Structural Insights into Endostatin-Heparan Sulfate Interactions Using Modeling Approaches.

Urszula Uciechowska-Kaczmarzyk, Martin Frank, Sergey A Samsonov, Martyna Maszota-Zieleniak

Abstract read

In one paragraph

Article in Molecules (Basel, Switzerland), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Urszula Uciechowska-KaczmarzykLaboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland.

Martin FrankBiognos AB, P.O. Box 8963, 40274 Göteborg, Sweden.

Sergey A SamsonovLaboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0002-5166-4849

Martyna Maszota-ZieleniakLaboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0002-1206-5624

Funding

National Science Center UMO-2023/49/B/ST4/00041

6 · The paper itself

Abstract

Glycosaminoglycans (GAGs) play a key role in a variety of biological processes in the extracellular matrix (ECM) via interactions with their protein targets. Due to their high flexibility, periodicity and electrostatics-driven interactions, GAG-containing complexes are very challenging to characterize both experimentally and in silico. In this study, we, for the first time, systematically analyzed the interactions of endostatin, a proteolytic fragment of collagen XVIII known to be anti-angiogenic and anti-tumoral, with heparin (HP) and representative heparan sulfate (HS) oligosaccharides of various lengths, sequences and sulfation patterns. We first used conventional molecular docking and a docking approach based on a repulsive scaling-replica exchange molecular dynamics technique, as well as unbiased molecular dynamic simulations, to obtain dynamically stable GAG binding poses. Then, the corresponding free energies of binding were calculated and the amino acid residues that contribute the most to GAG binding were identified. We also investigated the potential influence of Zn

Indexed as

EndostatinsHeparan SulfateMolecular Docking SimulationMolecular Dynamics SimulationProtein BindingBinding SitesCollagen Type XVIIIGlycosaminoglycansHeparinHumansModels, MolecularThermodynamicsZincCollagen Type XVIIIEndostatinsGlycosaminoglycansHeparan SulfateHeparinZincendostatinglycosaminoglycansmolecular dockingprotein–glycosaminoglycan interactionsrepulsive scaling–replica exchange molecular dynamics

Identifiers

PMID39274888

DOI10.3390/molecules29174040

PMCPMC11397277

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