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Multiple solvent crystal structures of ribonuclease A: an assessment of the method.

Dechene M, Wink G, Smith M, Swartz P, Mattos C
Proteins 76 861-81 (2009)
Related entries: 3eux, 3euy, 3euz, 3ev1, 3ev2, 3ev3, 3ev4, 3ev5, 3ev6

Cited: 20 times
EuropePMC logo PMID: 19291738

Abstract

The 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.

Reviews citing this publication (3)

  1. Protein flexibility in docking and surface mapping. Lexa KW, Carlson HA. Q Rev Biophys 45 301-343 (2012)
  2. Thermodynamics and solvent linkage of macromolecule-ligand interactions. Duff MR, Howell EE. Methods 76 51-60 (2015)
  3. Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology. Grasso D, Galderisi S, Santucci A, Bernini A. Int J Mol Sci 24 5819 (2023)

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  2. Analysis of binding site hot spots on the surface of Ras GTPase. Buhrman G, O'Connor C, Zerbe B, Kearney BM, Napoleon R, Kovrigina EA, Vajda S, Kozakov D, Kovrigin EL, Mattos C. J Mol Biol 413 773-789 (2011)
  3. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. Raman EP, Yu W, Yu W, Guvench O, Mackerell AD. J Chem Inf Model 51 877-896 (2011)
  4. New Frontiers in Druggability. Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. J Med Chem 58 9063-9088 (2015)
  5. 1,6-Hexanediol, commonly used to dissolve liquid-liquid phase separated condensates, directly impairs kinase and phosphatase activities. Düster R, Kaltheuner IH, Schmitz M, Geyer M. J Biol Chem 296 100260 (2021)
  6. Lipase in aqueous-polar organic solvents: activity, structure, and stability. Kamal MZ, Yedavalli P, Deshmukh MV, Rao NM. Protein Sci 22 904-915 (2013)
  7. DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site. Kearney BM, Johnson CW, Roberts DM, Swartz P, Mattos C. J Mol Biol 426 611-629 (2014)
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  9. Cosolvent Analysis Toolkit (CAT): a robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome. Sabanés Zariquiey F, de Souza JV, Bronowska AK. Sci Rep 9 19118 (2019)
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  12. ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures. Sekiyama N, Takaba K, Maki-Yonekura S, Akagi KI, Ohtani Y, Imamura K, Terakawa T, Yamashita K, Inaoka D, Yonekura K, Kodama TS, Tochio H. Proc Natl Acad Sci U S A 119 e2122523119 (2022)
  13. The use of a ditopic Gd(III) paramagnetic probe for investigating α-bungarotoxin surface accessibility. Bernini A, Spiga O, Venditti V, Prischi F, Botta M, Croce G, Tong AP, Wong WT, Niccolai N. J Inorg Biochem 112 25-31 (2012)
  14. Site-Resolved and Quantitative Characterization of Very Weak Protein-Ligand Interactions. Fuglestad B, Kerstetter NE, Wand AJ. ACS Chem Biol 14 1398-1402 (2019)
  15. Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium. Fermani S, Calvaresi M, Mangini V, Falini G, Bottoni A, Natile G, Arnesano F. Chemistry 24 4140-4148 (2018)
  16. Biased Docking for Protein-Ligand Pose Prediction. Arcon JP, Turjanski AG, Martí MA, Forli S. Methods Mol Biol 2266 39-72 (2021)
  17. Structure-based identification of a potential non-catalytic binding site for rational drug design in the fructose 1,6-biphosphate aldolase from Giardia lamblia. Méndez ST, Castillo-Villanueva A, Martínez-Mayorga K, Reyes-Vivas H, Oria-Hernández J. Sci Rep 9 11779 (2019)


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