Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

Modeling glycosaminoglycan–protein complexes

MM Kogut, M Marcisz, SA Samsonov - Current Opinion in Structural Biology, 2022 - Elsevier
Glycosaminoglycans are long linear and complex polysaccharides that are fundamental
components of the mammalian extracellular matrix. Therefore, it is crucial to appropriately …

Solvent model benchmark for molecular dynamics of glycosaminoglycans

M Marcisz, SA Samsonov - Journal of chemical information and …, 2023 - ACS Publications
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear
polysaccharides, so far there has been very little discussion about the role of solvent models …

GlycoTorch Vina: docking designed and tested for glycosaminoglycans

ED Boittier, JM Burns, NS Gandhi… - Journal of Chemical …, 2020 - ACS Publications
Glycosaminoglycans (GAGs) are a family of anionic carbohydrates that play an essential
role in the physiology and pathology of all eukaryotic life forms. Experimental determination …

Modeling protein–glycosaminoglycan complexes: does the size matter?

M Marcisz, M Zacharias… - Journal of Chemical …, 2021 - ACS Publications
Docking glycosaminoglycans (GAGs) has been challenging because of the complex nature
of these long periodic linear and negatively charged polysaccharides. Although standard …

Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling–the beginning of a …

G Künze, D Huster, SA Samsonov - Biological chemistry, 2021 - degruyter.com
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored
glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing …

Development and Evaluation of GlycanDock: a protein–glycoligand docking refinement algorithm in Rosetta

ML Nance, JW Labonte, J Adolf-Bryfogle… - The Journal of Physical …, 2021 - ACS Publications
Carbohydrate chains are ubiquitous in the complex molecular processes of life. These
highly diverse chains are recognized by a variety of protein receptors, enabling glycans to …

Construction of Histone–Protein Complex Structures by Peptide Growing

BZ Zsidó, B Bayarsaikhan, R Börzsei… - International Journal of …, 2023 - mdpi.com
The structures of histone complexes are master keys to epigenetics. Linear histone peptide
tails often bind to shallow pockets of reader proteins via weak interactions, rendering their …

A Bittersweet Computational journey among glycosaminoglycans

G Paiardi, M Milanesi, RC Wade, P D'Ursi, M Rusnati - Biomolecules, 2021 - mdpi.com
Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are
attached to a core protein. GAGs and PGs can be found as free molecules, associated with …

Regulation of Intersubunit Interactions in Homotetramer of Glyceraldehyde-3-Phosphate Dehydrogenases upon Its Immobilization in Protein—Kappa-Carrageenan …

O Makshakova, M Antonova, L Bogdanova, D Faizullin… - Polymers, 2023 - mdpi.com
Polysaccharides, being biocompatible and biodegradable polymers, are highly attractive as
materials for protein delivery systems. However, protein–polysaccharide interactions may …