Protein schematic representation

Figure C3.2.18.(a) Model a-helix, (b) hydrogen bonding contacts in tire helix, and (c) schematic representation of tire effective Hamiltonian interactions between atoms in tire protein backbone. From [23].

Fig. 10.27 Schematic representation of the energy landscape for protein folding. (Figure adapted from Onuchic ] N, Z Luthcy-Schulten and P Wolynes 1997. Theory of Protein Folding The Energy Landscape Perspective. Annual Reviews in Physical Chemistry 48 545-600.)...

Several human receptors for the neurohypophyseal hormones have been cloned and the sequences elucidated. The human V2 receptor for antidiuretic hormone presumably contains 371 amino acids and seven transmembrane segments and activates cycHc AMP (76). The oxytocin receptor is a classic G-protein-coupled type of receptor with a proposed membrane topography also involving seven transmembrane components (84). A schematic representation of the oxytocin receptor stmcture within the membrane is shown in Eigure 4 (85). 

Figure 3.6 Four-helix bundles frequently occur as domains in a proteins. The arrangement of the a helices is such that adjacent helices in the amino acid sequence are also adjacent in the three-dimensional structure. Some side chains from all four helices are buried in the middle of the bundle, where they form a hydrophobic core, (a) Schematic representation of the path of the polypeptide chain in a four-helrx-bundle domain. Red cylinders are a helices, (b) Schematic view of a projection down the bundle axis. Large circles represent the main chain of the a helices small circles are side chains. Green circles are the buried hydrophobic side chains red circles are side chains that are exposed on the surface of the bundle, which are mainly hydrophilic.

Figure 15.14 Schematic representation of the specific interactions between phosphoryicholine (orange) and the protein side groups (green) in Fab. The binding cavity is in a cleft between the light and the heavy chains. Choiine binds in the interior while the phosphate group is toward the surface. (Adapted from E.A. Padlan et al., Immunochemistry 13 945-949, 1976.)...

Figure 15.18 (a) Schematic representation of the path of the polypeptide chain in the structure of the class I MHC protein HLA-A2. Disulfide bonds are indicated as two connected spheres. The molecule is shown with the membrane proximal immunoglobulin-like domains (a3 and Pzm) at the bottom and the polymorphic al and a2 domains at the top. 

Figure 15.19 Schematic representation of the peptide-binding domain of a class I MHC protein. The al and a2 domains are viewed from the top of the molecule, showing the empty antigen-binding site as well as the surface that is contacted by a T-cell receptor. (Adapted from P.J. Bjdrkman et al.. Nature 329 506-512, 1987.)...

Antisense Oligonucleotides. Figure 1 Schematic representation of the action of antisense oligonucleotides. They bind to their respective target mRNA preventing protein translation. 

Caspases. Figure 2 Caspase activating complexes. Schematic representation of all described long prodomain caspase activation complexes. Each complex contains essentially three functionally different building blocks a sensor/platform, an adaptor and an effector in the form of a particular caspase. Some instigating ligands, possible outcomes and regulatory proteins are indicated. 

Figure 3 provides a very general overview of transcriptional activation in response to a PPAR ligand. Fig. 3a shows the schematic representation of a PPAR target gene in the absence of PPAR ligand. Co-repressor proteins bound to both unliganded PPAR and RXR... 

Peroxisome Proliferator-Activated Receptors. Figure 3 Transcription of PPAR target genes. A schematic representation of the transcription of PPAR-regulated genes in the absence (a) and presence (b) of PPAR ligand. Abbreviations PPAR-RE, peroxisome proliferator-activated receptor-response element RNA Pol II, RNA polymerase II TATA-BP, TATA-binding protein. 

Fig. 1 Heterocycles bearing a 2-pyridone moiety with wide range of medicinal applications. Amrinone WIN 40680 1 is a cardiotonic agent for the treatment of heart failure. ZAR-NESTRA 2 is a selective farnesyl protein inhibitor and NP048 3 is a pilicide with novel antibacterial properties. The 2-pyridones 4, 5 and 6 are schematic representations of the three categories of 2-pyridones that wiU be covered in this chapter i.e., substituted 2-pyridones 4, 2-quinolones 5 and other ring-fused 2-pyridones 6...

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

Figure 39-18. Schematic representation of the amplification of chorion protein genes s36 and s38. (Reproduced, with permission, from Chisholm R Gene amplification during development. Trends Biochem Sci 1982,7 161.)...

Figure 46-5. Variations in the way in which proteins are inserted into membranes. This schematic representation, which illustrates a number of possible orientations, shows the segments of the proteins within the membrane as a-helicesand the other segments as lines. The LDL receptor, which crosses the membrane once and has its amino terminal on the exterior, is called a type I transmembrane protein. The asialoglycoprotein receptor, which also crosses the membrane once but has its carboxyl terminal on the exterior, is called a type II transmembrane protein. The various transporters indicated (eg, glucose) cross the membrane a number of times and are called type III transmembrane proteins they are also referred to as polytopic membrane proteins. (N, amino terminal C, carboxyl terminal.) (Adapted, with permission, from Wickner WT, Lodish HF Multiple mechanisms of protein insertion into and across membranes. Science 1985 230 400. Copyright 1985 by the American Association for the Advancement of Science.)...

