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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 ...
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 ...
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 ...
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 ...