Crystal structure peptides

Superposition of BACE crystal structure with homology model of BACE. The crystal structure of BACE (PDB entry 1 FKN) was superimposed on the model using the MIDAS program [290]. The model peptide is shown in green stick figure and the crystal structure peptide is shown in red. 

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

Fig. 2. Conformational free energy of closed, intermediate and open protein kinase conformations. cAPK indicates the unbound form of cAMP-dependent protein kinase, cAPKiATP the binary complex of cAPK with ATP, cAPKiPKP the binary complex of cAPK with the peptide inhibitor PKI(5-24), and cAPK PKI ATP the ternary complex of cAPK with ATP and PKI(5-24). Shown are averaged values for the three crystal structures lATP.pdb, ICDKA.pdb, and ICDKB.pdb. All values have been normalized with respect to the free energy of the closed conformations.

The catalytic subunit then catalyzes the direct transfer of the 7-phosphate of ATP (visible as small beads at the end of ATP) to its peptide substrate. Catalysis takes place in the cleft between the two domains. Mutual orientation and position of these two lobes can be classified as either closed or open, for a review of the structures and function see e.g. [36]. The presented structure shows a closed conformation. Both the apoenzyme and the binary complex of the porcine C-subunit with di-iodinated inhibitor peptide represent the crystal structure in an open conformation [37] resulting from an overall rotation of the small lobe relative to the large lobe. 

An impressive example of the application of structure-based methods was the design of a inhibitor of the HIV protease by a group of scientists at DuPont Merck [Lam et al. 1994 This enzyme is crucial to the replication of the HIV virus, and inhibitors have bee shown to have therapeutic value as components of anti-AIDS treatment regimes. The star1 ing point for their work was a series of X-ray crystal structures of the enzyme with number of inhibitors boimd. Their objective was to discover potent, novel leads whid were orally available. Many of the previously reported inhibitors of this enzyme possessei substantial peptide character, and so were biologically unstable, poorly absorbed am rapidly metabolised. 

Fairall, L., et al. The crystal structure of a two zinc finger peptide reveals an extension to the rules for zinc finger/DNA recognition. Nature 366 483-487, 1993. 

Waksman, G., et al. Binding of a high affinity phosphoty-rosyl peptide to the Src SH2 domain crystal structures of the complexed and peptide-free forms. Cell 72 779-790, 1993. 

Fremont, D.H., Matsumura, M., 5tura, E.A., Peterson, P.A., Wilson, I.A. Crystal structures of two viral peptides in complex with murine MHC class I H2-K . Science 257 919-927, 1992. 

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. 

Stern, L.J., Brown, J.H., Jardetzky, T.S., Gorga, J.C., Urban, R.G., Strominger, J.L., Wiley, D.C. Crystal structure of the human class 11 MHC protein HLA-DRl complexed with an influenza virus peptide. Nature 368 215-221,... 

Figure 17.12 Ribbon diagram of EMPl bound to the extracellular domain of the erythropoietin receptor (EBP). Binding of EMPl causes dimerization of erythropoietin receptor. The x-ray crystal structure of the EMPl-EBP complex shows a nearly symmetrical dimer complex in which both peptide monomers interact with both copies of EBP. Recognition between the EMPl peptides and EBP utilizes more than 60% of the EMPl surface and four of six loops in the erythropoietin-binding pocket of EBP.

Lee TW, Chemey MM, Huitema C, Liu J, James KE, Powers JC, Eltis LD, James MN (2005) Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-fike aza-peptide epoxide. J Mol Biol 353 1137-1151 Liang PH (2006) Characterization and inhibition of SARS-coronavirus main protease. Curr Top Med Chem 6 361-376... 

Fig. 2.11 Preferential conformations around the C(a)-C(/9) bond in the crystal structures of /9-alanine-containing peptides [158]...

Interestingly, the 28-hehcal fold identified by NMR analysis of /9-peptide 109 compares well with the model of a /9 -peptide consisting of 1-aminomethylcyclo-propanecarboxylic acid residues (Fig. 2.24). This model was generated using ideal torsion angle values ( = + 120°, 9i=-72°, ii/=0°, and < =180°) derived from crystal structures of dimer 110, trimer 111 and tetramer 112 [163] (Fig. 2.25). 

Fig. 2.25 Conformational preferences and eight-membered turn motif of jS -peptides with 1 -aminomethylcyclopropanecarboxylic acid residues. X-ray crystal structures of dimer no, trimer m and tetramer 112 together with a model constructed using...

A //-peptidic parallel sheetiike conformation with characteristic intermolecular 14-membered H-bonded rings was first observed in the crystal structure of -peptide Boc-/ -HVal-/ -HAla-/l -HLeu-OMe 116 (Fig. 2.28A) [10]. However, the struc-... 

Fig. 2.28 X-ray crystal structures of parallel sheet-forming and all-un//fce-/F -peptides 116 and 117 [10, 191]. Views along the parallel amide planes and crystal packing diagram show the parallel pleated sheet arrangement (view perpendicular to the amide planes).

N-H--0) are 149.7° (inner H-bond) and 144.7° (outer H-bond). (B) Hybride -peptide 120 with a D-Pro-Gly type IT -turn segment (gray color) X-ray crystal structure [192]. The intramolecular H-bond N---0 distances are shown. The angles (N-H---0) are 147° (inner H-bond) and 155° (outer H-bond). The inter-molecular NH-0=C H-bonds (with N-H -O angles of 160 and 133 °) connect the hairpin into an infinitely extended -sheet... 

Adapted from [200]). (B) Top view of 141 (derived from NMR restraints) [200]. (C) X-ray crystal structure of y -peptide 146 built with (/ ,/ ,R)-amino acids 138a and 138c [206 207]. It is characterized by two H-bonded 14-membered pseudocycles. H-bond N--0 dis-... 

Fig. 2.38 sheet forming y-peptides. (A) Crystal structure of the two stranded antiparallel sheet formed by a,j -unsaturated y-dipeptide 152 with a-methyl substituted residues [208], Both intermolecular H-bonds are characterized by a N---0 distance of 2.84 A and an angle (N-H- -O) ofl54.2°. (B) Crystal structure of the infinite parallel sheet arrangement formed by vinylogous dipeptide 153 [208], Intermolecular H-bonds are characterized by a N -O distance of 2.88 A and 3.24 A and an... 

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