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Transcript
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.