Download Chemotaxis pahtway How can physics help?

Chemotaxis Pathway
How can physics help?
Davi Ortega
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
Vocabulary
• Amino Acids
In Biology
– In chemistry, an amino acid is a molecule that contains both amine and
•20 Amino
Acids groups. In biochemistry, this term refers to alphacarboxyl functional
amino acids with the general formula NH2CHRCOOH.
• Identified by three Letter code or one Letter
Code
•Classified by biochemistry properties: Polar,
Hydrophobic and Charged
Vocabulary
• Peptides
– Chain of Amino Acids connected by the peptide bonds
…FSEK…
Vocabulary
• Proteins
– Chain of Amino Acids that when folded execute a biological
function.
Vocabulary
• Pathway
– Set of protein that works cooperatively with the same objective
Vocabulary
Constant probability of mutations at any Residue.
• Genome: the whole hereditary information encoded on the DNA
Conserved residues
must
be extremely
important
to from
the biological
• Sequence:
Sequence
of the
amino acids
decoded
the DNA.
function
• Multiple Alignment: Alignment of different sequences of the same
protein.
E. Coli
• Chemotaxis pathway
– Senses the external environment and
actuates on the motility system
Bacteria Flagella Motility
Movie
The interaction problem
• The structures of CheA, CheW and MCP
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 ?
Methods: Multiple Alignment
CheA
MCP
CheW
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.
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.
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.