GlyProt: in silico glycosylation of proteins

Abstract

GlyProt () is a web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The probabilities of physicochemical properties such as mass, accessible surface and radius of gyration are calculated. The purpose of this service is to provide rapid access to reliable 3D models of glycoproteins, which can subsequently be refined by using more elaborate simulations and validated by comparing the generated models with experimental data.

Engineering the Pattern of Protein Glycosylation Modulates the Thermostability of a GH11 Xylanase

“…Molecular Dynamics Simulations-The initial atomic coordinates of the glycosylated xylanases were obtained from the GH11 xylanase from B. subtilis (Protein Data Bank code 1XXN) using the GlyProt tool (42). GlyProt works with the SWEET DB to build three-dimensional structures of glycoproteins, taking into account the stereochemical criteria for a given glycan composition.…”

Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity

“…A highly conserved, hydrophobic fusion loop composed of 13 amino acids is located at the The HIV glycan shield is highlighted in red on the Env trimer (PDB accession number 4TVP) from a side view (left) and top view (right). The model was generated by using GlyProt (298).…”

Structural Basis for Penetration of the Glycan Shield of Hepatitis C Virus E2 Glycoprotein by a Broadly Neutralizing Human Antibody

“…1E). A glycan chain can be attached to the side chain amide of Asn-415, based on modeling using the GlyProt server (48), indicating that glycosylation of E2 at Asn-415 would not prevent binding of HC33.1 (Fig. 5C).…”