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Solution structure and basis for functional activity of stromal cell‐derived factor‐1; dissociation of CXCR4 activation from binding and inhibition of HIV‐1
Open accessAbstract
The three-dimensional structure of stromal cell-derived factor-1 (SDF-1) was determined by NMR spectroscopy. SDF-1 is a monomer with a disordered N-terminal region (residues 1-8), and differs from other chemokines in the packing of the hydrophobic core and surface charge distribution. Results with analogs showed that the N-terminal eight residues formed an important receptor binding site; however, only Lys-1 and Pro-2 were directly involved in receptor activation. Modification to Lys-1 and/or Pro-2 resulted in loss of activity, but generated potent SDF-1 antagonists. Residues 12-17 of the loop region, which we term the RFFESH motif, unlike the N-terminal region, were well defined in the SDF-1 structure. The RFFESH formed a receptor binding site, which we propose to be an important initial docking site of SDF-1 with its receptor. The ability of the SDF-1 analogs to block HIV-1 entry via CXCR4, which is a HIV-1 coreceptor for the virus in addition to being the receptor for SDF-1, correlated with their affinity for CXCR4. Activation of the receptor is not required for HIV-1 inhibition.
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“The protein product of CCL11 resulting from differential signal peptide cleavage is predicted to retain additional amino-acid residues at its N terminus, a key region specifying binding and activity of chemokines.44”
From Whole-genome sequencing suggests a chemokine gene cluster that modifies age at onset in familial Alzheimer's disease (2015) · cites this paper as [44]
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BackgroundSustained Delivery of Chemokine CXCL12 from Chemically Modified Silk Hydrogels
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BackgroundNMR Solution Structure and Backbone Dynamics of the CC Chemokine Eotaxin-3,
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BackgroundResultChemoselective Copper-Mediated Modification of Selenocysteines in Peptides and Proteins
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The N-terminal ectodomain of Ninjurin1 liberated by MMP9 has chemotactic activity
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“Indeed, after the multiple alignments of mNinj11–56 with well-known chemokines including SDF-1α [16], fractalkine [17], and MIP-1β [18] using T-coffee software, a consistency-based multiple sequence alignment program [19], the comparison of their secondary structures revealed a close structural similarity (Fig.”
MethodPhotoactivatable Chemokines – Controlling Protein Activity by Light
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“In order to assess ACKR3-mediated chemokine binding and internalization in the presence of CXCR4, an ACKR3-specific chimeric chemokine (CXCL11_12), consisting of CXCL12 body with the N-terminal sequence of CXCL11, the second ligand of ACKR3 was generated, in line with the notion that modifications of the N-terminus ab…”
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“The binding of a chemokine to its cognate receptor is most often described by a two-step, two-site model, where the chemokine globular core fi rst engages the receptor N-terminus at CRS1, followed by insertion of the chemokine N-terminus into the orthosteric core of the receptor at CRS2 47 – 49 .”
BackgroundHuman CC Chemokine I-309, Structural Consequences of the Additional Disulfide Bond,
Keizer, D. W., Crump, M. P., Lee, T. W., Slupsky, C. M., Clark‐Lewis, I., & Sykes, B. D. (2000) · Biochemistry · doi:10.1021/bi000089l · Cited by 29
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“Moreover, 387 in this case, the two N-terminals domains of CXCL12, crucial for CXCR4 triggering [53], 388 are oriented in the same direction, and the resulting heterocomplexes have an optimal 389 conformation to bind a CXCR4 dimer.”
BackgroundBrennecke, P., Arlt, M., Muff, R., Campanile, C., Gvozdenovic, A., Husmann, K., Holzwarth, N., Cameroni, E., Ehrensperger, F., Thelen, M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074045 · Cited by 28
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Optimal Superpositioning of Flexible Molecule Ensembles
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“CXCL12 (3–67) retains significant binding affinity for the receptor and thus antagonizes the binding of biologically active CXCL12 (1–67) [72].”
BackgroundThe heterodimerization of platelet-derived chemokines
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“, the suggested “two-site” binding of chemokine CXCL12 to the CXCR4 receptor (59)].”
BackgroundStructural Analysis of a Novel Small Molecule Ligand Bound to the CXCL12 Chemokine
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Metadata
- Authors
- Crump, M. P., Gong, J., Loetscher, P., Rajarathnam, K., Amara, A., Arenzana‐Seisdedos, F., Virelizier, J., Baggiolini, M., Sykes, B. D., & Clark‐Lewis, I.
- Affiliations
- University of Alberta (CA)
- University of British Columbia (CA)
- University of Bern (CH)
- Institut Pasteur (FR)
- Corresponding author
- Sykes, Brian D.
- Clark‐Lewis, Ian
- Venue
- The EMBO Journal
- Published
- 1997-12-01
- Volume
- 16
- Issue
- 23
- Pages
- 6996-7007
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC1170303
- OpenAlex
- W1964083898
- Cited by
- 731
- References
- 45
- Citations by year
- 2026: 10 · 2025: 12 · 2024: 19 · 2023: 14 · 2022: 17 · 2021: 15 · 2020: 29 · 2019: 32 · 2018: 20 · 2017: 35 · 2016: 26 · 2015: 34 · 2014: 30 · 2013: 44 · 2012: 35
- FWCI
- 10.34
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Medical Research Council Canada
- Medical Research Council
- Topics
- Health Sciences › Medicine › Oncology › Chemokine receptors and signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- CXCL12, chemokine structure, N-terminal disordered region, receptor binding sites, CXCR4, HIV-1 coreceptor, HIV-1 entry inhibition, receptor activation, chemokine antagonists
- MeSH terms
- Amino Acid Sequence, Binding Sites, Models, Biological, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Structure-Activity Relationship, Virus Replication, HIV-1, Sequence Homology, Amino Acid, Chemokines, Anti-HIV Agents, Receptors, CXCR4, Chemokines, CXC, Nuclear Magnetic Resonance, Biomolecular, Chemokine CXCL12
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