ArticleJournal of chemical information and modeling2014
Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 55 citations in OpenAlex.
- Deciphering the Interlinked CXCR4-Mediated Feedback Loop Among Signaling Pathways in Diabetic Wound Healing.Current diabetes reviews · 2026Review
- Interaction and dynamics of chemokine receptor CXCR4 binding with CXCL12 and hBD-3.Communications chemistry · 2024Article
- Assessing Protein-Protein Docking Protocols: Case Studies of G-Protein-Coupled Receptor Interactions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy.Frontiers in physiology · 2024Article
- CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs.BMC bioinformatics · 2023Article
- Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery.The journal of physical chemistry. B · 2023Review
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Identify potential prognostic indicators and tumor-infiltrating immune cells in pancreatic adenocarcinoma.Bioscience reports · 2022Review
- Single-cell sequencing demonstrates complex resistance landscape in CLL and MCL treated with BTK and BCL2 inhibitors.Blood advances · 2022Article
- Protease-Triggered Release of Stabilized CXCL12 from Coated Scaffolds in an Ex Vivo Wound Model.Pharmaceutics · 2021Article
- Non-full-length Water-Soluble CXCR4iScience · 2020Article
- Internal water channel formation in CXCR4 is crucial for GCommunications chemistry · 2020Article
- Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis.Science signaling · 2020Article
- Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity.PLoS biology · 2020Article
- Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2020Article
- Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr.Biophysical journal · 2020Article
- Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding.Computational and structural biotechnology journal · 2020Article
- Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles.Biomolecules · 2019Article
- QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships.Chemical research in toxicology · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The chemotactic signaling induced by the binding of chemokine CXCL12 (SDF-1α) to chemokine receptor CXCR4 is of significant biological importance and is a potential therapeutic axis against HIV-1. However, as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4 signaling is involved in tumor metastasis, progression, angiogenesis, and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis in cancer, we employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular dynamics simulations, to obtain insights into the molecular recognition of CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally derived CXCL12:CXCR4 complex structure which is in remarkable agreement with experimental findings and sheds light into the functional role of CXCL12 and CXCR4 residues which are associated with binding and signaling. Our results reveal that the CXCL12 N-terminal domain is firmly bound within the CXCR4 transmembrane domain, and the central 24-50 residue domain of CXCL12 interacts with the upper N-terminal domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure is attributed to an abundance of nonpolar and polar intermolecular interactions, including salt bridges formed between positively charged CXCL12 residues and negatively charged CXCR4 residues. The success of the computational protocol can mainly be attributed to the nearly exhaustive docking conformational search, as well as the heterogeneous dielectric implicit water-membrane-water model used to simulate and select the optimum conformations. We also recently utilized this protocol to elucidate the binding of an HIV-1 gp120 V3 loop in complex with CXCR4, and a comparison between the molecular recognition of CXCR4 by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly interact with the same CXCR4 residues.
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Registered trials
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.