DRoP: Automated detection of conserved solvent‐binding sites on proteins
| Autor: | Michelle Dechene, Kendra Marcus, Bradley M. Kearney, Michael Schwabe, Daniel M. Roberts, Paul Swartz, Carla Mattos |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular Protein Conformation RNase P Population Protein Data Bank (RCSB PDB) Crystallography X-Ray Ligands Bovine pancreatic ribonuclease Biochemistry 03 medical and health sciences Structural Biology Animals Humans Molecule Organic Chemicals Binding site Databases Protein education Molecular Biology 030304 developmental biology 0303 health sciences education.field_of_study Binding Sites biology Chemistry 030302 biochemistry & molecular biology Proteins Water Ribonuclease Pancreatic Solvent Solvation shell Solvents biology.protein Cattle Biological system Software Protein Binding |
| Zdroj: | Proteins: Structure, Function, and Bioinformatics. 88:152-165 |
| ISSN: | 1097-0134 0887-3585 |
| DOI: | 10.1002/prot.25781 |
| Popis: | Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X-ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein-protein or protein-ligand interactions, as well as conserved water-binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Plný text