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The influence of n-linked glycans on the molecular dynamics of the hiv-1 gp120 v3 loop
(Public Library of Science (PLoS), 2013-11-26)
N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising ...
A chromatin-independent role of polycomb-like 1 to stabilize p53 and promote cellular quiescence
(Cold Spring Harbor Laboratory, 2015-10-22)
Polycomb-like proteins 1-3 (PCL1-3) are substoichiometric components of the Polycomb-repressive complex 2 (PRC2) that are essential for association of the complex with chromatin. However, it remains unclear why three ...
Defining the structural origin of the substrate sequence independence of o-glcnacase using a combination of molecular docking and dynamics simulation
(Oxford University Press (OUP), 2013-10-16)
Protein glycosylation with O-linked N-acetylglucosamine (O-GlcNAc) is a post-translational modification of serine/threonine residues in nucleocytoplasmic proteins. O-GlcNAc has been shown to play a role in many different ...
On the molecular basis of uracil recognition in dna: comparative study of t-a versus u-a structure, dynamics and open base pair kinetics
(Oxford University Press (OUP), 2010-09-28)
Uracil (U) can be found in DNA as a mismatch paired either to adenine (A) or to guanine (G). Removal of U from DNA is performed by a class of enzymes known as uracil-DNA-glycosylases (UDG). Recent studies suggest that ...
Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects
(Elsevier BV, 2010-08-01)
The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting ...
Conformational determinants for the recruitment of ercc1 by xpa in the nucleotide excision repair (ner) pathway: structure and dynamics of the xpa binding motif
(Elsevier BV, 2013-06-01)
XPA is an essential protein in the nucleotide excision repair (NER) pathway, in charge of recruiting the ERCC1-XPF endonuclease complex to the DNA damage site. The only currently available structural insight into the binding ...
On the role of water models in quantifying the binding free energy of highly conserved water molecules in proteins: the case of concanavalin a
(American Chemical Society (ACS), 2011-10-11)
The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in ...
Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase qm calculations
(Canadian Science Publishing, 2013-09-01)
In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative ...
Structure and binding analysis of polyporus squamosus lectin in complex with the neu5acα2-6galβ1-4glcnac human-type influenza receptor
(Oxford University Press (OUP), 2011-03-24)
Glycan chains that terminate in sialic acid (Neu5Ac) are frequently the receptors targeted by pathogens for initial adhesion. Carbohydrate-binding proteins (lectins) with specificity for Neu5Ac are particularly useful in ...