GTP-binding-protein ras, a signal-transducing protein involved in many
cancers.
red: GTP-bound, active form (GTP analog in sticks), 1LFO.pdb.
green: GDP-bound, inactive form,
1LF5.pdb.
Proper function of cells and organisms requires
cells from different parts of the organism to act synchronously, and proteins
within cells to communicate with each other through a process known as signal
transduction. These signaling pathways are involved in such processes
as cell division regulation, optical and olfactory response, and hormone
response. Improper functioning of these pathways can lead to disease;
for example, the malfunction of cell cycle control is the primary cause
of many cancers. Signal transduction is a higher-level form of enzyme
regulation, not involving just the response of a single protein to environmental
conditions, but often a whole network of proteins. My research focuses
on the use of biomolecular modeling techniques to predict the molecular mechanisms
of signal transduction from known protein structures. That is, given
a perturbation in one portion of a protein structure, how do other portions
of that protein’s structure respond? Two major models for this allostery
in protein structures exist, mechanical perturbation and effector-induced
shift in a preexisting conformational ensemble. Using the Rosetta biomolecular
modeling package, which predicts protein structures and protein-protein
complexes to within 5A RMSD in 50-70 percent of targets, I intend to simulate
how binding of allosteric effectors to proteins causes them to change conformations.
I intend to compare results from simulations based on the mechanical perturbation
model to results from simulations based on the conformational ensemble model
to shed light on which model is more biologically relevant. My model
systems will include such well-studied signal-transducing proteins like
GTP-binding proteins (G-proteins) and MAP kinase, and possibly also well-studied
allosteric enzymes like phosphofructokinase and hemoglobin.
Shown above is the α subunit of the GTP-binding protein
ras, an important intermediate in multiple signal-transduction pathways
in inactive (GDP-bound) and active (GTP-bound) forms. For example,
ras is dysfunctional (unconditionally active) in 40-60 percent of cancer
cases. In its inactive (GDP-bound) state, ras exists as a heterotrimer,
with the α subunit bound to Gβγ. Three main regions of conformation
change, called switch I, II, and III, respectively, can be observed. It
is the goal of this project to develop a simulation strategy based on Rosetta
that will simulate the conformational change that occurs when ras exchanges
GDP for GTP.
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. M.D. Daily, D. Masica, A. Sivasubramanian,
S. Somarouthu, and J.J. Gray (2005). Proteins 60(2), 181-186.
webPDF.
2004 Institute for Biophysical Research Retreat. M. Daily, A. Sivasubramanian,
D. Masica, and J. Gray. "New Challenges in Protein Assembly and Function."
September 2004, Baltimore, MD. (poster). PDF.
Biophysical Society 48th Annual Meeting: J. Gray & D.
Baker, "Protein-Protein Docking Predictions with RosettaDock."
February 2004, Baltimore, MD. PDF
Modeling
of Protein Interactions in Genomes: M. Daily, M. Ostermeier &
J. Gray, "Modeling the Structural and Energetic Basis for Functional
Coupling in Two Engineered Maltose Binding Protein/TEM-1 B-Lactamase
Molecular Switches." June 2003, Stony Brook, NY. (poster) PDF
Prior to Hopkins:
Huyghues-Despointes, B.M., Thurlkill R.L., Daily, M.D.,
Schell, D., Briggs, J.M., Antiosewicz, J.M., Pace, C.N., and Scholtz.,
J.M. (2003). pK Values of Histidine Residues in Ribonuclease
Sa: Effect of Salt and Net Charge. JMB 325, 1093-1105.
Daily, M.D. Local and Long-Range Electrostatic Interactions
in Denatured RNase Sa: Comparing the Denatured Protein with
Model Peptides. (Spring 2002). Senior Thesis. Texas
A&M University. J.M. Scholtz, advisor.
