Peptide complexation

Ikura, M., et al. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science 256 632-638, 1992. 

Meador, W.E., Means, A.R., Quiocho, F.A. Target enzyme recognition by calmodulin 2.4 A stmcture of a calmodulin-peptide complex. Science 257 1251-1255, 1992. 

Inhibitors as well as substrates bind in this crevice between the domains. From the numerous studies of different inhibitors bound to serine pro-teinases we have chosen as an illustration the binding of a small peptide inhibitor, Ac-Pro-Ala-Pro-Tyr-COOH to a bacterial chymotrypsin (Figure 11.9). The enzyme-peptide complex was formed by adding a large excess of the substrate Ac-Pro-Ala-Pro-Tyr-CO-NHz to crystals of the enzyme. The enzyme molecules within the crystals catalyze cleavage of the terminal amide group to produce the products Ac-Pro-Ala-Pro-Tyr-COOH and NHs. The ammonium ions diffuse away, but the peptide product remains bound as an inhibitor to the active site of the enzyme. 

I MHC-peptide complexes and those that recognize class 11 MHC-peptide complexes utilize the same set of Va and Vp genes, and the principal feature that defines the site of class 1 MHC-TCR interaction, the cleft formed by the a and az subunits of the MHC molecule, is shared by both class 1 and class... 

Scott, C.A., Peterson. P.A., Teyton, L., Wilson, LA. Crystal structures of two 1-A -peptide complexes reveal that high affinity can be achieved without large anchor residues. Immunity 8 319-329, 1998. 

Amini, F., Denison, C., Lin, H.J., Kuo, L., and Kodadek, T., Using oxidative crosslinking and proximity labelling to quantitatively characterize protein-protein and protein-peptide complexes, Chem. Biol., 10(11), 1115-1127, 2003. 

Strange and Dark demonstrated the presence of a hexosamine containing peptide in the spore coats of B. megaterium and B. subtilis. The breakdown of an insoluble peptide complex might well be one of the first steps of the germination process. It was believed that the release of the hexosamine-amino acid complex was the result of the action of lysozyme present in the spores. 

Kalkhof, S. et al. (2005a) Chemical cross-linking and high-performance fourier transform ion cyclotron resonance mass spectrometry for protein interaction analysis Application to a calmodulin/target peptide complex. Anal. Chem. 77, 495-503. 

Fig. 6. Schematic diagram of the peptide-protein interaction mode as seen in the crystallo-graphically refined structured of the Lck SH2 domain-peptide complex, Protein Databank entry code 1 LKK.PDB. The residues directly engaged in intramolecular hydrogen bonds (dotted lines) are labeled explicitly... 

Fig. 8. Lck SH2 domain-peptide complex (Ac-cmF-Glu-Glu-Ile-OH, 12) revealing the twopronged plug engaging a two-holed socket 1 binding mode, reminiscent of the majority of SH2 domains (Protein Databank entry code 1BHF.PDB [118]). The protein is depicted in a Connolly surface mode, the ligand is given in a ball-and-stick representation. The cmF residue is deeply buried in its binding pocket (left)...

Due to the changed backbone conformation, several key interactions normally found in SH2 domain-peptide complexes are not formed, thus demanding further optimization in order to meet the spatial requirements of the target more precisely [153]. 

Parke-Davis targeted a template structure with no formal charge replacing the Glu-Glu dipeptide bridging pTyr with lie (pTyr+3), since the X-ray structure of SH2-peptide complexes suggested that the contribution of the two charged... 

The Novartis group used the X-ray structure of a Grb2-peptide complex [68] as the structural basis for a design attempt that yielded entirely new non-peptide SH2 domain ligands [164]. As mentioned several times throughout this contribution, the interaction of the pTyr sidechain and the Asn sidechain in pTyr+2 position of the peptide ligand have been identified as key elements for molecular recognition (see Fig. 10). The obvious relevance of these two sidechain functionalities allowed the definition of a minimal pharmacophore pattern that... 

The kinetics and mechanisms of substitution reactions of metal complexes are discussed with emphasis on factors affecting the reactions of chelates and multidentate ligands. Evidence for associative mechanisms is reviewed. The substitution behavior of copper(III) and nickel(III) complexes is presented. Factors affecting the formation and dissociation rates of chelates are considered along with proton-transfer and nucleophilic substitution reactions of metal peptide complexes. The rate constants for the replacement of tripeptides from copper(II) by triethylene-... 

The sluggish substitution properties of copper(III) and nickel(III) peptide complexes have permitted the isolation of complexes with these oxidation states (14, 15). Thus, the tri-valent peptide complexes pass through a cation exchange resin which readily strips copper(II) or nickel(II) from the corresponding complexes. We now have a little more information about the substitution characteristics of the trivalent metal complexes. 

Nickel(III) peptide complexes have a tetragonally-distorted octahedral geometry as shown by electron spin resonance studies (19) and by reaction entropies for the Ni(III,II) redox couple (17). Axial substitutions for Ni(III)-peptide complexes are very fast with formation rate constants for imidazole greater... 

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