A5061022607- Protein Structure and Dynamics
- Enzyme Structure and Function
- ATP Synthase and ATPases Research
- SARS-CoV-2 and COVID-19 Research
- Force Microscopy Techniques and Applications
- Pharmacogenetics and Drug Metabolism
- Pharmacological Effects of Natural Compounds
- Lipid Membrane Structure and Behavior
- Glycosylation and Glycoproteins Research
- Heat shock proteins research
- Botanical Research and Chemistry
- Proteins in Food Systems
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- Biochemical and Molecular Research
- Venomous Animal Envenomation and Studies
- Monoclonal and Polyclonal Antibodies Research
- RNA modifications and cancer
- Ion channel regulation and function
- Microbial Metabolic Engineering and Bioproduction
- Cardiac electrophysiology and arrhythmias
- Bioactive Compounds and Antitumor Agents
- Mechanical and Optical Resonators
- Protein Interaction Studies and Fluorescence Analysis
- Inflammatory mediators and NSAID effects
Institute of Fundamental Technological Research
2024-2025
Polish Academy of Sciences
2024-2025
Universidad Nacional Autónoma de México
2021-2023
ABSTRACT Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency accurate representation of protein dynamics with the capabilities studying proteins in different biological environments. This paper introduces enhanced model, which a virtual-site implementation Gō...
We present a review of series contact maps for the determination native interactions in proteins and nucleic acids based on distance threshold. Such are mostly physical chemical construction, yet they sensitive to some parameters (e.g., distances or atomic radii) can neglect key interactions. Furthermore, we also comment new class that only requires geometric arguments. The map is necessary ingredient build robust Go-Martini model their complexes Martini 3 force field. extension popular...
Biomolecular simulations have been paramount in advancing our understanding of the complex dynamics biological systems. They played a crucial role various applications, including drug discovery and molecular characterization virus-host interactions. Despite their success, biomolecular face inherent challenges due to multiscale nature processes, which involve intricate interactions across wide range length time scales. All-atom (AA-MD) provides detailed insights at atomistic resolution, yet...
Prostaglandin reductase 1 (PTGR1) is an NADPH-dependent enzyme critical to eicosanoid metabolism. Its elevated expression in malignant tumors often correlates with poor prognosis due its role protecting cells against reactive oxygen species. This study explores the inhibitory potential of licochalcone A, a flavonoid derived from Xinjiang licorice root, on human PTGR1. Using molecular dynamics simulations, we mapped enzyme's conformational landscape, revealing low-energy, rigid-body-like...
We performed a comprehensive structural analysis of the conformational space several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known (Delta, BA.1, XBB.1.5, and JN.1) alongside wild-type (WT) form SARS-CoV-2. The states each variant were characterized by analyzing their distributions within selected collective variables (CVs), such as inter-domain distances between receptor-binding domain (RBD) N-terminal (NTD). Our primary focus...
Wheat germ agglutinin (WGA) demonstrates potential as an oral delivery agent owing to its selective binding carbohydrates and capacity traverse biological membranes. In this study, we employed differential scanning calorimetry molecular dynamics simulations comprehensively characterize the thermal unfolding process of both complete lectin four isolated domains. Furthermore, present nuclear magnetic resonance structures three domains that were previously lacking experimental in their forms....
With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, develop drugs with novel modes bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as attractive antimicrobial target, validated by pharmaceutical approval inhibitor treat tuberculosis. In this work, we aimed design, through two types silico strategies, allosteric inhibitors ATP synthase, targeting...
Molecular dynamics simulations revealed variations in mechanostability among different SARS-CoV-2 variants complex with the H11-H4 nanobody.
In addition to playing a central role in the mitochondria as main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions cell membrane. Its malfunction has been linked growing number human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, aging diseases. Furthermore, inhibition this enzyme jeopardizes survival several bacterial pathogens public health concern. Therefore, emerged novel drug target both treat diseases...
We present a review of series contact maps for the determination native interactions in proteins and nucleic acids based on distance-threshold. Such are mostly physical chemical construction, yet they sensitive to some parameters (e.g. distances or atomic radii) can neglect key interactions. Furthermore, we also comment new class that only requires geometric arguments. The map is necessary ingredient build robust G\=oMartini model their complexes Martini 3 force field. extension popular...