A5041030878- Protein Structure and Dynamics
- Enzyme Structure and Function
- Molecular Junctions and Nanostructures
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Photochemistry and Electron Transfer Studies
- Computational Drug Discovery Methods
- Spectroscopy and Quantum Chemical Studies
- Biochemical and Molecular Research
- Advanced Chemical Physics Studies
- Amino Acid Enzymes and Metabolism
- DNA Repair Mechanisms
- Electrochemical Analysis and Applications
- DNA and Nucleic Acid Chemistry
- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Magnetism in coordination complexes
- Metabolism and Genetic Disorders
- Chemical Synthesis and Analysis
- Advanced Thermodynamics and Statistical Mechanics
- Genomics and Phylogenetic Studies
- Receptor Mechanisms and Signaling
- Career Development and Diversity
- Neuroscience and Neuropharmacology Research
- Bioinformatics and Genomic Networks
Northeastern University
2015-2025
Universidad del Noreste
2020-2024
Budapest University of Technology and Economics
2022
Eastern University
2015
Scripps Research Institute
2011
Simon Fraser University
2008
Northwest University
2008
University of Calgary
2008
Brandeis University
2001
Howard Hughes Medical Institute
2001
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermodynamics for processes in finite timeBjarne Andresen, R. Stephen Berry, Mary Jo Ondrechen, and Peter SalamonCite this: Acc. Chem. Res. 1984, 17, 8, 266–271Publication Date (Print):August 1, 1984Publication History Published online1 May 2002Published inissue 1 August 1984https://pubs.acs.org/doi/10.1021/ar00104a001https://doi.org/10.1021/ar00104a001research-articleACS PublicationsRequest reuse permissionsArticle...
We show that theoretical microscopic titration curves (THEMATICS) can be used to identify active-site residues in proteins of known structure. Results are featured for three enzymes: triosephosphate isomerase (TIM), aldose reductase (AR), and phosphomannose (PMI). note TIM AR have similar structures but catalyze different kinds reactions, whereas PMI reactions. Analysis the all ionizable these shows a small fraction (3–7%) possess flat region where residue is partially protonated over wide...
Salts of the form 1,2‐dimethyl‐3‐propylimidazolium X [where , and were prepared purified. Linear sweep voltammetry was conducted at 80°C, a temperature which all four salts molten, Pt, W, glassy carbon working electrodes. We found that intrinsic anodic stability these anions in order . These experimental solution‐phase oxidation potentials correlated well with gas‐phase highest occupied molecular orbital energies calculated by an ab initio technique.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel calculations of potential surfaces van der Waals complexes containing large aromatic moleculesMary Jo Ondrechen, Ziva Berkovitch-Yellin, and Joshua JortnerCite this: J. Am. Chem. Soc. 1981, 103, 22, 6586–6592Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/ja00412a009https://doi.org/10.1021/ja00412a009research-articleACS PublicationsRequest...
The production of work from a heat source with finite capacity is discussed. We examine the conversion such first by single Carnot engine and then sequence engines. optimum values operating temperatures these engines are calculated. efficiency an arbitrary number derived, it shown that maximum available can be extracted only when cycles in becomes infinite. results illustrate importance recovery or bottoming processes optimization work-producing systems. In addition, present model...
The production of work in finite time from a reservoir with heat capacity is studied. A model system, for which the only irreversibilities result rates conduction, adopted. maximum obtainable such system derived, and found to be strongly dependent upon capacity. cycle producing derived an arbitrary one-component working fluid; no equation state assumed. In optimum cycle, when substance contact reservoir, then temperature fluid exponential function entropy linear time. While single fixed-time...
We report on the synthesis, identification, excited-state energetics, interstate electronic relaxation and intrastate nuclear dynamics in electronically–vibrationally excited states of Van der Waals molecules, consisting a large aromatic molecule bound to inert-gas atoms.
This study describes the design and implementation of remote Summer undergraduate research programs during COVID-19 pandemic, including program strengths recommendations for improvement from perspectives researchers.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA model for the optical absorption spectrum of (.mu.-pyrazine) decaamminediruthenium(5+): What hath Creutz and Taube wrought?Mary Jo Ondrechen, Jaeju Ko, Li Tai ZhangCite this: J. Am. Chem. Soc. 1987, 109, 6, 1672–1676Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/ja00240a012https://doi.org/10.1021/ja00240a012research-articleACS PublicationsRequest...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic structure of the Creutz-Taube ionLi Tai Zhang, Jaeju Ko, and Mary Jo OndrechenCite this: J. Am. Chem. Soc. 1987, 109, 6, 1666–1671Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://doi.org/10.1021/ja00240a011RIGHTS & PERMISSIONSArticle Views708Altmetric-Citations82LEARN ABOUT THESE METRICSArticle Views are COUNTER-compliant sum full text article downloads since...