Figure 48-5. Schematic representation of fibronectin interacting with an integrin fibronectin receptor situated in the exterior of the plasma membrane of a cell of the ECM and of various attachment proteins interacting indirectly or directly with an actin microfilament in the cytosol. For simplicity, the attachment proteins are represented as a complex.

Figure 49-3. Schematic representation of the thin fiiament, showing the spatiai configuration of its three major protein components actin, myosin, and tropomyosin. The upper panei shows individual molecules of G-actin. The middle panel shows actin monomers assembled into F-actin. Individual molecules of tropomyosin (two strands wound around one another) and of troponin (made up of its three subunits) are also shown. The lower panel shows the assembled thin filament, consisting of F-actin, tropomyosin, and the three subunits of troponin (TpC, Tpl, andTpT).

Schematic representation of ferritin, the iron storage protein, (a) The protein contains 24 neariy identical polypeptides, (b) A ribbon stmcture of one of the polypeptide chains.

Fig. 9.1 Schematic representation of possible mechanisms of resistance in Gram-negative and Gram-positive bacteria. 1, antibiotic-inactivating enzymes 2, antibiotic efflux proteins 3, alteration or duplication of intracellular targets 4, alteration of the cell membrane reducing antibiotic uptake 5, alterations in porins or lipopolysaccharide reducing antibiotic uptake or binding.

Figure 3.1 Schematic representation of a generic excitatory synapse in the brain. The presynaptic terminal releases the transmitter glutamate by fusion of transmitter vesicles with the nerve terminal membrane. Glutamate diffuses rapidly across the synaptic cleft to bind to and activate AMPA and NMDA receptors. In addition, glutamate may bind to metabotropic G-protein-coupled glutamate receptors located perisynaptically to cause initiation of intracellular signalling via the G-protein, Gq, to activate the enzyme phospholipase and hence produce inositol triphosphate (IP3) which can release Ca from intracellular calcium stores...

Figure 6.4 Schematic representation of the muscarinic receptor. All muscarinic receptors have seven transmembrane domains and the major difference between them is within the long cytoplasmic linkage connecting the fifth and sixth domains. This implies different G-protein connections and functions. Some possibilities are shown although the position of the Mi and M2 boxes is not intended to indicate their precise structural differences within the loop...

Figure 18.5 Schematic representation of possible cleavage sites of APP by a, and y-secretase and the production of j5-amyloid protein. (I) This shows the disposition of APP molecules in 695, 751 and 770 amino-acid chain lengths. Much of it is extracellular. The /1-amyloid (A/I4) sequence is partly extracellular and partly in the membrane. (II) An enlargement of the /1-amyloid sequence. (Ill) Normal cleavage of APP by a-secretase occurs in the centre of A/I4 sequence to release the extracellular APP while the remaining membrane and intracellular chain is broken down by y-secretase to give two short proteins that are quickly broken down. (IV) In Alzheimer s disease ji rather than a-secretase activity splits off the extracellular APP to leave the full AP4 sequence remaining attached to the residual membrane and intracellular chain. 42/43 amino acid )S-amyloid sequence is then split off by y-secretase activity...

Figure 3. Schematic representation of the PGII, PGI, PGC [13] and PGE proteins from A. niger, indicating the putative processing sites for the signal peptide ( ) and the mono- and dibasic processing site for the propeptide ( ). The position of introns (lA, IB and IC) are indicated ( [) and variation of amino acids number is shown in different parts of protein. The putative N-glycosylation sites are marked ( ).

Fig. 1.1 ATP bound to cAMP protein kinase and a schematic representation indicating the non-conserved regions (hydrophobic pocket and specificity surface) of the pocket utilised in the development of protein kinase inhibitors.

The human oxytocin receptor gene was isolated and characterised in 1994 [122], heralding the development of modern cloned receptor screening. The oxytocin receptor belongs to the Family A series of G-protein coupled 7-transmembrane receptors (GPCRs). A schematic representation of the generic structure of 7TM receptors is shown in Figure 7.3. 

Fig. 2 A schematic representation of an HTRF assay for a protein-protein interaction. One protein is tagged with a fluorescent molecule whose emission spectra overlaps with the excitation of another fluorescent molecule. When they are in close proximity (above) the energy is transferred. When they diffuse apart (below) or are inhibited from coming together by a small molecule no FRET occurs...

Fig. 8 Schematic representation of the binding of a small molecule (left) or a fragment (right) to a hypothetical protein active site...

FIGURE 98-1. Schematic representation of carbohydrate, fat, and protein digestion. (From KumpfVJ, Chessman KH. Enteral nutrition. In DiPiro JT, Talbert RL, Yee GC, et al, (eds.) Pharmacotherapy A Pathophysiologic Approach. 6th ed. New York McGraw-Hill 2005 2616.)... 

Figure 1.6 Schematic representation of the changes in protein conformational microstate distribution that attend ligand (i.e., substrate, transition state, product and inhibitor) binding during enzyme catalysis. For each step of the reaction cycle, the distribution of conformational microstates is represented as a potential energy (PE) diagram.

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