A5088500200- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- HIV/AIDS drug development and treatment
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- HIV Research and Treatment
- Antimicrobial Peptides and Activities
- Porphyrin Metabolism and Disorders
- Spectroscopy and Quantum Chemical Studies
- RNA Interference and Gene Delivery
- Enzyme Structure and Function
- Protein purification and stability
- Nanopore and Nanochannel Transport Studies
- Monoclonal and Polyclonal Antibodies Research
- Lipid Membrane Structure and Behavior
- Biochemical and Molecular Research
- Folate and B Vitamins Research
- Computational Drug Discovery Methods
- Various Chemistry Research Topics
- Electrostatics and Colloid Interactions
- Protease and Inhibitor Mechanisms
University of Warsaw
2016-2025
Centrum Kopernika Badań Interdyscyplinarnych
1996-2012
University of Virginia
2010
Howard Hughes Medical Institute
2005-2006
University of California, San Diego
2004-2006
Center for Theoretical Biological Physics
2004-2006
National Institute of Standards and Technology
1999
Abstract Short modified oligonucleotides targeted at bacterial DNA or RNA could serve as antibacterial agents provided that they are efficiently taken up by cells. However, the uptake of such is hindered cell wall. To overcome this problem, oligomers have been attached to cell-penetrating peptides, but efficiency delivery remains poor. Thus, we investigated ability vitamin B 12 transport peptide nucleic acid (PNA) into cells Escherichia coli and Salmonella Typhimurium. Vitamin was covalently...
High macromolecular concentrations, or crowded conditions, have been shown to affect a wide variety of molecular processes, including diffusion, association and dissociation, protein folding stability. Here, we model the effect crowding on internal dynamics protein, HIV-1 protease, using Brownian simulations. protease possesses pair flaps which are postulated open in early stages its catalytic mechanism. Compared low close-packed concentrations repulsive agents found significantly reduce...
Abstract A coarse‐grained simulation model for the nucleosome is developed, using a methodology modified from previous work on ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse nonbonded) potentials. Force‐field parameters were estimated by Boltzmann inversion of corresponding radial distribution functions obtained 5‐ns all‐atom molecular dynamics (MD) simulation, refined to produce agreement with MD simulation....
Biochemical reactions in living systems occur complex, heterogeneous media with total concentrations of macromolecules the range 50 - 400 . Molecular species occupy a significant fraction immersing medium, up to 40% volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between may hinder diffusion major process determining metabolism, transport, signaling. Also, can alter, both qualitatively...
Multiscale simulations (coarse‐grained Brownian dynamics and all‐atom molecular in implicit solvent) were applied to reveal the binding processes of ligands as they enter site HIV‐1 protease. The initial structures used for generated based on trajectories, this is first simulation modeling association a ligand with We found that protease substrate successfully binds protein when flaps are fully open. Surprisingly, smaller cyclic urea inhibitor (XK263) can reach not However, if nearly closed,...
Abstract There has been growing interest in simulating biological processes under vivo conditions due to recent advances experimental techniques dedicated study single particle behavior crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse‐grained bead models. is written C and employs modern computer...
Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve inside cell. After uptake, bacteria extract soluble iron(II) siderophore. Ferric siderophores are transported cell via TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack transport system for hydroxamate-type deliver peptide nucleic acid oligomers into...
Study of N^C^NPt( ii )-peptide nucleic acid bioconjugates as a potential tool in bioimaging and targeted therapies due to their interesting phosphorescent features, good recognition properties towards natural acids, lack cytotoxicity.
The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. approximate valence bond method applied to active site atoms participating directly rearrangement chemical bonds. rest protein with explicit solvent treated a classical mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) Asp 25 protonated at inner oxygen, and direct nucleophilic attack 25....
Abstract Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic (CMV) were investigated using numerical solutions to the Poisson–Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in absence divalent cations when pH is raised from 5 7. CMV, although structurally homologous, does not undergo this transition. An analysis calculated electrostatic potential confirms a strong repulsion at calcium‐binding sites capsid most likely driving...
Many aminoglycosidic antibiotics target the A-site of 16S RNA in small ribosomal subunit and affect fidelity protein translation bacteria. Upon binding, aminoglycosides displace two adenines (A1492 A1493 for E. coli numbering) that are involved tRNA anticodon loop recognition. The major difference binding site between prokaryota eukaryota is an adenine into guanine substitution position 1408. This mutation likely affects dynamics near A1492 hinders to eukaryotic ribosomes. With multiple 20...
Huntington's disease is a neurodegenerative disorder caused by polyglutamine (polyQ) expansion in the N-terminal fragment of Huntingtin (Htt) protein. Structural properties Htt regions and molecular mechanism leading to protein aggregation have not been fully explained yet. We performed all-atom replica exchange dynamics investigate structures parts with polyQ tracts nonpathogenic pathogenic lengths. The monomers were composed headpiece (17 residues), tract (polyQ(17) for native polyQ(55)...