Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes

Abstract

In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing in N- and O-glycosylated proteins using a bottom up approach. We report the conformational free-energy landscapes of all relevant glycosidic linkages as obtained from local elevation simulations and subsequent umbrella sampling. To the best of our knowledge, this represents the first complete conformational library for the construction of N- and O-glycan structures. Next, we systematically study the effect of neighboring residues, by extensively simulating all relevant trisaccharides and one tetrasaccharide. This allows for an unprecedented comparison of disaccharide linkages in large oligosaccharides. With a small number of exceptions, the conformational preferences in the larger structures are very similar as in the disaccharides. This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples.

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

“…Representative glycan structures were added from a library created through enhanced sampling to get a large variety of conformers, as explained in reference. 15 As a putative interaction partner, a homology model of the extracellular domain of FEI1 was modelled based on the structure of the extracellular domain of Brassinosteroid Insensitive 1- Associated Kinase 1 (BAK1, PDB code 4MN8; 16 32.6% sequence identity with FEI1, corresponds to LRR 1–5 domains).…”

An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra‐ and hexa‐N‐acetylchitohexaose

“…The carbohydrate content of the complex was parameterized with the 53A6glyc parameter set of the GROMOS force field for carbohydrates. Parameters for the N‐acetyl group in NAG have been adjusted to the current protein force field previously . For the modeling of the initial conformations, two crystal structures of λ lysozyme with PDB ID: 3D3D (molecule B) and 1AM7 (molecule A) were used as closed and open conformations, respectively.…”

“…The initial structure of the hexasaccharide bound to the closed λ lysozyme was modeled by using the crystallographic NAG6 conformation for sugars 1 to 4 which occupy subsites A to D. The tetrasaccharide was then extended by adding two NAG units with PyMOL . While adding these two NAG residues, the glycosidic angles at the linkage were set according to their most favorable energetic state with φ , ψ angles of −84°, 102° which have been identified previously . This places the final two sugar units 5 and 6 into subsites that we refer to as E and F while the subsites populated by the second NAG6 molecule in the crystal structure are referred to as E′ and F′ (Figure B).…”

Structural Aspects of the O‐glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments

“…All MD simulations were performed using the GROMOS11 biomolecular simulation package (http://www.gromos.net) and the 54A8 GROMOS force field . For compatibility with the protein force field minor modifications to the original 53A6glyc carbohydrate parameter set were applied . Initial structures of the studied units were modeled in the molecular operating environment (MOE) by setting their glycosidic dihedral angles to their respective free‐energy minima, which have been previously reported .…”

“…They used 2D biasing potentials which have been previously studied in the content of peptidic and oligosaccharide systems . The GROMOS force field for carbohydrates 53A6GLYC was recently validated for N‐glycans and cyclodextrin …”