Protein permissive sites

Fig. 13. The secondary structure of the E. colt ribosomal 16 S RNA, showing protein-binding sites, RNA—protein cross-link sites, and intra-RNA cross-link sites. The relations between a, b, and c are represented as in Figs. 2 and 3. Reproduced with permission from Brimacombe et al. (1983). 

Manoil, C., and Bailey, J. (1997). A simple screen for permissive sites in proteins analysis of Escherichia coli lac permease./ Mol. Biol., 267, 250—263. 

FIGURE 16-6 Structures of Fe — S Protein-Active Sites, (a) Ferredoxin. (From E.-I. Ochiai, Bioinorganic Chemistry, Allyn and Bacon, Boston, 1977, p. 184.) (b) Clostridial ferredoxin. (Reproduced with permission from E. T. Adman, L. C. Sicker, and L. H. Jensen, J. Biol. Chem., 1973, 248, 3987.) (c) A model for the structure of the Fe Sg active unit. (Reproduced with permission from E.-I. Ochiai, Bioinorganic Chemistry, Allyn and Bacon, Boston, 1977, p. 192.)... 

The Gram-negative bacteria have two membranes separated by the periplasmic space (Figure 6). Short peptides can be inserted into some surface exposed loops of outer membrane proteins (OMPs). The most used proteins are the maltoporin LamB, the outer membrane protein OmpA, and the phosphate-inducible porin PhoE. LamB is an E. coli protein. Some permissive sites have been identified [10,11], but the insertion of peptides longer than 60 amino acids perturbs its conformation and assembly. Another protein used is OmpA, which tolerates larger inserts [12,13]. Lipoproteins (Lpp, TraT, and PAL) have also been used [14-16], as well as proteins present in the filamentous structures present... 

In 1966, Koshland, Nemethy, and Filmer described several models for oligomeric proteins or enzymes with different permissible site-site interactions (Koshland et al, 1966). The KNF models avoid the assumption of symmetry of the MWC model, but use another simplifying features. They assume that the progress fromT to the ligand-bound R state is a sequential process. The conformation of each subunit changes in turn as it binds the ligand, and there is no dramatic switch from... 

Ribosomal Protein Synthesis Inhibitors. Figure 3 The chemical structure of tetracycline and possible interactions with 16S rRNA in the primary binding site. Arrows with numbers indicate distances (in A) between functional groups. There are no interactions obseived between the upper portion of the molecule and 16S rRNA consistent with data that these positions can be modified without affecting inhibitory action (from Brodersen et al. [4] with copynght permission). 

Ribosomal Protein Synthesis Inhibitors. Figure 4 The binding site of pactamycin on the 30S subunit. The positions of mRNA, the RNA elements H28, H23b, H24a, and the C-terminus of protein S7 are depicted in the E-site of the native 30S structure (left) and in the 30S-pactamycin complex (right). In the complex with pactamycin, the position of mRNA is altered (from Brodersen etal. [4] with copyright permission). 

Fig. 2. Stereo view of the active site off), gigas hydrogenase (reprinted with permission from (65) copyright 1997, American Chemical Society). LI and L2 are diatomic ligands that form hydrogen bonds with the protein- they are supposed to be the two CN s molecules. The third ligand L3 sits in a hydrophobic pocket and is assumed to be the CO. The designates the putative oxo bridging ligand.

Fig. 3 Binding and release of tropoelastin. The elastin receptor consists of a 67 kDa peripheral subunit (EBP) with two transmembrane proteins of 61 and 55 kDa. The 67 kDa protein binds tropoelastin and galactosugars through two separate sites, (a) Tropoelastin binds to the intact EBP complex, (b) Upon binding of a galactosugar, the EBP loses its affinity for both tropoelastin and the membrane-bound protein, which leads to the release of tropoelastin. Reproduced from [8] with permission from John Wiley and Sons, copyright 1998...

Fig. 15 Amino acid sequences of artificial extracellular matrix (aECM) proteins. Each protein contains a TV tag, a histidine tag, a cleavage site, and elastin-like domains with lysine residues for crosslinking. The RGD cell-binding domain is found in aECM 1, whereas aECM 3 contains the CS5 cell-binding domain. aECM 2 and aECM 4 are the negative controls with scrambled binding domains for aECM 1 and aECM 3, respectively. Reprinted from [121] with permission from American Chemical Society, copyright 2004...

