CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate–protein modeling

O Guvench, SS Mallajosyula, EP Raman… - Journal of chemical …, 2011 - ACS Publications
Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-
acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid …

Sulfated glycosaminoglycans as promising artificial extracellular matrix components to improve the regeneration of tissues

M Schnabelrauch, D Scharnweber… - Current medicinal …, 2013 - ingentaconnect.com
Glycosaminoglycans (GAG) such as hyaluronan (HA) or chondroitin/dermatan sulfate
(CS/DS) occur in many connective tissues, for instance, in bone, cartilage and skin. Due to …

[HTML][HTML] Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy

M Yusupov, A Privat-Maldonado, RM Cordeiro… - Redox biology, 2021 - Elsevier
Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here
we investigated the biological and molecular effect of oxidative stress on the interaction …

Atomic-resolution experimental structural biology and molecular dynamics simulations of hyaluronan and its complexes

O Guvench - Molecules, 2022 - mdpi.com
This review summarizes the atomic-resolution structural biology of hyaluronan and its
complexes available in the Protein Data Bank, as well as published studies of atomic …

CHARMM additive all-atom force field for phosphate and sulfate linked to carbohydrates

SS Mallajosyula, O Guvench, E Hatcher… - Journal of Chemical …, 2012 - ACS Publications
Presented is an extension of the CHARMM additive all-atom carbohydrate force field to
enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are …

Comparison of carbohydrate force fields in molecular dynamics simulations of protein–carbohydrate complexes

A Plazinska, W Plazinski - Journal of chemical theory and …, 2021 - ACS Publications
In this paper, we present the results of molecular dynamics simulations aimed at critical
comparison of classical, biomolecular force fields (FFs) in the context of their capabilities to …

N-Glycosylation can selectively block or foster different receptor–ligand binding modes

J Vuorio, J Škerlová, M Fábry, V Veverka… - Scientific Reports, 2021 - nature.com
While DNA encodes protein structure, glycans provide a complementary layer of information
to protein function. As a prime example of the significance of glycans, the ability of the cell …

What is special about 200 kDa hyaluronan that activates hyaluronan receptor signaling?

PH Weigel, BA Baggenstoss - Glycobiology, 2017 - academic.oup.com
The polydispersity of hyaluronan (HA) presents challenges for analyzing its solution
properties, such as the relationship between mass and particle size. The broad mass range …

Atomistic fingerprint of hyaluronan–CD44 binding

J Vuorio, I Vattulainen… - PLoS computational …, 2017 - journals.plos.org
Hyaluronan is a polyanionic, megadalton-scale polysaccharide, which initiates cell signaling
by interacting with several receptor proteins including CD44 involved in cell-cell interactions …

Terminal sialic acids on CD44 N‐glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains

CE Faller, O Guvench - Proteins: Structure, Function, and …, 2014 - Wiley Online Library
Specific sugar residues and their linkages form the basis of molecular recognition for
interactions of glycoproteins with other biomolecules. Seemingly small changes, like the …