NSF Sumer School on Theoretical and Computational Biophysics 2003

Beauty Contest Finalists


Karunesh Arora and Yanli Wang
Studying the Docking of ATP Analogue in the Binding Pocket of Raf-1 Kinase using Molecular Dynamics Simulations



Phillip Fowler and Shantenu Jha.
DNA, SMD and Force Fields (...or how I learned to stop worrying and love SMD)




Han Liang
Molecular Dynamics of Release Factor (eRF1)



Zhanwu Liu
SMD study of sodium ion permeation across a gramicidin A channel




Will Sheffler
Rational design of Snake Toxin as Molecular Marker




Scott Stagg
Molecular simulation of distorted tRNA: Is tRNA a molecular spring?








Yanli Wang and Karunesh Arora
Studying the Docking of ATP Analogue in the Binding Pocket of Raf-1 Kinase using Molecular Dynamics Simulations


The identification of cognate substrates for kinases is a known problem in protein kinase research. One possible solution is to engineer the kinase of interest to accept an ATP analogue which is orthogonal (unable to fit into the ATP-binding site) for the wild type enzyme. The acceptance of radioisotropically labeled nucleotide analogue by active site modified kinase provides a unique way to trace the direct substrates of any particular kinase. This approach has been successfully applied to study serine/threonine kinase Raf-1.

In this work, a three dimensional structure model for Raf-1 was built by homology modeling. Three residues in the ATP binding pocket were mutated based on the model and sequence alignment. Experimentally determined orthogonal analogue (N6-(2-phenethyl)-ATP) was placed in the binding pocket of mutant Raf-1 by superimposing with ATP. Room temperature molecular dynamics simulation in NPT ensemble was performed with NAMD using CHARMM forcefield. Our preliminary results show the opening of the binding pocket and large conformational change of the analogues, to accommodate substrate in the active site.



Phillip Fowler and Shantenu Jha
DNA, SMD and Force Fields (...or how I learned to stop worrying and love SMD)

We compare the dynamic behaviour of DNA system (see below) using two different force fields (Amber 94 and Charmm 27) under exactly the same conditions. A more destructive, yet fun and useful method of comparing the FFs is to rip the DNA asunder using SMD. Finally, we'll demonstrate a transcontinental distributed steering experiment*
System:  A 12 base pair DNA helix of pharmacological significance, solvated with 22 Na+ ions to maintain electrical neutrality.
*Time and colour for the moon permitting.



Han Liang
Molecular Dynamics of Release Factor (eRF1)


eRF1 (eukaryotic release factor 1) plays a very important role in terminating protein translation. Domain 1 in eRF1 is responsible for stop codons recognition, but the specific binding sites have not yet been identified.
The binding sites have been suggested to experience conformational changes in order to perform their function, when binding to the ribosome.
In this study simulations of  MD of eRG1 domain 1 under two conditions,  normal water solution and solution with high negative charge, which corresponds to ribosome density, are performed. The files of which RMSD are compared, and the biological important sites has been suggested.



Zhanwu Liu
SMD study of sodium ion permeation across a gramicidin A channel

Gramicidin A is a small model ion channel that allows sodium ions to permeate. In this simulation, I build a system consisting of gA channel as well as small box of water to save computer time. Potential of mean force will be constructed through simulation. Results expected from the simulation:
1. Explore the optimal parameters to perform SMD in this system and the expanded system (which will include the lipid bilayer).
2. The energy change of sodium ion permeation through gA channel.
Future research will focus on how small anesthetic dry molecules affect the energetics of ion permeation.



Will Sheffler
Rational design of Snake Toxin as Molecular Marker

I present models of nicotinic AcetylCholine Receptors, which mediate post-synaptic transmission in the brain and in neuro-muscular junctions, in complex with the snake toxin protein alpha-bungarotoxin, one type to which the toxin shows native affinity, and the other to which it does not. Models are based on receptor homology to a soluble protein of known structure and NMR data of alpha-bungarotoxin in complex with a small receptor peptide fragment. I equilibrate the two systems and then use SMD to pull the toxin away from each receptor, allowing qualitative analysis of why alpha-bungarotoxin binds to one receptor type and not the other. Ultimately, our group wishes to design and express a mutated version of th toxin which will bind to different acetylcholine receptor types, facilitating the use of radio-labeled toxin as a molecular marker in acetylcholine receptor expression pattern studies of interest in neuroscience.



Scott Stagg
Molecular simulation of distorted tRNA: Is tRNA a molecular spring?

A recent cryo-EM study showed that when the ternary complex of EF-Tu, GTP and tRNA binds to the ribosome, the anticodon of the tRNA is bent nearly 45°. It was suggested that the tRNA is acting as a molecular spring, and that this distortion is important for the selection of the correct tRNA.  I have modeled the distorted tRNA and I am using MD to test whether the tRNA will return to its undistorted state. If so, I will repeat this simulation in the context of the ribosome and determine the regions in which the tRNA is interacting with the ribosome. This should help elucidate the mechanism of translational fidelity.