Simulations of Biological Macromolecules
Vaidehi Nagarajan, Wely Floriano, Joyce Peng, Derek Debe and William Goddard III
Design of inhibitors for E.coli invasion of the brain endothelial cells in neonatal infants ( NIH- NICHD in collaboration with Dr. Prasadarao and Dr. Kim of the Children's Hospital, Los Angeles)
- Building three dimensional structures for odor receptors and study the binding characteristics of the odorants to the odor receptors.(Floriano, Vaidehi, Debe, Goddard, Singer, Shepherd, Manic, Buck)
- Understanding of the stability of amyloid fibrils in Alzheimer's and Huntington's diseases.(Peng, Vaidehi and Goddard)
- Dimerization and stability of fluorinated zippers (collaboration with Y.Tang &D.Tirrell, Chem. Engg. Caltech)
Inhibitors for E.coli invasion of the brain microvascular endothelial cells
Bacterial meningitis in neonatal infants is caused by the E.coli invasion of the brain microvascular endothelial cells.
The OmpA on E.coli recognizes the GlcNac-GlcNac epitopes on the glycoproteins (Prasadarao, Wass and Kim, Infection and Immunity, 1996, 64, 154.)
OmpA binding Studies
Glycosylation( especially chitobiose) of peptides has been observed to induce the formation of a b
turn in protein folding process (Connor and Imperiali, 1998).
- GlcNac-GlcNac dimers or NAG dimers are known to be Asparagine linked in glycoproteins.
- It is known that while E.coli invades the brain microvascular endothelial cells it doesnot invade systemic endothelial cells- may be to a fucosyl substitution in the chitobiose for the systemic cells.
- We need to investigate the binding determinants in the binding of chitobiose and its derivatives
Crystal Structure of OmpA.
Possible Binding Pockets in OmpA.
Preliminary Results on Binding
Binding energies (estimate) from Annealing MD simulations
10 cycles of Annealing simulations done from 300 to 600K.
- protein fixed and only the ligand and waters movable
- all residues within 5A distance from the ligand are movable with ligand and waters.
Binding energy for N-acetyl glucosamine trimer = -4.1056 Kcals/mole
Binding energy for fucosyl substituted NAG oligomer = -5.2735 Kcals/mole
The binding of fucosyl and NAG oligomer do not show much difference in this binding pocket.
Other binding pockets would be tried and binding energy estimated with MD and then using QM calculations.
Restraint Generic Protein_Loop Builder
This past year we have developed the RGP_loop builder for building loops in membrane proteins.
- Loops are extracellular in membrane proteins and highly variable in structure and sequence.
- Most of the short loops (< 10 residues) do not have secondary structure characteristics but longer loops like the 3rd loop in OmpF (porin) have a few residues in helical or sheet regions( torsion angles).
- The commercial loop builders such the protein data bank for sequence similarity hits which is not suitable for longer loops( no hits).
- We need a generic loop builder especially to automate the procedure of building loops with varying lengths for about 1000 proteins( odor receptors).
- We started this to predict loop structures for OmpA where loop region is the binding pocket.
RGP for Membrane Proteins
- Grows loops within 120% of the membrane volume which allows the loops to be within the hydrophobic region.
- The angles at the start and the end of the loop are extended(pdb) and biased towards growing it extended for short loops (<15 res).
- Longer loops are grown without condition 2 and with condition 1.
RGP Predictions for OmpF short loops
Structure Prediction, Molecular Dynamics and Function Correlations
Wely Floriano, Vaidehi Nagarajan & William Goddard III (Caltech)
Bettina Malnic & Linda Buck ( Harvard Medical)
Mike Singer & Gordon Shepherd (Yale Medical)
Mammalian Olfaction is a complex phenomenon- distiguishes thousands of odorants - and at few ppt concentration.
Understanding of the binding of odors to the receptors. The binding may not be specific or tight since it could be reversible.
- Assembly of odor receptor structures. Seven helical trans membrane proteins coupled to G-proteins.
- Harvard: sequences the odor receptors
- Yale: Identify the secondary structure parts.
- Caltech: packing and MD of the receptors.
Details will be given in talk D1 (Floriano).
Heirarchical NEIMO Method
Torsional dynamics method- with large domains of proteins as rigid bodies and loops as flexible regions.
It would be possible to study large motions ( required for packing helices) by keeping only the degrees of motion necessary to pack the helices as flexible torsions
- Dofs reduced from 1247 to 266 in the case of bacteriorhodopsin. 5fs timestep Nose-TVN
- small dihedral motions causes large displacements in helices
- slow down the dynamics with all cartesian and restore H-NEIMO dynamics
- Massively Parallel Simulation Package (MPSim)
- Would perform simulations with water in the barrel and a high dielectric SGB solvation(Dan Mainz) in the membrane region.
H-NEIMO Model for Odor Receptors