine Hydrochloride/therapeutic use , Disease Management , Female , Humans , Treatment Outcome
19.
BMJ Open ; 4(9): e005628, 2014 Aug 14.
Article in English | MEDLINE | ID: mdl-25239291

ABSTRACT

OBJECTIVES: To document overall, racial, ethnic and intent-specific spatiotemporal trends of firearm-related fatality rates (FRF rates) in the USA. DESIGN: Cross-sectional study per year from 2000 to 2010. SETTING USA PARTICIPANTS: Aggregate count of all people in the USA from 2000 to 2010. OUTCOME MEASURES: Data from the Web-based Injury Statistics Query and Reporting System from 2000 to 2010 was used to determine annual FRF rates per 100,000 and by states, race, ethnicity and intent. RESULTS: The average national 11-year FRF rate was 10.21/100,000, from 3.02 in Hawaii to 18.62 in Louisiana: 60% of states had higher than national rates and 41 states showed no temporal change. The average national FRF rates among African-Americans and Caucasians were 18.51 and 9.05/100,000 and among Hispanics and non-Hispanics were 7.13 and 10.13/100,000; Hispanics had a decreasing change of -0.18, p trend<0.0001. In states with increasing trends (Florida and Massachusetts), Caucasians and non-Hispanics drove the rise; while in states with decreasing trends (California, North Carolina, Arizona, Nevada, New York, Illinois, Maryland), Hispanics and African-Americans drove the fall. The average national FRF rates due to homicides (4.1/100,000) and suicides (5.8/100,000) remained constant, but varied between states. CONCLUSIONS: Endemic national FRF rates mask a wide variation in time trends between states. FRF rates were twice as high in African-Americans than Caucasians but decreased among Hispanics. Efforts to identify state-specific best practices can contribute to changes in national FRF rates that remain high.


Subject(s)
Black or African American , Firearms , Hispanic or Latino , White People , Wounds, Gunshot/mortality , Cross-Sectional Studies , Humans , Time Factors , United States/epidemiology
20.
Biochim Biophys Acta ; 1838(3): 910-20, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24269200

ABSTRACT

The regulatory protein of the squid nerve sodium calcium exchanger (ReP1-NCXSQ) is a 15kDa soluble, intracellular protein that regulates the activity of the Na(+)/Ca(2+) exchanger in the squid axon. It is a member of the cellular retinoic acid-binding proteins family and the fatty acid-binding proteins superfamily. It is composed of ten beta strands defining an inner cavity and a domain of two short alpha helix segments. In this work, we studied the binding and orientation of ReP1-NCXSQ in anionic and zwitterionic lipid membranes using molecular dynamics (MD) simulations. Binding to lipid membranes was also measured by filtration binding assay. ReP1-NCXSQ acquired an orientation in the anionic membranes with the positive end of the macrodipole pointing to the lipid membrane. Potential of mean force calculations, in agreement with experimental measurements, showed that the binding to the anionic interfaces in low ionic strength was stronger than the binding to anionic interfaces in high ionic strength or to zwitterionic membranes. The results of MD showed that the electrostatic binding can be mediated not only by defined patches or domains of basic residues but also by a global asymmetric distribution of charges. A combination of dipole-electric field interaction and local interactions determined the orientation of ReP1-NCXSQ in the interface.


Subject(s)
Electricity , Fatty Acid-Binding Proteins/metabolism , Lipid Bilayers/metabolism , Membrane Lipids/metabolism , Sodium-Calcium Exchanger/metabolism , Animals , Decapodiformes , Fatty Acid-Binding Proteins/chemistry , Lipid Bilayers/chemistry , Membrane Lipids/chemistry , Molecular Dynamics Simulation , Protein Conformation , Sodium-Calcium Exchanger/chemistry
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