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Updated: May 4, 2026
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
Published on: January 10, 2018
New conformational state of NHERF1-CXCR2 signaling complex captured by crystal lattice trapping
Yuanyuan Jiang1, Guorong Lu, Laura R Trescott
1Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America.
Abstract:
NHERF1 is a PDZ adaptor protein that scaffolds the assembly of diverse signaling complexes and has been implicated in many cancers. However, little is known about the mechanism responsible for its scaffolding promiscuity or its ability to bind to multiple targets. Computational studies have indicated that PDZ promiscuity may be attributed to its conformational dynamics, but experimental evidence for this relationship remains very limited. Here we examine the conformational flexibility of the NHERF1 PDZ1 domain using crystal lattice trapping via solving PDZ1 structure of a new crystal form. The structure, together with prior PDZ1 structures of a different space group, reveals that 4 of 11 ligand-interacting residues undergo significant crystal packing-induced structural changes. Most of these residues correspond to the residues involved in allosteric transition when a peptide ligand binds. In addition, a subtle difference in ligand conformations causes the same peptide to bind in slightly different modes in different crystal forms. These findings indicate that substantial structural flexibility is present in the PDZ1 peptide-binding pocket, and the structural substate trapped in the present crystal form can be utilized to represent the conformational space accessible to the protein. Such knowledge will be critical for drug design against the NHERF1 PDZ1 domain, highlighting the continued need for experimentally determined PDZ1-ligand complexes.
Insights
The NHERF1 PDZ1 domain exhibits significant structural flexibility, crucial for its ability to bind multiple targets in cancer signaling. Understanding this flexibility is key for developing targeted cancer therapies.
Area of Science:
- Biochemistry
- Structural Biology
- Cancer Biology
Background:
- NHERF1 (EBP50) is a PDZ adaptor protein involved in cancer signaling.
- Its scaffolding promiscuity, or ability to bind multiple targets, is poorly understood.
- Computational studies suggest conformational dynamics contribute to PDZ promiscuity, but experimental evidence is limited.
Purpose of the Study:
- To investigate the conformational flexibility of the NHERF1 PDZ1 domain.
- To provide experimental evidence linking conformational dynamics to PDZ domain promiscuity.
- To inform drug design strategies targeting NHERF1 in cancer.
Main Methods:
- Crystal lattice trapping to solve the NHERF1 PDZ1 domain structure in a new crystal form.
- Comparison of the new structure with previously solved PDZ1 structures (different space group).
- Analysis of ligand-interacting residues and their conformational changes.
Main Results:
- Four of eleven ligand-interacting residues in PDZ1 undergo significant crystal packing-induced structural changes.
- These altered residues are involved in allosteric transitions during peptide ligand binding.
- Subtle differences in peptide conformations lead to varied binding modes across different crystal forms.
- The NHERF1 PDZ1 peptide-binding pocket displays substantial structural flexibility.
Conclusions:
- The NHERF1 PDZ1 domain possesses significant conformational flexibility.
- Crystal packing can induce structural changes in ligand-interacting residues, reflecting accessible conformational states.
- This flexibility and the trapped substates are critical for understanding NHERF1's scaffolding promiscuity.
- Experimental determination of PDZ1-ligand complexes is essential for NHERF1-targeted drug design in cancer therapy.
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