This proposed project seeks to develop the recent paradigm that protein complexes can be multi-configurational, if not highly dynamic entities. The biophysical and functional features of such dynamic complexes need to be understood. We chose heterodimer complexes involving Eph-family SAM domains as an example. SAM domains are important as they occur in over 200 human proteins, most notably in all 14 members of human Eph receptor tyrosine kinases. These receptors function in the development of the nervous and cardiovascular systems, and recent studies have shown that the SAM domain of EphA2 is mutated in a variety of human tumors as well as cataract, both linked to EphA2 dysregulation. However, the molecular basis of the normal and abnormal function of EphA2 SAM domain is not yet understood. Using a three-pronged approach, involving biophysical, computational and cell biology methods we will characterize the multi-configurational features of EphA1-SHIP2 and EphA2-SHIP2 SAM:SAM complexes. Furthermore, we will study how tumor associated mutations affect not just protein folding, stability and aggregation, but likely affect SAM domain-protein interactions via alterations of the configurational and internal dynamics of SAM domains. We will study the effect of specific tyrosine phosphorylation in the same manner, revealing the molecular basis of these functionally important posttranslational modifications. Investigations of Eph-related SAM domain conformational dynamics and protein-protein interactions have shifted our perspective on the normal and disease function of the domain. The knowledge obtained from this basic science research will serve as a general model for other dynamic protein complexes. Furthermore, the insights obtained, may eventually lead to the design of diagnostic and therapeutic agents.
Configurational and internal dynamics of protein-protein complexes This proposed project is a basic science study of fundamental importance: We will characterize the critical biophysical features that determine the multi-configurational nature of a model for a dynamic protein-protein complex. The results will have a broad impact on the understanding of protein-protein interactions, particularly of the over 200 SAM domains found in human proteins. The model system that we chose, the EphA1-SHIP2 and EphA2-SHIP2 SAM:SAM complex is significant for its biomedical relevance. Specifically, Eph receptors function in the development of the nervous and cardiovascular systems, and recent studies have shown that the SAM domain of EphA2 is mutated in a variety of human tumors as well as cataract, both linked to EphA2 dysregulation. The effect of 18 tumor associated and 2 cataract associated mutations as well as specific tyrosine phosphorylation will be examined on the domain's biophysical features, its complex formation in vitro as well as in cells, revealing the mechanism of these functionally important modifications. The knowledge obtained from this basic science research will serve as a general model for other dynamic protein complexes. The insights obtained could lead to the development of diagnostic and therapeutic agents.
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|Li, Zhen-Lu; Prakash, Priyanka; Buck, Matthias (2018) A ""Tug of War"" Maintains a Dynamic Protein-Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane. ACS Cent Sci 4:298-305|
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|Zhang, Liqun; Buck, Matthias (2017) Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1. J Phys Chem B 121:1485-1498|
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|Li, Zhen-Lu; Buck, Matthias (2017) Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology. Structure 25:679-689.e2|
|Won, Seoung Youn; Kim, Cha Yeon; Kim, Doyoun et al. (2017) LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate. Front Mol Neurosci 10:327|
|Shengjuler, Djoshkun; Chan, Yan Mei; Sun, Simou et al. (2017) The RNA-Binding Site of Poliovirus 3C Protein Doubles as a Phosphoinositide-Binding Domain. Structure 25:1875-1886.e7|
|Li, ZhenLu; Cao, Shufen; Buck, Matthias (2016) K-Ras at Anionic Membranes: Orientation, Orientation…Orientation. Recent Simulations and Experiments. Biophys J 110:1033-5|
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