Proteins bottom

Figure 10.11 MS/MS spectra of a tryptic piece of the 11,222 Da protein (top spectrum) and the 11,236 Da protein (bottom spectrum). Both proteins were identified as homologous to a conserved hypothetical protein of Salmonella enterica serovar Typhi. The only difference observed in the sequence is that of a substitution of valine with leucine, which increases the molecular weight of the protein by 14 Da.

Figure 7.9 The high- and low-affinity copper transporters in S. cerevisiae (top) (From Cobine et al., 2006, Copyright 2006, with permission from Elsevier.) and a topological model for the hCtrl protein (bottom). (From Petris et al., 2004. With kind permission of Springer Science and Business Media.)...

Fig. 1. Nucleotide sequence of the SFV 26 S RNA (top row), the corresponding amino acid sequence (middle row), and the amino acid sequence of the Sindbis virus structural proteins (bottom row). Nucleotides are numbered from the 5 end of the RNA molecule and all amino adds from the amino terminus of each protein. The amino- and the carboxyl-terminal ends of each protein are indicated hy arrows, glycosylation sites by triangles, and membrane-spanning regions of the viral glycoproteins by underlines for Sindbis virus and overlines for SFV. Amino acids in boxes are negatively charged (Asp and Glu), and those circled are positively charged (Lys and Arg). Some restriction endonuclease cleavage sites are shown on the nucleotide sequence. The alignment of the amino acid...

Figure 8 The effect of mild acid hydrolysis on amides in HMW DOM. Two potentially important classes of biochemicals that likely contribute to HMW DOM are (poly)-N-acetyl amino sugars (top) and proteins (bottom). Mild acid hydrolysis of (poly)-iV-acetyl amino sugars will yield free acetic acid, but will not depolymerize the polysaccharide. The generation of acetic acid will be accompanied by a shift in the N-NMR from amide to amine. In contrast, mild acid hydrolysis of proteins does not yield acetic acid, but may depolymerize the protein macromolecular segments to yield free amino acids. Free amino acids can be quantified by chromatographic techniques and compared to the shift from amide (protein) to amine (free amino acid) in N-NMR.

Top, right P. furiosus ferredoxin. Bottom, left 4-a-helix-bnndle synthetic protein. Bottom right A xylosoxidans Cu-nitrite reductase. 

Fig. 3. (A) Autoradiograms of Northern blots (top), and mRNA levels normalized to mRNA for P-actin (bottom) for cPLA and iPLA in brains of control rats and rats treated with lithium for 6 wk. Means SEM ( = 5). p < 0.001. (B) Autoradiograms of Western blots (top) and levels of cPLAj protein (bottom) in brains from control and chronic lithium-treated rats. Means SEM (n = 8). p < 0.001. (From Rintala et al., 1999).

FIG. 3 Variation of the intrinsic viscosity of long alkyl-modified polyacrylic acids as a function of the concentration of bovine serum albumin in the solvent. Solvent used for dilutions 30 mM borate buffer pH 9 and protein (top curves) or same buffer plus 0.3 M NaCl and protein (bottom curves). Black circles polymer modified with 4 mol% of C18 side groups squares polymer modified with 3 mol% of C12 groups cross-circles unmodified poly (sodium acrylate). (Reprinted with permission from Ref. 33. Copyright 1998 American Chemical Society.)... 

Figure 7.11. Penicillinases and penicillinase-resistant penicillins. Top Penicillins destroy bacteria after binding to penicillin binding proteins (PBPs). Middle Penicillinases are enzymes produced by bacteria that destroy penicillins by cleaving the beta-lactam ring of the drug. Penicillins are "lured" into the active site because they are chemically similar to penicillin binding proteins. Bottom Clavulinic acid is a "decoy" drug that enhances the activity of penicillins. Clavulinic acid binds to the active sites of penicillinases rendering the enzyme inactive.

Figure B2.1.7 Transient hole-burned speetra obtained at room temperature with a tetrapyrrole-eontaining light-harvesting protein subunit, the a subunit of C-phyeoeyanin. Top fluoreseenee and absorption speetra of the sample superimposed with die speetnuu of the 80 fs pump pulses used in the experiment, whieh were obtained from an amplified CPM dye laser operating at 620 mn. Bottom absorption-diflferenee speetra obtained at a series of probe time delays.

Figure B2.1.10 Stimulated photon-echo peak-shift (3PEPS) signals. Top pulse sequence and iuterpulse delays t and T. Bottom echo signals scaimed as a fiinction of delay t at tluee different population periods T, obtained with samples of a tetrapyrrole-containing light-harvesting protein subunit, the a subunit of C-phycocyanin.

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

Alpha helices in proteins are found when a stretch of consecutive residues all have the 0, y angle pair approximately -60° and -50°, corresponding to the allowed region in the bottom left quadrant of the... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

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 16.2 The icosahedron (top) and dodecahedron (bottom) have identical symmetries but different shapes. Protein subunits of spherical viruses form a coat around the nucleic acid with the same symmetry arrangement as these geometrical objects. Electron micrographs of these viruses have shown that their shapes are often well represented by icosahedra. One each of the twofold, threefold, and fivefold symmetry axes is indicated by an ellipse, triangle, and pentagon, respectively.

FIGURE 21.11 The structure of UQ-cyt c reductase, also known as the cytochrome hci complex. The alpha helices of cytochrome b (pale green) define the transmembrane domain of the protein. The bottom of the structure as shown extends approximately 75 A into the mitochondrial matrix, and die top of the structure as shown extends about 38 A into the intermembrane space. (Photograph kindly provided by Di Xia and Johann Deismhofer [From Xia, D., Yn, C.-A., Kim, H., Xia,J-Z., Kachnrin, A. M., Zhang, L., Yn,... 

Consider, for example, the protein shown in Figure 15.7. The bottom left-hand amino acid is valine, which is linked to proline. Suppose for the sake of argument that we wanted to treat this valine quantum-mechanically and the rest of the protein chain according to the methods of molecular mechanics. We would have to draw a QM/MM boundary somewhere between valine and the rest of the protein. The link atoms define the boundary between the QM and the MM regions. A great deal of care has to go into this choice of boundary. The boundary should not give two species whose chemical properties are quite different from those implied by the structural formulae on either side of this boundary. 

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