Reactive center loop

The crystal structure of native hen ovalbumin shows an intact reactive center loop in the form of an exposed a-helix of three turns that protrudes from the main body of the molecule on two peptide stalks. The ovalbumin structure includes four crystallographically independent ovalbumin molecules and the position of the helical reactive center loop relative to the protein core differs by 2-3 A between molecules. Although this shift is probably due to the different environments of the helices in the crystal lattice, it suggested that the reactive center loop is flexible in solution. Structural studies of serpins in various conformations have shown how the exceptional mobility of the serpin reactive center loop and their unique flexibility is essential for function. In contrary to inhibitory serpins, ovalbumin does not show evidence for a large conformational change following cleavage at its putative reactive center and appears to have lost the extreme mobility which is characteristic for its inhibitory ancestors. 

Biol. Chem. 269, 15957-15960, 1994 Lawrence, D.A., The role of reactive-center loop mobility in the serpin inhibitory mechanism, Adv. Exp. Med. Biol. 425, 99-108,1997 Whisstock, J., Skinner, R., and Lesk, A.M., An atlas of serpin conformations. Trends Biochem. Sci. 23, 63-67, 1998 Gettins, P.G., Serpin stractnre, mechanism, and fnnction, Chem. Rev. 102, 4751 804, 2002 Hnntington, J.A., Shape-shifting serpins — advantages of a mobile mechanism. Trends Biochem. Sci. 31, 427 35, 2006. 

Figure 5 Serpins inhibit serine proteases by binding a reactive center loop in the active site, forming a covalent complex with the enzyme, undergoing a large conformational change, and irreversibly distorting the active site of the protease.

Serpins consist of a conserved core of three P-sheets and eight or nine a-helices that act collectively in the inhibitory mechanism. As with the Kazal- and Kunitz-type inhibitors, the mechanism involves a surface exposed loop that is termed the reactive center loop (RCL). The RCL presents a short stretch of polypeptide sequence bearing the Pl-Pl scissile bond. Like other serine protease inhibitor families, the PI residue dominates the thermodynamics that govern the interaction between protease and inhibitor. Exposure of the PI residue to solvent is typically brokered by 15 amino acids N-terminal to the PI residue and 5 residues on the C-terminal prime side of the scissile bond. Evidence for dramatic conformational change in the inhibitory mechanism was first provided by the crystal structure of the cleaved form of ai-antitrypsin (37). In this structure and unlike the native form, the reactive center loop was not solvent exposed but occurred as an additional P-strand within the core of the structure. 

Pi Z, Pi Pi Mmaiton, and Pi Md te are synthesized by the fiver in relatively normal amounts but are only partially secreted, resulting in accumulation within the endoplasmic reticulum of hepatic parenchymal cells and low plasma levels. As a result of a glu lys substitution in Pi Z, the reactive center loop on one molecule can insert into the P-pleated sheet of a second molecule, resulting in polymerization and retention within the pre-Golgi endoplasmic reticulum. Similar alterations have been shown to be present in Pi and Pi The amino acid substi-... 

CHAPTER 36, FIGURE 7 A group of structurally similar protein inhibitors of the serine proteinases known as SERPINS (SERine Proteinase INhibitors). The structure shown is human antithrombin. The reference SERPIN, a j-proteinase inhibitor or a. -antitrypsin contains -30% a helix (9 helices) and 40% sheet (5 3 sheets). Other members of the SERPIN family contain both additional helices and p sheets. The reactive center loop of antithrombin, residues 378-396, contains the reactive site residues Arg and Ser . Upon reaction with the target proteinase or after cleavage by the target proteinase (a reaction that inactivates the inhibitor without inactivating the proteinase), the reactive center loop folds between the S3 and S5 sheets. 

Figure 3 The heparin-binding mechanism of AT III. p-sheet A facing A-helix in the back, D-helix to the right, the reactive center loop (RCL) at the top, and Arg399 displayed in spacefill. Heparin pentasaccharide showed in stick. In native AT, the N-terminal region of the RCL is incorporated as strand 4 in P-sheet A, which constrains the RCL and the PI Arg393 side chain.

Lawrence DA, Olson ST, Muhammad S et aL Partitioning of serpin-proteinase reactions between stable inhibition and substrate cleavage is regulated by the rate of serpin reactive center loop insertion into fl-sheet A. J Biol Chem 2000 275 5839-5844. 

Theoretically, all of the proteinaceous inhibitors act by presenting a loop portion of their chains as an idealized, that is, pre-organized for optimal interactions, substrate for elastase. Conformational analysis of the inhibitor residues P P3 and P1-P3 for a series of proteinaceous, serine protease inhibitors showed that there is little difference between their free and/or complexed states [63]. In aj-PI, the loop contains as its elastase reactive center (see Table 2.2) a Met-Ser linkage. The importance of the P,-substituent in a PI for its enzyme specificity characteristics is exempli-... 

Atoms and free radicals are highly reactive intermediates in the reaction mechanism and therefore play active roles. They are highly reactive because of their incomplete electron shells and are often able to react with stable molecules at ordinary temperatures. They produce new atoms and radicals that result in other reactions. As a consequence of their high reactivity, atoms and free radicals are present in reaction systems only at very low concentrations. They are often involved in reactions known as chain reactions. The reaction mechanisms involving the conversion of reactants to products can be a sequence of elementary steps. The intermediate steps disappear and only stable product molecules remain once these sequences are completed. These types of reactions are refeiTcd to as open sequence reactions because an active center is not reproduced in any other step of the sequence. There are no closed reaction cycles where a product of one elementary reaction is fed back to react with another species. Reversible reactions of the type A -i- B C -i- D are known as open sequence mechanisms. The chain reactions are classified as a closed sequence in which an active center is reproduced so that a cyclic reaction pattern is set up. In chain reaction mechanisms, one of the reaction intermediates is regenerated during one step of the reaction. This is then fed back to an earlier stage to react with other species so that a closed loop or... 

Ribosomal Protein Synthesis Inhibitors. Figure 5 Nucleotides at the binding sites of chloramphenicol, erythromycin and clindamycin at the peptidyl transferase center. The nucleotides that are within 4.4 A of the antibiotics chloramphenicol, erythromycin and clindamycin in 50S-antibiotic complexes are indicated with the letters C, E, and L, respectively, on the secondary structure of the peptidyl transferase loop region of 23S rRNA (the sequence shown is that of E. coll). The sites of drug resistance in one or more peptidyl transferase antibiotics due to base changes (solid circles) and lack of modification (solid square) are indicated. Nucleotides that display altered chemical reactivity in the presence of one or more peptidyl transferase antibiotics are boxed. 

Therefore, the control loop shown in Fig. 5.28 was developed to solve the problem of symmetry control [121]. Two additional PID control loops are used to control the homogeneity of the reactive gas partial pressure because of appropriate regulation of the threefold gas inlet (top/center/bottom). The... 

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