Summary of current projects

RAS GTPases (in collaboration with the group of Prof. John Hancock)
A host of proteins within the Ras superfamily of GTPases act as molecular switches in signaling pathways that control cell growth and proliferation. Mutations in Ras account for about a third of all human cancers. Understanding the mechanism by which individual Ras proteins control specific signal flows is critical for the development of malignancy-specific anticancer agents. The widely studied and highly homologous H-, N- and K-Ras isoforms provide a suitable model for studying signaling specificity. That the isoforms promote specific signaling outputs is now clear, but it is not clear how. A significant body of cell-biological and biochemical data suggests that different membrane microdomain compartmentalization of the isoforms determines their effector specificity. Other clues suggest that specificity can be achieved independently of Ras location to membrane subdomains. The differences in amino acid sequence at the membrane-binding C-terminus as well as in posttranslational modifications support the former argument. However, subtle structural and/or dynamical differences could also play a significant role. Structures are available for truncated H-Ras in the inactive (GDP-bound) or active (GTP-bound) states and in isolation or in complex with effectors or activators. However, no structural characterization has been made for the full-length protein either in solution or in its membrane-associated state. It would be interesting to computationally probe into the specificity determinants through detailed characterization of the dynamics and energetics of each Ras isoform (in different mediums and with/without their interaction partners)


1. Gorfe AA, Grant B and McCammon JA Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins Structure,  in press  (2008).
2. Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF. A novel switch region regulates H-ras membrane orientation and signal output EMBO J.,    (2008).
3. Gorfe AA, Babakhani A and McCammon JA. H-ras Protein in a Bilayer: Interaction and Structure Perturbation (J. Am. Chem. Soc.; published online 09/19/2007  
   
4. Gorfe AA, Babakhani A and McCammon JA. Free Energy Profile of H-ras Membrane Anchor upon Membrane Insertion (Angew. Chem. Int. Ed.; published online 09/21,  
   
5. Abankwa D, Gorfe AA, Hancock JF. Ras nanoclusters : molecular structure and assembly Seminars in Cell and Developmental Biology,   (   2007).
   
6. Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF and McCammon JA. Structure and dynamics of the full-length lipid-modified H-Ras protein in complex with a DMPC bilayer. J. Med. Chem.,   2007 Feb 22;50(4):674-84   (2007).[pdf]
   
7. Gorfe AA, Pellarin R and Caflisch A. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J. Am. Chem. Soc.,   126(46):15277-15286   (2004).[pdf]


Acetylcholinesterase (with Dr. Chia-en Chang)
Acetylcholinesterase is an enzyme in the cholinergic synapses, including the neuromuscular junction, which very rapidly hydrolyzes the neurotransmitter acetylcholine. The crystallographic structure of the tetramer, which is the most important functional form, has been solved in two low-resolution crystal forms. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. Rate caculations and some experiments suggested that occlusion by complemenmtary subunits may reduce catalysis efficiency. Furthermore, the x-ray structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). Therefore, a complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer and normal mode analysis carried out on this model also suggested that the subunits could indeed fluctuate relative to one another. To understand the extent and significance of these motions, we investigate the large scale inter-subunit dynamics by a multi-scale simulation approach.


Gorfe AA, Chang CA, Ivanov I and McCammon JA. Dynamics of acetylcholinesterase tetramer (    2007).



Peptide-membrane interactions (with Arneh Babkhani)
Please visit Arneh's page for more!

Babakhani A, Gorfe AA, Gullingsrud J, Kim J and McCammon JA. Peptide Insertion, Positioning, and Stabilization in a Memberane: Insight From an All-Atom Melecular Dynamics Simulation Biopolymers,   85(5-6):490-497  (2007). [pdf]