A5042385218- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Computational Drug Discovery Methods
- Bacterial Genetics and Biotechnology
- Analytical Chemistry and Chromatography
- Chemical Synthesis and Analysis
- Crystallization and Solubility Studies
- Machine Learning in Bioinformatics
- DNA and Nucleic Acid Chemistry
- Biofuel production and bioconversion
- Enzyme Production and Characterization
- Plant Pathogenic Bacteria Studies
- Influenza Virus Research Studies
- Cellular Automata and Applications
- Carbohydrate Chemistry and Synthesis
- Plant Surface Properties and Treatments
- DNA and Biological Computing
- Microbial Metabolic Engineering and Bioproduction
- Legume Nitrogen Fixing Symbiosis
- Genomics and Phylogenetic Studies
- Mass Spectrometry Techniques and Applications
- Biochemical and Structural Characterization
- Plant pathogens and resistance mechanisms
Democritus University of Thrace
2013-2024
University of Crete
2003-2009
University of Ioannina
2009
National Centre of Scientific Research "Demokritos"
2006
FORTH Institute of Molecular Biology and Biotechnology
1999-2004
University of Leeds
1998-2003
Foundation for Research and Technology Hellas
1999-2000
Abstract A computer program has been developed to aid the analysis of molecular dynamics trajectories. The is tuned for macromolecular large‐scale problems and supports features such as removal global translations‐rotations solute, calculation average distance maps their corresponding standard deviations, variance‐covariance cross‐correlation matrices, principal component trajectories with added ability create artificial based on selected eigenvectors. Limited graphics (trajectory viewing)...
We report the availability of grcarma, a program encoding for fully automated set tasks aiming to simplify analysis molecular dynamics trajectories biological macromolecules. It is cross-platform, Perl/Tk-based front-end carma and designed facilitate needs novice as well those expert user, while at same time maintaining user-friendly intuitive design. Particular emphasis was given automation several tedious tasks, such extraction clusters structures based on dihedral Cartesian principal...
Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum diseases including bacteremia, septicemia, typhoid fever, bubonic plague in mammals, localized lesions, systemic wilting, blights plants. In addition, type are also required for biogenesis flagellum. The HrcQ B protein, component apparatus Pseudomonas syringae with homologues all systems, has variable N-terminal conserved...
Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source controversy (and various ad hoc solutions) in the field. Clearly, only reasonable, consistent, satisfying way to infer (or otherwise) trajectory must be based on probability theory. Ideally, question we would wish answer following: "What that configuration important for analysis hand has yet been observed ?". Here propose method answering variant this by using...
Folding molecular dynamics simulations amounting to a grand total of 4 μs simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 the vammin protein results compared with experimentally known peptide stabilities structures. The faithfully accurately reproduce major experimental findings show that (a) is mostly disordered in solution, (b) mutant has well-defined stable structure, (c) structure an irregular β-hairpin non-glycine β-bulge, excellent...
We examine the sensitivity of folding molecular dynamics simulations on choice between three variants same force field (the AMBER99SB and its ILDN, NMR-ILDN, STAR-ILDN variants). Using two different peptide systems (a marginally stable helical a β-hairpin) grand total more than 20 μs simulation time we show that even relatively minor changes can lead to appreciable differences in behavior.
In the Gram-positive bacterium Bacillus subtilis concentration of amino acid l-arginine is controlled by transcriptional regulator AhrC. The hexameric AhrC protein binds in an l-arginine-dependent manner to pseudo-palindromic operators within promoter regions arginine biosynthetic and catabolic gene clusters. binding results repression transcription genes activation genes. crystal structure has been determined at 2.7 Å resolution. Each subunit two domains. C-terminal domains are arranged...
Bacillus cereus is an opportunistic pathogenic bacterium closely related to anthracis , the causative agent of anthrax in mammals. A significant portion B. chromosomal genes are common including which code for putative virulence and surface proteins. thus provides a convenient model organism studying proteins potentially associated with pathogenicity highly infectious . The zinc‐binding protein Bc ZBP, encoded from bc1534 gene has three homologues exhibits deacetylase activity N ‐acetyl...
A computational solution to the protein folding problem is holy grail of biomolecular simulation and corresponding force fields. The complexity systems used for simulations precludes a direct feedback between fields, thus necessitating study simpler with sufficient experimental data allow field optimization validation. Recent studies on short polyalanine peptides increasing length (up penta-alanine) indicated presence systematic deviation (NMR-derived) J-couplings great majority χ(2) values...
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens putative models the C-terminal domain protein were constructed multitude homology-modelling algorithms, and these tested for presence signal in calculations. Of these, only model calculated by SAM-T08 server gave consistent convincing solution, but resulting was too inaccurate to allow phase determination proceed completion. application...
The full extent of proline (Pro) hydroxylation has yet to be established, as it is largely unexplored in bacteria. We describe here a so far unknown Pro activity which occurs active sites polysaccharide deacetylases (PDAs) from bacterial pathogens, modifying the protein backbone at Cα atom residue produce 2-hydroxyproline (2-Hyp). This process modifies with high specificity conserved Pro, shares deacetylation reaction same site and one catalytic residue, utilizes molecular oxygen source for...
Short peptides serve as minimal model systems to decipher the determinants of foldability due their simplicity arising from smaller size, ability echo protein-like structural characteristics, and direct implication in force field validation. Here, we describe an effort identify small that can still form stable structures aqueous solutions. We followed silico folding a selected set 8640 tryptophan-containing tetra- pentapeptides through 15 210 molecular dynamics simulations amounting total...
The villin headpiece helical subdomain (HP36) is one of the best known model systems for computational studies fast-folding all-α miniproteins. HP21 a peptide fragment-derived from HP36-comprising only first and second helices full domain. Experimental showed that although mostly unfolded in solution, it does maintain some persistent native-like structure as indicated by analysis NMR-derived chemical shifts. Here we compare experimental data with results obtained 15-μs long folding molecular...
The classical approach to the problem of placing n copies a search model in asymmetric unit target crystal structure is divide this 6n-dimensional optimization into succession three-dimensional searches (rotation-function followed by translation-function for each models). Here, it shown that structure-determination method based on reverse Monte Carlo minimization suitably chosen statistic space defined rotational and translational parameters molecules both feasible practical, at least small...
Conventional wisdom has it that the presence of disordered regions in three-dimensional structures polypeptides not only does contribute significantly to thermodynamic stability their folded state, but, on contrary, disorder leads a decrease corresponding proteins' stability. We have performed extensive 3.4 µs long folding simulations (in explicit solvent and with full electrostatics) an undecamer peptide experimentally known helical structure, both without its (four residue long) C-terminal...
The repressor of primer (Rop) protein has become a steady source surprises concerning the relationship between sequences and structures several its mutants variants. Here we add another piece to puzzle Rop by showing that an engineered deletion mutant (corresponding residues 30-34 wild-type designed restore heptad periodicity at turn region) results in complete reorganization bundle which is converted from homodimer homotetramer. In contrast (and as previously shown), two-residue insertion,...
Regulation of nuclear receptors by their coactivators involves the recognition and binding a specific sequence motif contained in coactivator sequence. This is known as receptor (NR) box contains conserved LxxLL subsequence, where L leucine x any amino acid residue. Crystallographic studies have shown that motifs adopt an α-helical conformation when bound to cognate receptors. Here we use extensive set folding molecular dynamics simulations examine whether demonstrated state may represent...