A5048374538- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Enzyme Structure and Function
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Lipid Membrane Structure and Behavior
- Protein Structure and Dynamics
- Microfluidic and Capillary Electrophoresis Applications
- Nanopore and Nanochannel Transport Studies
- Hepatitis C virus research
- Biochemical and Molecular Research
- thermodynamics and calorimetric analyses
- Genomics and Phylogenetic Studies
- Surface Modification and Superhydrophobicity
- Microfluidic and Bio-sensing Technologies
- RNA modifications and cancer
- Ion channel regulation and function
- Biosensors and Analytical Detection
- Computational Geometry and Mesh Generation
- Thermodynamic properties of mixtures
- Advanced Chemical Physics Studies
- Computer Graphics and Visualization Techniques
- Spectroscopy and Quantum Chemical Studies
Instituto Politécnico Nacional
2014-2025
Center for Research and Advanced Studies of the National Polytechnic Institute
2016-2025
Instituto de Estudios Avanzados
2025
Centro de Investigación en Materiales Avanzados
2016-2022
Integral University
2022
Istanbul Medeniyet University
2022
Cukurova University
2022
Instituto Tecnológico Superior de Irapuato
2012-2017
Scripps Research Institute
2008
University of Michigan
2008
VIPERdb (http://viperdb.scripps.edu) is a relational database and web portal for icosahedral virus capsid structures. Our aim to provide comprehensive resource specific the needs of virology community, with an emphasis on description comparison derived data from structural computational analyses capsids. In current release, VIPERdb2, we implemented useful novel method represent protein residues in asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ...
The hydrations of Na+ and K+ were investigated by means Monte Carlo simulations with refined ab initio based potentials. These interaction potentials include intramolecular relaxation, polarizability many-body nonadditive effects. Care was taken to ensure proper convergence the MC runs that statistical samples large enough. As a result, agreement attained all experimental data available for hydration ions. water molecules in first shell found have same geometries dipole moments as those...
Abstract VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and database structure-derived along with various specific information. VIPERdb has been continuously improved for over 20 years contains number structure analysis tools. The release v3.0 new structure-based analytics tools like Multiple Structure-based Sequence Alignment (MSSA) to identify hot-spot residues within selected group an anomaly detection...
Amphotericin B is the most potent antimycotic known to date. However due its large collateral toxicity, use, although long standing, had been limited. Many attempts have made produce derivatives with reduced damage. The molecular mechanism of polyene has also closely studied for this purpose and understanding it would contribute development safe derivatives. Our study examined action, including chemical synthesis, electrophysiology, pharmacology, toxicology dynamics. results were used...
We have calculated the lateral pressure profile from well-converged, experimentally validated, molecular dynamics simulations of hydrated lipid bilayer membranes containing highly polyunsaturated fatty acids. The three simulations, each 30 ns in length, contain ω-3 acids, ω-6 and a mixture acids cholesterol were continued previously published that demonstrated excellent agreement with wide variety experimental measurements. find distribution stress within hydrophobic core membrane is...
Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about impact HGT on evolution enzyme function. Specifically, what influence a recently acquired function an existing gene? For example, certain members genus Corynebacterium have horizontally whole l-tryptophan biosynthetic operon, whereas closely related actinobacteria, for Mycobacterium, trpF missing. In performed by dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also...
The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization analysis tools accessed through set of interfaces. Our aim in developing VIPERdb to provide comprehensive on viruses comprising simple detailed attributes such as size (diameter), architecture T number), genome type, taxonomy, intersubunit association energies, surface-accessible...
Using a simple model it is shown that the cost of constraining hydrated potassium ion inside narrow nanopore smaller than sodium ion. The former allows for greater distortion its hydration shell and can therefore maintain better coordination. We propose in this way larger go through pores more easily. This relevant to molecular basis selective nanopores since mechanism does not depend on details pore, could also operate all sorts nanotubes, from biological synthetic.
Drug-resistant tuberculosis is a pressing global health issue that requires the development of new drugs or identification therapeutic targets. The ESX-3 secretion system essential for Mycobacterium growth and plays role in iron/zinc homeostasis virulence. aim this study was to evaluate quaternary interface EccD3, component system, association an eccD3 mutant with drug resistance. molecular structures EccD3 protein other proteins M. were predicted based homology Mycolicibacterium smegmatis...
The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics metabolic modeling to detect bacterial species that are evolving by loss, with finding Actinomycetaceae genomes from human cavities undergoing sizable reductions, including L-histidine L-tryptophan biosynthesis. observe dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears coevolve occurrence trp his genes....
Current sequence-based approaches to identify enzyme functional shifts, such as promiscuity, have proven be highly dependent on a priori knowledge, hampering our ability reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used classify families, can useful distinguish between closely related families with different specificities. The (βα)8-isomerase HisA/PriA family, involved in L-histidine (HisA, mono-substrate) biosynthesis most bacteria...
Amphotericin B (AmB) is still the most effective drug for treatment of systemic fungal infections in humans. Despite significant theoretical and experimental efforts trying to understand its molecular mechanism action, answer has remained elusive. In this work, we present a computational methodology test current membrane related hypotheses, namely, transmembrane ion channel, adsorption, sterol sponge. We use thermodynamic approach which represent by multiphase solvation model with atomic...
Mitochondria are quantitatively the most important sources of reactive oxygen species (ROS) which formed as by-products during cellular respiration. ROS generation occurs when single electrons transferred to molecular oxygen. This leads a number different types, among them superoxide. Although studies focus on in mitochondrial matrix, intermembrane space (IMS) is also this regard. The main scavengers for detoxification superoxide IMS Cu, Zn dismutase (SOD1) and cytochrome-c. Similar ROS,...
Viral capsids are composed of multiple copies one or a few chemically distinct capsid proteins and mostly stabilized by inter subunit protein-protein interactions. There have been efforts to identify analyze these interactions, in terms their extent similarity, between the interfaces related quasi- icosahedral symmetry. Here, we describe new method map quaternary interactions spherical virus onto polar angle space with respect symmetry axes using azimuthal orthographic diagrams. This...
Abstract Porcine circovirus type 2 (PCV2) still represents a major problem to the swine industry worldwide, causing high mortality rates in infected animals. Virus‐like particles (VLPs) have gained attention for vaccine development, serving both as scaffolds epitope expression and immune response enhancers. The commercial subunit vaccines against PCV2 consist of VLPs formed by self‐assembly capsid protein (CP) expressed baculovirus vector system. In this work, protective was inserted into...