Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Structures of Human CCL18, CCL3, and CCL4 Reveal Molecular Determinants for Quaternary Structures and Sensitivity to Insulin-Degrading Enzyme

Journal Article · · Journal of Molecular Biology
 [1];  [1];  [1];  [1]
  1. Univ. of Chicago, IL (United States). Ben-May Dept. for Cancer Research
CC chemokine ligands (CCL) are 8-14 kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here in this paper, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small angle X-ray scattering (SAXS) analyses. Our data shows that CCL18 adopts an α-helical conformation at its N-terminus that weakens its dimerization, explaining CCL18’s preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4, but is replaced by lysine in human CCL18. Our structural analyses suggest that a proline 8 to alanine mutation stabilizes a type I β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme (IDE) degrades CCL3 and CCL4 but not CCL18. Lastly, our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function.
Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1194229
Alternate ID(s):
OSTI ID: 1233993
Journal Information:
Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Journal Issue: 6B Vol. 427; ISSN 0022-2836
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
ENGLISH

References (62)

MassMatrix: A database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data journal March 2009
Amyloid β-degrading cryptidases: insulin degrading enzyme, presequence peptidase, and neprilysin journal May 2008
Thermofluor-based high-throughput stability optimization of proteins for structural studies journal October 2006
Chemokines and Cancer: A Fatal Attraction journal April 2011
Structural Insights into Biological Roles of Protein-Glycosaminoglycan Interactions journal March 2005
Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-β hydrolysis journal May 2014
The chemokine system in diverse forms of macrophage activation and polarization journal December 2004
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-α, and Amylin by Human Insulin-Degrading Enzyme journal January 2010
Structural basis for high selectivity of anti-CCL2 neutralizing antibody CNTO 888 journal June 2012
Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data journal August 2011
Effect of posttranslational processing on the in vitro and in vivo activity of chemokines journal March 2011
Chemokine oligomerization and interactions with receptors and glycosaminoglycans: The role of structural dynamics in function journal March 2011
The Phenix software for automated determination of macromolecular structures journal September 2011
Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor journal November 2002
Macrophage inflammatory protein-1 journal December 2002
Structural Comparison of Monomeric Variants of the Chemokine MIP-1β Having Differing Ability To Bind the Receptor CCR5 , journal August 2001
A dendritic-cell-derived C–C chemokine that preferentially attracts naive T cells journal June 1997
Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme journal October 2010
Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones journal May 2014
Glycosaminoglycan binding and oligomerization are essential for the in vivo activity of certain chemokines journal February 2003
Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme journal August 2013
Monomeric Monocyte Chemoattractant Protein-1 (MCP-1) Binds and Activates the MCP-1 Receptor CCR2B journal December 1998
Tyrosine Sulfation of Chemokine Receptor CCR2 Enhances Interactions with Both Monomeric and Dimeric Forms of the Chemokine Monocyte Chemoattractant Protein-1 (MCP-1) journal April 2013
The Core Domain of Chemokines Binds CCR5 Extracellular Domains while Their Amino Terminus Interacts with the Transmembrane Helix Bundle journal February 2003
Phaser crystallographic software journal July 2007
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates journal December 1995
The CCP 4 molecular-graphics project journal October 2002
Coot model-building tools for molecular graphics journal November 2004
Structural Plasticity in Actin and Tubulin Polymer Dynamics journal August 2009
High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR journal March 1994
Protein Misfolding, Functional Amyloid, and Human Disease journal June 2006
Chemokine:Receptor Structure, Interactions, and Antagonism journal April 2007
A Vicious Circle of Alveolar Macrophages and Fibroblasts Perpetuates Pulmonary Fibrosis via CCL18 journal April 2006
Oligomerization of RANTES is required for CCR1-mediated arrest but not CCR5-mediated transmigration of leukocytes on inflamed endothelium journal September 2003
Marked elevation of the chemokine CCL18/PARC in Gaucher disease: a novel surrogate marker for assessing therapeutic intervention journal January 2004
Designed Inhibitors of Insulin-Degrading Enzyme Regulate the Catabolism and Activity of Insulin journal May 2010
Aggregation of the chemokine MIP-1 alpha is a dynamic and reversible phenomenon. Biochemical and biological analyses. journal February 1994
Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor journal November 2002
Macrophage inflammatory protein-1 journal December 2002
CCL18 from Tumor-Associated Macrophages Promotes Breast Cancer Metastasis via PITPNM3 journal April 2011
Structure–activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme journal January 2015
Molecular Bases for the Recognition of Short Peptide Substrates and Cysteine-Directed Modifications of Human Insulin-Degrading Enzyme journal December 2008
β-Chemokines are released from HIV-1-specific cytolytic T-cell granules complexed to proteoglycans journal February 1998
Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism journal October 2006
Tyrosine Sulfation of Chemokine Receptor CCR2 Enhances Interactions with Both Monomeric and Dimeric Forms of the Chemokine Monocyte Chemoattractant Protein-1 (MCP-1) journal April 2013
The Core Domain of Chemokines Binds CCR5 Extracellular Domains while Their Amino Terminus Interacts with the Transmembrane Helix Bundle journal February 2003
Identification of human CCR8 as a CCL18 receptor journal September 2013
PRIMUS: a Windows PC-based system for small-angle scattering data analysis journal September 2003
Phaser crystallographic software journal July 2007
New developments in the ATSAS program package for small-angle scattering data analysis journal March 2012
Determination of the regularization parameter in indirect-transform methods using perceptual criteria journal August 1992
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates journal December 1995
The CCP 4 molecular-graphics project journal October 2002
Coot model-building tools for molecular graphics journal November 2004
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution journal May 2012
International Union of Basic and Clinical Pharmacology. LXXXIX. Update on the Extended Family of Chemokine Receptors and Introducing a New Nomenclature for Atypical Chemokine Receptors journal November 2013
A Vicious Circle of Alveolar Macrophages and Fibroblasts Perpetuates Pulmonary Fibrosis via CCL18 journal April 2006
An engineered monomer of CCL2 has anti-inflammatory properties emphasizing the importance of oligomerization for chemokine activity in vivo journal July 2008
Involvement of CC chemokine ligand 18 (CCL18) in normal and pathological processes journal April 2005
Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data dataset January 2011

Cited By (5)

SNPs in inflammatory genes CCL11, CCL4 and MEFV in a fibromyalgia family study journal June 2018
PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection journal February 2018
Chemokine CXCL7 Heterodimers: Structural Insights, CXCR2 Receptor Function, and Glycosaminoglycan Interactions journal April 2017
Discovery of CCL18 antagonist blocking breast cancer metastasis journal May 2019
Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3 journal April 2016

Similar Records

Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3
Journal Article · Sun Apr 17 20:00:00 EDT 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1254500

Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme
Journal Article · Mon Dec 06 23:00:00 EST 2010 · EMBO J. · OSTI ID:1002901

Novel antiviral activity of chemokines
Journal Article · Wed Jul 05 00:00:00 EDT 2006 · Virology · OSTI ID:20850530