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.