Application of the Multiple Solvent Crystal Structures Method to Analyze the Protein Binding Surface of H-Ras Protein

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Title: Application of the Multiple Solvent Crystal Structures Method to Analyze the Protein Binding Surface of H-Ras Protein
Author: Buhrman, Gregory Kale
Advisors: Carla Mattos, Committee Chair
Abstract: H-Ras is a member of the small, monomeric GTPase protein superfamily. H-Ras functions as a 'molecular switch', using nucleotide dependent conformational changes to relay signals in a number of signal transduction pathways. Mutations in codons 12, 13 and 61 creates an oncogenic version of the protein which does not hydrolyze GTP, resulting in the constitutive activation of downstream effector proteins. Ras proteins participate in multiple protein : protein interactions in the cell, making Ras a good candidate protein to extend the Multiple Solvent Crystal Structures method (MSCS) to the analysis and prediction of protein binding surfaces. MSCS involves solving the crystal structure of the protein after soaking the protein crystal in a variety of organic solvent molecules. Replacing an aqueous solvent with an organic solvent affects the Ras protein structure in several ways. The disordered Switch II region of Ras is ordered in the presence of 2,2,2-trifluoroethanol or 1,6-hexanediol. Polar interactions that stabilize the ordered switch are enhanced in the presence of hydrophobic co-solvents. This suggests that hydrophobic solvents can be used in general to order short biologically relevant segments of disordered regions in protein crystals. We have used MSCS to study two crystal forms of active H-Ras bound to a nonhydrolyzable GTP analog (GMPPNP). We have also solved the structure of an oncogenic mutant of H-Ras (Q61L) in a non-canonical crystal form. This crystal form of H-Ras shows a new conformation for the flexible Switch II region that is not affected by crystal packing forces. This provides a structural explanation for the oncogenic properties of the Q61L mutation, showing that the Q61L mutation stabilizes a non-catalytic conformation of Switch II. MSCS analysis of Ras identifies the known Ras-effector binding domain as a site of protein: protein interaction and predicts a new protein binding site that is located in a large, solvent exposed pocket between Switch II and helix 3. In applying MSCS to the Ras protein, we show that by using polar organic solvent molecules as probes, we can identify binding sites that are highly charged and dynamic.
Date: 2006-05-02
Degree: PhD
Discipline: Biochemistry

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