Multiple solvent crystal structures of ribonuclease A: An assessment of the method

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2009-09, Vol.76 (4), p.861-881
• Main Authors: Dechene, Michelle, Wink, Glenna, Smith, Mychal, Swartz, Paul, Mattos, Carla
• Format: Article
• Language: English
• Subjects: Animals; Catalytic Domain; CATTLE; Computer Simulation; CRYSTAL STRUCTURE; Crystallography, X-Ray; DIOXANE; HOT SPOTS; HYDRATION; MATERIALS SCIENCE; Models, Molecular; ORGANIC SOLVENTS; Pancreas - enzymology; PLASTICITY; Protein Binding; protein binding sites; Protein Conformation; PROTEINS; Ribonuclease, Pancreatic - chemistry; Ribonuclease, Pancreatic - metabolism; RNA-ASE; solvent mapping; SOLVENTS; Solvents - chemistry; Solvents - metabolism; WATER; Water - chemistry; Water - metabolism
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.22393

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. Proteins 2009. © 2009 Wiley‐Liss, Inc.