Search
Close this search box.

Molecular dynamics simulations enlight glycosaminoglycan interactions in the free- and protein-bound states

Author(s)

B. Nagarajan, S.G. Holmes, N.V. Sankaranarayanan & U.R. Desai

Sources

Current Opinion in Structural Biology 2022, 74:102356

Glycosaminoglycans (GAGs) are informational molecules with astounding structural diversity. Understanding the behaviour of GAGs in the free and protein-bound states is critical for harnessing this diversity. Molecular dynamics (MD) offers atomistic insight into principles governing GAG recognition by proteins. Here, we discuss how MD can be used to understand the local and global properties of GAGs in free solutions, including torsions, puckering, hydrogen bonding, flexibility, and energetics. The authors discuss MD studies on GAG–protein complexes, which help elucidate the strength of interacting residues, the role of water, energetics, and so on.
gags_enews_4july2022.png
The MD results suggest that GAG recognition of proteins is a continuum from the highly selective end to the fully non-selective on the other with intermediate levels of selectivity, including moderately selective and plastic. The advancements in MD technology, such as coarse-grained MD, coupled with really long simulations will help understand macroscale molecular movements in the future.

Latest news

In biological systems, vascular networks play a pivotal role in regulating the chemical compositions of...

Amylose, a linear polymer comprised of α-1,4-linked glucopyranose units, is renowned for its propensity to...

Algae play an important ecological role as oxygen producers and carbon sequesters and are the...

Streptococcus gordonii is a Gram-positive bacterial species that typically colonizes the human oral cavity, but...