ArticleJournal of computer-aided molecular design2011
Docking glycosaminoglycans to proteins: analysis of solvent inclusion.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 73 citations in OpenAlex.
- Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.Biomolecules · 2023Article
- Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.Journal of chemical information and modeling · 2023Article
- Antiviral Disaccharide Lead Compounds against SARS-CoV-2 through Computer-Aided High-Throughput Screen.Chembiochem : a European journal of chemical biology · 2022Article
- Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states.Current opinion in structural biology · 2022Review
- In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism.Biomolecules · 2022Article
- Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System.International journal of molecular sciences · 2021Article
- A Bittersweet Computational Journey among Glycosaminoglycans.Biomolecules · 2021Review
- A Systems View of the Heparan Sulfate Interactome.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2021Review
- Carbohydrate-Protein Interactions: Advances and Challenges.Communications in information and systems · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools.Glycobiology · 2020Article
- Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study.Journal of chemical information and modeling · 2020Article
- Syntheses of defined sulfated oligohyaluronans reveal structural effects, diversity and thermodynamics of GAG-protein binding.Chemical science · 2019Article
- Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin.The Journal of biological chemistry · 2018Article
- So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again!Current opinion in structural biology · 2018Review
- Targeting cancer-specific glycans by cyclic peptide lectinomimics.Amino acids · 2017Article
- Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains.Open biology · 2017Article
- Glycosaminoglycanomics: where we are.Glycoconjugate journal · 2017Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein-protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.