Chemotaxis Pathway How can physics help

1
Chemotaxis PathwayHow can physics help?

• Davi Ortega

2
Summary

• Vocabulary
• Pathway, Proteins, Peptides, Amino acids.
• Genome, Sequences, Multiple Alignment.
• Bacteria (E. Coli)
• Chemotaxis pathway.
• Motility, Substances gradient recognition.
• The proteins interaction problem
• CheA, CheW and MCP
• Methods and Evidences
• Multiple Alignment
• Docking
• Molecular Dynamics.
• Conclusions

3
Vocabulary

• In Biology
• 20 Amino Acids
• Identified by three Letter code or one Letter
  Code
• Classified by biochemistry properties Polar,
  Hydrophobic and Charged

• Amino Acids
• In chemistry, an amino acid is a molecule that
  contains both amine and carboxyl functional
  groups. In biochemistry, this term refers to
  alpha-amino acids with the general formula
  NH2CHRCOOH.

4
Vocabulary

• Peptides
• Chain of Amino Acids connected by the peptide
  bonds

FSEK
5
Vocabulary

• Proteins
• Chain of Amino Acids that when folded execute a
  biological function.

6
Vocabulary

• Pathway
• Set of protein that works cooperatively with the
  same objective

7
Vocabulary
Constant probability of mutations at any
Residue. Conserved residues must be extremely
important to the biological function

• Genome the whole hereditary information encoded
  on the DNA
• Sequence Sequence of the amino acids decoded
  from the DNA.
• Multiple Alignment Alignment of different
  sequences of the same protein.

8
E. Coli

• Chemotaxis pathway
• Senses the external environment and actuates on
  the motility system

9
Bacteria Flagella Motility
10
Movie
11
The interaction problem

• The structures of CheA, CheW and MCP

12
The interaction problem

• The same organism has several CheA, CheW and MCP.
• How do they interact!?
• How do they cluster?
• What kind of signal is transmitted?
• Which CheA interacts with which CheW and MCPs ?

13
Methods Multiple Alignment
CheA
CheW
MCP
14
3D Structures Molecular Dynamics

• Molecular Dynamics
• Force Field techniques.
• 3D Structures are snapshots
• Few structures available
• Need to have energy minimized
• Simulation with non zero temperature.

15
Docking (by biochemistry and sequences)

• Based on affinity of amino acids.
• 1) Define the contacts aminoacids
• 2) Produce a score based on the affinity for each
  sequence.
• 3) Score the possible matches
• 4) Select the best scores.

16
Conclusion

• Chemotaxis Pathway Interactions between proteins
  are still a open problem
• Physics, Biology (and Genomics), Chemistry and
  Computation can solve the mystery.
• Solutions can leads to better antibiotics or
  bioengineering bacteria to increase biofuel
  efficiency.