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Salt Dependent Association of Novel Mutants of TATA-Binding Proteins to DNA:Predictions from Theory and Experiments

Communications in Computational Physics 2008年第5期3卷 1132-1153页

作者： Johan H.Bredenberg marcia o.fenley Institute of Molecular Biophysics Florida State UniversityTallahasseeFL 32306USA. Department of Physics Florida State UniversityTallahasseeFL 32306USA.

The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA,SKpred,are fairly insensitive to the choice of atomic charges,radii,interior dielectric constant and treatment of the boundary between a biomolecule and the *** this study we show that the SKpred is highly correlated with the conformational adaptability of the partners involved in the biomolecular binding *** is demonstrated for the wild-type and mutant forms of the archaeon Pyrococcus woesi TATA-binding protein(PwTBP)in complex with DNA,on which we performed molecular mechanics energy minimizations with different protocols,and molecular dynamics simulations and then computed the SKpred on the resulting *** was found that the inter-molecular non bonded force field energy between the DNA and protein correlates linearly and significantly well with the *** correlation encompasses the wild-type and mutant variants of the PwTBP and provides us with a quick way to estimate the SKpred from a large ensemble of structures generated with Molecular Dynamics or Monte Carlo *** corresponding experimental SKobs should also correlate with the inter-molecular non bonded force field energy between the protein and DNA,given that the underlying mechanisms in binding and salt-dependent effects are in fact the main contributors in the association of proteins/peptides to nucleic *** show that it is possible to fit experiments versus the inter-molecular non bonded force field energy between the protein and DNA,and use this relation to predict the SKobs in absolute ***,we present two novel approaches to estimate both the SKpred and the SKobs for in silico modelled PwTBP novel mutants and even for TBPs from other *** is a simple but powerful tool to suggest new experiments on the TBP-DNA type of macromolecular *** conclude by suggesting some mutants and a possible biological interpretation of how changes in solvent

关键词： Poisson-Boltzmann equation electrostatics salt dependence binding molecular mechanics DNA TATA binding proteins.

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The Role of Anionic Protein Residues on the Salt Dependence of the Binding of Aminoacyl-tRNA Synthetases to tRNA:A Poisson-Boltzmann Analysis

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Communications in Computational Physics 2008年第5期3卷 1051-1070页

作者： Johan H.Bredenberg Alexander H.Boschitsch marcia o.fenley Institute of Molecular Biophysics Florida State UniversityTallahasseeFL 32306USA. Continuum-Dynamics Inc. 34 Lexington AvenueEwingNJ 08618USA. Department of Physics Florida State UniversityTallahasseeFL 32306USA.

Long-range electrostatic interactions in proteins/peptides associating to nucleic acids are reflected in the salt-dependence of the binding *** to the oligocationic binding model,which is based on counterion condensation theory,only the cationic residues of peptides/proteins near the binding interface are assumed to affect the salt dependence in the association of peptides and proteins to nucleic *** model has been used to interpret and predict the binding of oligocationic chains-such as oligoarginines/lysines-to nucleic acids,and does an excellent job in these kinds of *** simple relationship,which is used to compare or count the number of ionic interactions in protein-nucleic acid complexes,does not hold when acidic residues,*** and aspartate,are incorporated in the protein ***,we report a combined molecular mechanics(by means of energy-minimization of the structure under the influence of an empirical energy function)and Poisson-Boltzmann(PB)study on the salt-dependence in binding to tRNA of two important enzymes that are involved in the seminal step of peptide formation in the ribosome:Glutamine synthetase(GluRS)and Glutaminyl synthetase(GlnRS)bound to their cognate *** two proteins are anionic and contain a significant number of acidic residues distributed over the entire *** of these residues are located in the binding interface to *** computed the salt-dependence in association,SKpred,of these enzyme-tRNA complexes using both the linear and nonlinear solution to the PoissonBoltzmann Equation(PBE).our findings demonstrate that the SKpred obtained with the nonlinear PBE is in good agreement with the experimental SKobs,while use of the linear PBE resulted in the SKpred being *** conclude that electrostatic interactions between the binding partners in these systems are less favorable by means of charge-charge repulsion between negatively charged protein residues and phosphateoxygens in th

