SIP: Self-Inhibitory Peptides

Step 3: What protein will be your drug target? What property of that protein will you target? Design an assay/approach to identify an antidote for “degron”. (4 pts.)

toxin A and E cleave a bond in SNAP-25, but A cleaves the peptide bond between Gln197-Arg198 whilst E cleaves Arg180-Ile181. Only one peptide bond in the SNARE protein is cleaved by the catalytic domain of the light chain, even though there may be more occurrences of the same bond within the structure. The reason for this was speculated to be due to structural differences between the serotypes and that the binding domain of each may be in a different position so that when the toxin binds to its substrate it changes its orientation to cleave the peptide bond that is ideal in correspondence with the change in orientation. The effect of the peptide bond cleavage is revealed once an action potential reaches the neuron. An action potential at the neuron depolarises the membrane and this causes an influx of Ca2+ ions in the axon. The formation of a neurotransmitter occurs when acetyl-CoA and choline react to produce acetylcholine in a process catalysed by the enzyme choline acetyltransferase. The calcium ions stimulate neurotransmitter release and thus acetylcholine molecules want to leave the cell via

4a). This protein had the characteristics of two interactions and a 544 amino acid residue. To further support the claim of the TPP1 interaction with POT1, TPP1 antibody was pulled down with flag tagging POT1 (Fig. 4b). Hence, these data validate the claim of the POT1, and TPP1 form one complex [17].

Enhance the affinity of the recognition site for GABA by inducing conformational changes that make GABA binding more efficacious.

For the peptide-based drugs it is a rate-limiting step to cross the BBB. Chimaric peptides contain the drug in brain but are unable to cross the BBB so; we conjugate the drug with targeting vector. Now, these Chimaric proteins can easily pass through the BBB and can be detected by fluorescent markers in the

C-peptide is 31 amino acid chains that connect “A” chain of insulin to “B” chain of insulin in proinsulin molecules.

The concept of targeting PEP with specific inhibitors to control critical neuropeptide levels in the body is an intriguing one. However, a better understanding of the physiological function of PEP and its specific mechanism for regulating neuropeptide levels is critical to design appropriate inhibitors that target the proper region of the body.

For the second part of the experiment, one had to use the knowledge learn from viewing protein molecules in FirstGlance in Jmol to analyze the protein PDB ID: 4EEY. The analysis of this protein was done using the RSCB protein data bank (PDB) at (http://www.rcsb.org/pdb/home/home.do).2

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

in discrete sectors, and this cationic, amphipathic structural feature is critical for their activity and selectivity ( Zasloff, M., 2002). Most host defense peptides are believed to be membranolytic, with cationic residues selecting for anionic cellular membrane via electrostatic interactions and hydrophobic regions responsible for membrane permeation and disruption ( Melo, M.N., 2009).

The two active peptides; orexin A and orexin B are structurally related to each other but have no sequence similarity to any other known

As indicated previously,17 long alkyl chain and one of the diphenyl ether ring form hydrophobic interaction with Ala140, Met196, Tyr225, Thr231, Ala273, and Met285 that may provide better affinity toward inhibitor than triclosan (Figure 4). In addition, the ring that does not have alkyl chain binds to the pocket at ∼24° tilted position compared to that of the bound triclosan to FabI. Specifically, when the structures of FabIs and FabV were superimposed, conserved M206 through FabIs interfered the binding of the inhibitor of FabV (Figure 4).7,22 Therefore, we postulate that the hydrophobic pocket of FabV has a preference for the alkyl chain of inhibitor than triclosan.

The reason for increased toxicity, with highly hydrophobic peptides, in eukaryotic cells is that peptides with higher hydrophobicity experience poor solubility conditions in aqueous solution, therefore binding to (and disrupting) also eukaryotic cell membranes (Dennison, SR., 2005b). Thus, a strong correlation is observed between cytotoxicity and hydrophobicity (Blondelle, SE., 1992; Bessalle, R., 1993; Javadpour, MM., 1996; Skerlavaj, B., 1996; Pasupuleti, M., 2008).

After the QSAR studies, docking study is being carried out. The docking study will reveal the binding orientation of the active ligands on the protein which will be completed in BTP-phase II.

In a study where stimulations of XN1-P11-P10 peptides which are identical to XN1 but lack poly-P regions show that poly-P region protects XN1 by inhibiting aggregation of poly-Q region. Poly-P regions from PPII helices and overcome the likelihood of poly-Q residues in XN1 to adopt β-sheet dihedral angles (La khani et al, 2010). Therefore without poly-P regions aggregation will follow in poly-Q. Another study showed that a 23 aa-long hHtt peptide, P42, plays a defensive role with respect to polyQ-hHtt aggregation as well as cellular and