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J Mol Biol. 2014 Feb 6;426(3):611-29. doi: 10.1016/j.jmb.2013.10.036. Epub 2013 Nov 2.

DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

Author information

1
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.
2
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
3
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.
4
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA. Electronic address: c.mattos@neu.edu.

Abstract

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras.

KEYWORDS:

DRoP; DRoP software; Detection of Related Solvent Positions; GAP; GTPase activating protein; MSCS; PDB; Protein Data Bank; Ras GTPase; crystallographic water analysis; multiple solvent crystal structures; protein hydration; water-mediated networks in protein structure

PMID:
24189050
DOI:
10.1016/j.jmb.2013.10.036
[Indexed for MEDLINE]

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