关键词： Enzyme electrostatics molecular mechanics Poisson-Boltzmann equation oligocation salt-dependence aminoacyl-tRNA synthetase polyelectrolyte counterion condensation theory

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Numerical optimization of a Walk-on-Spheres Solver for the Linear Poisson-Boltzmann Equation

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Communications in Computational Physics 2013年第1期13卷 195-206页

作者： Travis Mackoy Robert C.Harris Jesse Johnson Michael Mascagni marcia o.fenley Institute of Molecular Biophysics Florida State UniversityTallahasseeFL 32306USA Department of Physics Florida State UniversityTallahasseeFL 32306USA Departments of Computer Science Mathematics and Scientific ComputingFlorida State UniversityTallahasseeFL 32306USA

Stochastic walk-on-spheres(WoS)algorithms for solving the linearized Poisson-Boltzmann equation(LPBE)provide several attractive features not available in traditional deterministic solvers:Gaussian error bars can be computed easily,the algorithm is readily parallelized and requires minimal memory and multiple solvent environments can be accounted for by reweighting ***,previouslyreported computational times of these Monte Carlo methods were not competitive with existing deterministic numerical *** present paper demonstrates a series of numerical optimizations that collectively make the computational time of these Monte Carlo LPBE solvers competitive with deterministic *** optimization techniques used are to ensure that each atom’s contribution to the variance of the electrostatic solvation free energy is the same,to optimize the bias-generating parameters in the algorithm and to use an epsilon-approximate rather than exact nearest-neighbor search when determining the size of the next step in the Brownian motion when outside the molecule.

关键词： Poisson-Boltzmann equation walk-on-spheres solvation

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Fecal calprotectin and endoscopic scores: The cornerstones in clinical practice for evaluating mucosal healing in inflammatory bowel disease

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World Journal of Gastroenterology 2024年第24期30卷 3022-3035页

作者： marcia Henriques de Magalhães Costa Ligia Yukie Sassaki Júlio Maria Fonseca Chebli Department of Clinical Medicine Fluminense Federal UniversityRio de Janeiro 24210-200Brazil Department of Internal Medicine Medical SchoolSão Paulo State University(Unesp)Botucatu 18618-686São PauloBrazil Division of Gastroenterology Department of MedicineUniversity Hospital of The Federal University of Juiz de ForaUniversity of Juiz de Fora School of MedicineJuiz de Fora 36036-247Minas GeraisBrazil

Managing inflammatory bowel disease(IBD)is becoming increasingly complex and personalized,considering the advent of new advanced therapies with distinct mechanisms of *** mucosal healing(MH)is a pivotal therapeutic goal in IBD management and can prevent IBD progression and reduce flares,hospitalization,surgery,intestinal damage,and colorectal *** proactive disease and therapy assessment is essential to achieve better control of intestinal inflammation,even if subclinical,to alter the natural course of *** monitoring of fecal calprotectin(FC)levels and interval endoscopic evaluations are cornerstones for evaluating response/remission to advanced therapies targeting IBD,assessing MH,and detecting subclinical ***,we comment on the article by Ishida et al Moreover,this editorial aimed to review the role of FC and endoscopic scores in predicting MH in patients with ***,we intend to present some evidence on the role of these markers in future targets,such as histological and transmural *** prospective multicenter studies with a stricter MH criterion,standardized endoscopic and histopathological analyses,and virtual chromoscopy,potentially including artificial intelligence and other biomarkers,are desired.

关键词： Fecal calprotectin Endoscopic scores Mucosal healing Histological healing Ulcerative colitis Inflammatory bowel diseases

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Feruloylation in Grasses： Current and Future Perspectives

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Molecular Plant 2009年第5期2卷 861-872页

作者： marcia M. de o. Buanafinat Department of Biology 208 Mueller Laboratory Pennsylvania University University Park PA 16802 USA

