Protein flexibility and enzymatic catalysis
M Kokkinidis, NM Glykos, VE Fadouloglou - Advances in protein chemistry …, 2012 - Elsevier
The dynamic nature of protein structures has been recognized, established, and accepted
as an intrinsic fundamental property with major consequences to their function. Nowadays …
as an intrinsic fundamental property with major consequences to their function. Nowadays …
Characterization of the N-Acetyl-α-d-glucosaminyl l-Malate Synthase and Deacetylase Functions for Bacillithiol Biosynthesis in Bacillus anthracis,
D Parsonage, GL Newton, RC Holder, BD Wallace… - Biochemistry, 2010 - ACS Publications
Bacillithiol (Cys-GlcN-malate, BSH) has recently been identified as a novel low-molecular
weight thiol in Bacillus anthracis, Staphylococcus aureus, and several other Gram-positive …
weight thiol in Bacillus anthracis, Staphylococcus aureus, and several other Gram-positive …
[HTML][HTML] Structure and function of the LmbE-like superfamily
S Viars, J Valentine, M Hernick - Biomolecules, 2014 - mdpi.com
The LmbE-like superfamily is comprised of a series of enzymes that use a single catalytic
metal ion to catalyze the hydrolysis of various substrates. These substrates are often key …
metal ion to catalyze the hydrolysis of various substrates. These substrates are often key …
[HTML][HTML] Cross Dimerization of Amyloid-β and αSynuclein Proteins in Aqueous Environment: A Molecular Dynamics Simulations Study
JC Jose, P Chatterjee, N Sengupta - PloS one, 2014 - journals.plos.org
Self-assembly of the intrinsically unstructured proteins, amyloid beta (A β) and alpha
synclein (αSyn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body …
synclein (αSyn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body …
On the application of Good-Turing statistics to quantify convergence of biomolecular simulations
PI Koukos, NM Glykos - Journal of chemical information and …, 2014 - ACS Publications
Quantifying convergence and sufficient sampling of macromolecular molecular dynamics
simulations is more often than not a source of controversy (and of various ad hoc solutions) …
simulations is more often than not a source of controversy (and of various ad hoc solutions) …
Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus
VE Fadouloglou, M Kapanidou… - … Section D: Biological …, 2013 - journals.iucr.org
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been
determined using an unconventional molecular-replacement procedure. Tens of putative …
determined using an unconventional molecular-replacement procedure. Tens of putative …
LmbE proteins from Bacillus cereus are de‐N‐acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis
A Deli, D Koutsioulis, VE Fadouloglou… - The FEBS …, 2010 - Wiley Online Library
The genomes of Bacillus cereus and its closest relative Bacillus anthracis each contain two
LmbE protein family homologs: BC1534 (BA1557) and BC3461 (BA3524). Only a few …
LmbE protein family homologs: BC1534 (BA1557) and BC3461 (BA3524). Only a few …
Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrP C: Insights from atomistic simulations
S Menon, N Sengupta - Molecular BioSystems, 2015 - pubs.rsc.org
Conversion of the predominantly α-helical cellular prion protein (PrPC) to the misfolded β-
sheet enriched Scrapie form (PrPSc) is a critical event in prion pathogenesis. However, the …
sheet enriched Scrapie form (PrPSc) is a critical event in prion pathogenesis. However, the …
Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations
A Stavrakoudis - Cell biochemistry and biophysics, 2011 - Springer
One key step in the immune response against infected or tumor cells is the recognition of the
T-cell receptor (TCR) by class I major histocompatibility complexes. The complex between …
T-cell receptor (TCR) by class I major histocompatibility complexes. The complex between …
Clustering of molecular dynamics trajectories via peak-picking in multidimensional PCA-derived distributions
AS Baltzis, PI Koukos, NM Glykos - arXiv preprint arXiv:1512.04024, 2015 - arxiv.org
We describe a robust, fast, and memory-efficient procedure that can cluster millions of
structures derived from molecular dynamics simulations. The essence of the method is …
structures derived from molecular dynamics simulations. The essence of the method is …