@article{dechene_wink_smith_swartz_mattos_2009, title={Multiple solvent crystal structures of ribonuclease A: An assessment of the method}, volume={76}, ISSN={["1097-0134"]}, DOI={10.1002/prot.22393}, abstractNote={AbstractThe multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6‐hexanediol, 70% isopropanol, 50% R,S,R‐bisfuran alcohol, 70% t‐butanol, 50% trifluoroethanol, or 1.0M trimethylamine‐N‐oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. © 2009 Wiley‐Liss, Inc.}, number={4}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Dechene, Michelle and Wink, Glenna and Smith, Mychal and Swartz, Paul and Mattos, Carla}, year={2009}, month={Sep}, pages={861–881} }
 @article{buhrman_wink_mattos_2007, title={Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf}, volume={15}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2007.10.011}, abstractNote={<h2>Summary</h2> Transformation efficiencies of Ras mutants at residue 61 range over three orders of magnitude, but the in vitro GTPase activity decreases 10-fold for all mutants. We show that Raf impairs the GTPase activity of RasQ61L, suggesting that the Ras/Raf complex differentially modulates transformation. Our crystal structures show that, in transforming mutants, switch II takes part in a network of hydrophobic interactions burying the nucleotide and precatalytic water molecule. Our results suggest that Y32 and a water molecule bridging it to the γ-phosphate in the wild-type structure play a role in GTP hydrolysis in lieu of the Arg finger in the absence of GAP. The bridging water molecule is absent in the transforming mutants, contributing to the burying of the nucleotide. We propose a mechanism for intrinsic hydrolysis in Raf-bound Ras and elucidate structural features in the Q61 mutants that correlate with their potency to transform cells.}, number={12}, journal={STRUCTURE}, author={Buhrman, Greg and Wink, Glenna and Mattos, Carla}, year={2007}, month={Dec}, pages={1618–1629} }