In the cell walls of forage grasses, ferulic acid is esterified to arabinoxylans and participates with lignin monomers in oxidative coupling pathways to generate ferulate-polysaccharide-lignin complexes that cross-link the cell wall. The accumulation of ferulates and the cross-linking of arabinoxylans via diferulate esters are hypothesized to function in various processes in plants. The specific roles of arabinoxylan feruloylation as well as the nature, cellular localization, and substrate for arabinoxylans feruloylation of cell walls are reviewed. The various approaches that have been used for assessing the specific roles of feruloylation are described and assessed. I argue that, until recently, the specific role of feruloylation in these various processes has been established largely by indirect experiments and, although these studies reached similar conclusions about the potential importance of wall feruloylation, they suffer from a common problem： namely they depend on correlations between two processes and do not stem from a detailed understanding of the mechanisms of feruloylation. I also argue that the nature of arabinoxylan feruloylation remains uncertain.

关键词： Cell wall feruloylation ferulic acid cross-link dehydrodiferulate grasses.

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Challenges in Implementing DVI Best Practice Guidelines Due to the Brumadinho Disaster

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Forensic Medicine and Anatomy Research 2024年第1期12卷 1-12页

作者： Reinaldo Moreira Silva Bruno Diniz Sander Morais Carlos Danilo Ruas Silva Elza Cristina Lopes de oliveira Fernando Pereira Macedo Giovanni Vitral Pinto Guadalupe Dell’Arret Coutinho Higgor Gonçalves Dornelas João Luiz Silva Moreira Laila Evangelista de Almeida Fernandes marcia Lobão Iannini Patrícia Siqueira Valéria Rosalina Dias e Santos Sordaini Maria Caligiorne Instituto de Criminalística Polícia Civil de Minas Gerais Belo Horizonte Brazil

The broke of a tailings dam from Vale S.A. destroyed a gigantic area killing 270 persons in Brumadinho/Brazil. organizing activities after a mass disaster is a complex process that requires the involvement of many people and resources in the laboratory. To DNA identification of the victims, a daunting work had to be made by DNA laboratory staff in a collaborative effort with many partners. Efforts to implement good practice guidelines in Disaster Victim Identification (DVI) have revealed several important aspects that need to change in the forensic DNA laboratory. This article highlights the challenges of implementing DVI best practice guidelines in resource-poor settings, but with professionals from different sectors engaged in the same goal of briefly identifying victims and helping families and society.

关键词： Disaster Victim Identification DNA Brumadinho

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Core-softened potentials, multiple liquid-liquid critical points, and density anomaly regions： An exact solution

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Frontiers of physics 2018年第1期13卷 85-94页

作者： Eduardo o. Rizzatti Marco Aurelio A. Barbosa marcia C. Barbosa Instituto de Fisica Universidade Federal do Rio Grande do Sul Porto Alegre-RS Brazil Programa de Pos-Graduacao em Ciencia de Materiais Universidade de Brasilia Planaltina-DF Brazil

The pressure versus temperature phase diagram of a shoulder-like potential is exactly computed in one system of particles interacting through a multiscale dimension. The N-shoulder potential exhibits N density anomaly regions in the phase diagram if the length scales can be connected by a convex curve The result is analyzed in terms of the convexity of the Gibbs free energy.

关键词： density anomalies regions

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Rapid acupuncture for musculoskeletal pain in the emergency room of the Hospital Servidor Publico Estadual, Brazil: A quasi-experimental study

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Journal of Integrative Medicine 2020年第4期18卷 313-318页

作者： Luciana Aikawa Alexandre Massao Yoshizumi Mirian Matsura Shirassu marcia Kiyomi Koike Programa de Pós-Graduação em Ciências da Saúde Instituto de Assistência Médica ao Servidor Público Estadual(IAMSPE)Vila ClementinoSão PauloSP 04029-000Brazil Associação Médica Brasileira de Acupuntura Vila MarianaSão PauloSP 04011-002Brazil