Fig. 2.3 The development of polarity and asymmetric division in Saccharomyces cerevisiae. The diagram is reproduced in a slightly simplified form from the work of Lew Reed (1995) with the permission of Current Opinion in Genetics and Development, (a) The F-actin cytoskeleton strands = actin cables ( ) cortical actin patches, (b) The polarity of growth is indicated by the direction of the arrows (arrows in many directions signifies isotropic growth), (c) 10-nm filaments which are assembled to form a ring at the neck between mother and bud. (d) Construction of the cap at the pre-bud site. Notice that the proteins of the cap become dispersed at the apical/isotropic switch, first over the whole surface of the bud, then more widely. Finally, secretion becomes refocussed at the neck in time for cytokinesis, (e) The status and distribution of the nucleus and microtubules of the spindle. Notice how the spindle pole body ( ) plays an important part in orientation of the mitotic spindle.

Figure 2-7. Origins of the increased O2 binding energy in IPNS when the protein is included in an ONIOM model. (A) A comparison of the optimized geometries from an active-site model (silver) and an ONIOM protein model (dark grey), show that the artificial structural relaxation of the active-site model is more pronounced for the reactant state than for the product state. (B) Contributions to O2 binding from the surrounding protein, evaluated only at the MM level (Adapted from Lundberg and Morokuma [26], Reprinted with permission. Copyright 2007 American Chemical Society.)...

Figure 6.8 Stereoscopic view of the dimeric building block of bacterioferritin (a) twofold axis horizontal (b) twofold axis approximately normal to the page. The protein is represented by a blue a-carbon trace, the haem by a stick model (pink) and the dinuclear metal site by dotted spheres (orange and yellow). From Frolow et ah, 1994. Reproduced by permission of Nature Publishing Group.

Figure 7.2 (a) Schematic representation of the structure of B. subtilis ferrochelatase. Domain I is coloured green and domain II blue. The parts of the chain in red build up the walls of the cleft, and the region in yellow makes the connection between the domains. The N- and C-termini are marked, (b) The proposed active site of ferrochelatase with protoporphyrin IX molecule (red) modelled into the site. The backbone atoms of the protein are in purple, the side-chains in blue. Reprinted from Al-Karadaghi et ah, 1997. Copyright (1997), with permission from Elsevier Science. 

Figure 2 Double-stranded oligonucleotide photoprobes that simulate modified DNA and intended to cross-link to DNA-binding proteins. (A) Probe modeling interstrand cross-linking by cisplatin Source From Ref. [63], with permission from the American Chemical Society via the Rightslink service (license number 2458870278307 granted June 30, 2010). The benzophenone probe prior to reaction with DNA is shown in the lower part of the panel. (B) Photoaffinity probe for bacterial DNA repair proteins. TT is a simulated thymine dimer intended to be recognized as a site of damage in DNA, and T (two instances) is the diazirine thymine derivative T Source From Ref. [64], with permission from Wiley.

FIGURE 1 2-2 Schematic diagram of the phosphorylation sites on each of the four 60kDa subunits of tyrosine hydroxylase (TOHase). Serine residues at the N-terminus of each of the four subunits of TOHase can be phosphorylated by at least five protein kinases. (J), Calcium/calmodulin-dependent protein kinase II (CaM KII) phosphorylates serine residue 19 and to a lesser extent serine 40. (2), cAMP-dependent protein kinase (PKA) phosphorylates serine residue 40. (3), Calcium/phosphatidylserine-activated protein kinase (PKC) phosphorylates serine 40. (4), Extracellular receptor-activated protein kinase (ERK) phosphorylates serine 31. (5), A cdc-like protein kinase phosphorylates serine 8. Phosphorylation on either serine 19 or 40 increases the activity of TOHase. Serine 19 phosphorylation requires the presence of an activator protein , also known as 14-3-3 protein, for the expression of increased activity. Phosphorylation of serines 8 and 31 has little effect on catalytic activity. The model shown includes the activation of ERK by an ERK kinase. The ERK kinase is activated by phosphorylation by PKC. (With permission from reference [72].)... 

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