A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge genomics. The input consists electrostatic geometric properties derived from structure query alone. Sequence-based conservation information, where available, may also be incorporated. Electrostatics features THEMATICS are combined with multidimensional isotonic...
Abstract One of the major challenges in genomics is to understand function gene products from their 3D structures. Computational methods are needed for high‐throughput prediction proteins structure. Methods that identify active sites important understanding and annotating proteins. Traditional exploiting either sequence similarity or structural can be unreliable cannot applied with novel folds low homology other Here, we present a machine‐learning application combines computed electrostatic,...
Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect these mutations is that SOD1, which normally stable dimer, dissociates into toxic monomers seed aggregates. Considerable research effort has been devoted to developing compounds stabilize dimer fALS SOD1 variants, but unfortunately, this not yet resulted treatment. We hypothesized cyclic thiosulfinate cross-linkers, selectively target rare,...
Abstract Background Methods are now available for the prediction of interaction sites in protein 3D structures. While many these methods report high success rates site prediction, often predictions not very selective and have low precision. Precision is addressed using Theoretical Microscopic Titration Curves (THEMATICS), a simple computational method identification active enzymes. Recall precision measured compared with other catalytic sites. Results Using test set 169 enzymes from original...
Genomics has posed the challenge of determination protein function from sequence and/or 3-D structure. Functional assignment relationships can be misleading, and structural similarity does not necessarily imply functional similarity. Proteins in DJ-1 family, many which are unknown function, examples proteins with both fold that span multiple classes. THEMATICS (theoretical microscopic titration curves), an electrostatics-based computational approach to site prediction, is used sort family...
Neglected tropical disease drug discovery requires application of pragmatic and efficient methods for development new therapeutic agents. In this report, we describe our target repurposing efforts the essential phosphodiesterase (PDE) enzymes TbrPDEB1 TbrPDEB2 Trypanosoma brucei , causative agent human African trypanosomiasis (HAT). We protein expression purification, assay development, benchmark screening a collection 20 established PDE inhibitors. disclose that PDE4 inhibitor piclamilast,...
Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also in a second shell and these turn third shell. These have distinct roles maintaining essential chemical properties first-shell catalytic particularly their spatial arrangement relative to binding pocket, electrostatic dynamic properties. The extent which remote participate catalysis precisely how they affect remains unexplored. To improve our understanding second- third-shell...
Monoacylglycerol lipase (MAGL) is the principle enzyme for metabolizing endogenous cannabinoid ligand 2-arachidonoyglycerol (2-AG). Blockade of MAGL increases 2-AG levels, resulting in subsequent activation endocannabinoid system, and has emerged as a novel therapeutic strategy to treat drug addiction, inflammation, neurodegenerative diseases. Herein we report new series inhibitors, which were radiolabeled by site-specific labeling technologies, including
Abstract Theoretical Microscopic Titration Curves (THEMATICS) may be used to identify chemically important residues in active sites of enzymes by characteristic deviations from the normal, sigmoidal Henderson–Hasselbalch titration behavior. Clusters such deviant physical proximity constitute reliable predictors location site. Originally with predicted behavior were identified human observation computed curves. However, it is preferable select unusual mathematically well‐defined criteria,...
Understanding the catalytic efficiency and specificity of enzymes is a fundamental question major practical conceptual importance in biochemistry. Although progress biochemical structural studies has enriched our knowledge enzymes, role enzyme catalysis residues that are not nearest neighbors reacting substrate molecule largely unexplored experimentally. Here computational active site predictors, THEMATICS POOL, were employed to identify functionally important direct contact with molecule....
Abstract Summary: We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information high-performance prediction of catalytic residues from 3D structures. Input features consist THEMATICS electrostatics data pocket ConCavity. measures deviation typical, sigmoidal titration behavior to identify functionally important ConCavity identifies binding pockets by analyzing the surface geometry...
The COVID-19 pandemic continues to pose a substantial threat human lives and is likely do so for years come. Despite the availability of vaccines, searching efficient small-molecule drugs that are widely available, including in low- middle-income countries, an ongoing challenge. In this work, we report results open science community effort, "Billion molecules against challenge", identify inhibitors SARS-CoV-2 or relevant receptors. Participating teams used wide variety computational methods...