objective:To compare differences in self-reported musculoskeletal pain before and after receiving rapid acupuncture for pain at an outpatient emergency ***:Exactly 102 patients presenting to the emergency room of the Hospital Servidor Publico Estadual in Sao Paulo,Brazil,participated in this before-and-after *** participants had musculoskeletal pain and were treated with the technique proposed by Marques *** emergency acupuncture involved inserting a needle at a point defined by traditional Chinese medicine and applying intense stimulation for 10 s;no more than two points were used on any individual *** was measured using a numerical visual scale before and immediately after the ***:Participants in this study were mostly women(78%),had a college degree(47%)and were below the age of 60(56%).The most common region of pain was the lower back(31%),and the most common type of pain was acute and exacerbated chronic *** meridians most commonly involved were the eight extra meridians(40%),and the points most often used for treatment were Houxi(SI3),Shenmai(BL62)and Zulinqi(GB41).Almost all participants reported a decrease in pain intensity,independent of sex,education level,pain site and pain type(acute/chronic;Pof the session,only4%of the participants reported a desire for allopathic ***:This emergency acupuncture technique for analgesia appears to reduce musculoskeletal *** registration:Brazilian Registry of Clinical Trials(http://***/)with ***-8 dmfjf.

关键词： Acupuncture analgesia Emergency medical services Acute pain Acupuncture therapy

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oxidative dehydrogenation of propane under steady-state and transient regimes over alumina-supported catalysts prepared from mixed V_2W_4o_(19)^(4-) hexametalate precursors

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Journal of Natural Gas Chemistry 2010年第2期19卷 123-133页

作者： Sébastien Paul Elise Berrier marcia Cristina Kaezer Frana Jean-Guillaume Eon Univ Lille Nord de France F-59000 LilleFrance ECLille UCCSF-59650 Villeneuve d'AscqFrance CNRS UMR 8181F-59650 Villeneuve d'AscqFrance USTL UCCSF-59650 Villeneuve d'AscqFrance Instituto de Quimíca Universidade Federal do Rio de Janeiro-Cidade UniversitáriaIlha do Fundo21945-970 Rio de JaneiroBrazil

An integrated approach combining the development of an innovative catalyst and the research of a set of adequate operating conditions for the propane oxidative dehydrogenation （oDH） is *** experimental set-up,specially designed for steady-state and transient studies is *** preparation method,the characterization and the performances in steady-state and transient regimes of catalysts based on V2W4o194-Lindqvist isopolyanion used as a precursor and supported on alumina are *** influence of the preparation method of the catalyst and the role of water in the feed gas are more particularly discussed.

关键词： propane oxidative dehydrogenation (oDH) transient regime pulsed reactor Lindqvist isopolyanion in-situ Raman

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Plant plasma membrane-resident receptors:Surveillance for infections and coordination for growth and development

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Journal of Integrative Plant Biology 2021年第1期63卷 79-101页

作者： Ana marcia Escocard de Azevedo Manhaes Fausto Andres ortiz-Morea Ping He Libo Shan Department of Plant Pathology and Microbiology Texas A&M UniversityCollege Station Texas77843USA Department of Biochemistry and Biophysics Texas A&M UniversityCollege Station Texas77843USA Centro de Investigaciones Amazonicas CIMAZ-MACAGUAL Universidad de la AmazoniaFlorencia 180002622Colombia

As sessile organisms, plants are exposed to pathogen invasions and environmental fluctuations. To overcome the challenges of their surroundings, plants acquire the potential to sense endogenous and exogenous cues, resulting in their adaptability. Hence, plants have evolved a large collection of plasma membrane-resident receptors, including RECEPToR-LIKE KINASEs(RLKs) and RECEPToR-LIKE PRoTEINs(RLPs) to perceive those signals and regulate plant growth,development, and immunity. The ability of RLKs and RLPs to recognize distinct ligands relies on diverse categories of extracellular domains evolved. Co-regulatory receptors are often required to associate with RLKs and RLPs to facilitate cellular signal transduction. RECEPToR-LIKE CYToPLASMIC KINASEs(RLCKs) also associate with the complex, bifurcating the signal to key signaling hubs, such as MIToGEN-ACTIVATED PRoTEIN KINASE(MAPK) cascades, to regulate diverse biological processes. Here, we discuss recent knowledge advances in understanding the roles of RLKs and RLPs in plant growth, development, and immunity, and their connection with co-regulatory receptors, leading to activation of diverse intracellular signaling pathways.

关键词： co-regulatory receptors plant growth and development plant immunity RECEPToR-LIKE KINASE(RLK) RECEPToR-LIKE PRoTEIN(RLP) signal transduction

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