Molecular Dynamics of the Avian Influenza Virus

Team Members: Ashvin Srivatsa, Michael Fu, Ellen Chuang, Ravi Sheth

Team Leader: Yuan Zhang

Contents

• Influenza Background• How Influenza Works• Molecular Dynamics• Objective• Procedure• Results• Conclusion

Influenza Background

The Influenza Problem

• “Flu”• Common viral infection of lungs• Many different strains which mutate regularly• Different levels of virulence• Kills roughly half a million people per year

Historical Flu Pandemics

• 1918 Spanish Flu (H1N1)– 500,000 deaths in U.S.

• 1957 Asian Flu (H2N2)– 69,800 deaths in U.S.

• 1968 Hong Kong Flu (H3N2)– 33,800 deaths in U.S.

Avian Influenza

• H5N1• Form of Influenza A Virus• One of the most virulent strains today, spreads

only from birds to humans• Similar to human “common flu”• Mutates frequently, makes it hard to develop

countermeasures• If a mutation allows for it to spread from human

to human, pandemic would follow

How Influenza Works

Structure of Bird Flu Virus

• Protein Coat– Hemagglutinin – bonds

virus to cell membrane– Neuraminidase – helps

virus reproduce in cell

• Lipid Membrane• RNA

Lifecycle of Bird Flu Virus

• Enters and infects cell

• Reproduce genetic material

• Cell lyses, releasing new viruses

Fusion Peptide

• Part of Hemagglutinin protein• Binds virus to cell membrane

Molecular Dynamics

Molecular Dynamics (MD)

• Involves study of computer simulations that allow molecules and atoms to interact

• Extremely complex, based on physics laws• Must be run on powerful supercomputers

MD Software

• Many different types of software solutions exist

• We utilized VMD and NAMD– VMD – Visual Molecular Dynamics– NAMD2 – Not (just) Another Molecular Dynamics

program

A silicon nanopore, rendered with VMD by the Theoretical and Computational Biophysics Group at

the University of Illinois at Urbana-Champaign

Objective

Objective1. Utilize VMD and NAMD2 to conduct

simulations of the influenza fusion peptide being inserted into a lipid membrane on OSC’s supercomputer clusters

2. Determine how various mutations of the fusion peptide affects its ability to penetrate a lipid membrane

Procedure

Procedure

1. Acquire protein structure files (.pdb) – pdb.org

2. Generate lipid membrane, position protein on membrane

3. Solvate (immerse in water) the protein4. Create batch files that tell supercomputer

what to do

Procedure (Cont.)

5. Perform an equilibration simulation to equilibrate protein

6. Execute simulation that pulls protein into membrane

7. Produce visualization

Results

Fusion Peptide Equilibration (H1N1)

Fusion Peptide Pulling (H1N1)

Fusion Peptide Pulling #2 (H1N1)

Next Step: Mutations

• Random change in genetic material• Changes amino acid structure in proteins• New strains of influenza arise through random

mutations as well as through natural selection

Comparison of Amino Sequences

• Different Strains of the 20 amino acid fusion peptide

• Mutation Names – based on original amino acid, position, and new amino acid

Mutation 1

• Mutation at the “head” of the protein• Variants G1V, G1S– (Changes to Valine, Serine)

• Changes way each peptide enters the membrane (Li, Han, Lai, Bushweller, Cafisso, Tamm)

G1V(green), G1S (red) mutants, H1N1 (orange)

G1V(green), G1S (red) mutants, H1N1 (orange)

Analysis

• The H1N1 maintains a straight structure• G1V, G1S variants bunch up – reduce

efficiency• Shows that the Glycine is important amino

acid on the “head”

Mutation 2

• Mutation near bend in peptide• W14A / H3N2• Boomerang structure is critical to peptide (Lai,

Park, White, Tamm)

W14A(green), H1N1 (blue)

W14A(green), H1N1 (blue)

Analysis

• W14A bunches up, after going in half way, comes back out

• H1N1 maintains structure• Shows that “boomerang” or bend is essential• Also could have contributed the success of the

1918 H1N1 outbreak, compared to H3N2

Mutation 3

• N12G• Affects Boomerang Structure• Chosen by team members (not previously

attempted)

N12G(orange), H1N1 (blue)

N12G(orange), H1N1 (blue)

Analysis

• N12G bunches up halfway through• Does not insert as much as H1N1• Further proves that proper bend is essential

Conclusion

Conclusions

• Boomerang structure of the fusion peptide is essential for proper insertion

• Glycine is essential in the “head” position of the fusion peptide

The Bigger Picture

• The fusion peptide process is a target for drug intervention

• Influenza mutates quickly• Deadly implications if H5N1 mutates to spread

from human to human• Further research is essential to protect

humans from another pandemic

Acknowledgements

Yuan Zhang(project leader)

Barbara Woodall(UNIX)

Elaine Pritchard(Organization)

Brianna, Daniel(Dorm Supervisors)

SI SponsorsParents

VMD(University of Illinois)

NAMD2(University of Illinois)

ClustalW(Amino Acid Alignment)

OSC(Supercomputing Time)

Questions?