Alpha-carbon plot

Figure 2-15 A stereoscopic alpha-carbon plot showing the three-dimensional structure of favin, a sugar-binding lectin from the broad bean (Viciafaba). In this plot only the a-carbon atoms are shown at the vertices. The planar peptide units are represented as straight line segments. Side chains are not shown. The protein consists of two identical subunits, each composed of a 20-kDa a chain and a 20-kDa 3 chain. The view is down the twofold rotational axis of the molecule. In the upper subunit the residues involved in the front 3 sheet are connected by double lines, while those in the back sheet are connected by heavy solid lines. In the lower subunit the a chain is emphasized. Notice how the back 3 sheet (not the chain) is continuous between the two subunits. Sites for bound Mn2+ (MN), Ca2+ (CA), and sugar (CHO) are marked by larger circles. From Reeke and Becker.112...

Figure 3-25 (A) Alpha-carbon plot of the structure of ribosomal protein L30 from E. coli as deduced by NMR spectroscopy and model building. (B) Combined COSY-NOESY diagram for ribosomal protein L30 used for elucidation of dm connectivities (see Fig. 3-27). The upper part of the diagram represents the fingerprint region of a COSY spectrum recorded for the protein dissolved in H20. The sequential assignments of the crosspeaks is indicated. The lower part of the diagram is part of a NOESY spectrum in H20. The dm "walks" are indicated by (->—) S11-A12 (—) H19 to L26 (-------)...

Figure 13-6 Stereoscopic view into the active site of triose phosphate isomerase showing side chains of some charged residues PGH, a molecule of bound phosphoglycolohydroxamate, an analog of the substrate enolate.138 The peptide backbone, as an alpha-carbon plot, is shown in light lines.147 The (a/ (S)8-barrel structure is often called a TIM barrel because of its discovery in this enzyme. Courtesy of M. Karplus.

Figure 16-31 (A) Structure of molybdopterin cytosine dinucleotide complexed with an atom of molybdenum. (B) Stereoscopic ribbon drawing of the structure of one subunit of the xanthine oxidase-related aldehyde oxidoreductase from Desulfo-vibrio gigas. Each 907-residue subunit of the homodimeric protein contains two Fe2S2 clusters visible at the top and the molybdenum-molybdopterin coenzyme buried in the center. (C) Alpha-carbon plot of portions of the protein surrounding the molybdenum-molybdopterin cytosine dinucleotide and (at the top) the two plant-ferredoxin-like Fe2S2 clusters. Each of these is held by a separate structural domain of the protein. Two additional domains bind the molybdopterin coenzyme and there is also an intermediate connecting domain. In xanthine oxidase the latter presumably has the FAD binding site which is lacking in the D. gigas enzyme. From Romao et al.633 Courtesy of R. Huber.

Allylic rearrangement 527,712 with condensation 527 Allysine 429 Alpha-carbon plot 64 Alpha effect on reaction rates 590 Alpha helix See a Helix Alport disease 438 Alternan 175... 

A more powerful technique is to compute the RMSDs for all pairs of snapshots from the trajectory and plot them on a single graph [28]. Figure 7 shows the results of such a plot, made using the alpha-carbon RMSD computed from a... 

FIGURE 13.7 Measuring the width of the tube as a function of five global collective torsions of the peptide. The torsions are examined sequentially, (a) shows torsion of the first four C atoms and (b) includes the next four alpha carbons and so on. The vertical axis is the sampling in the milestones in degrees. The sampled points are displayed as a function of the trajectory indices. The first 100 trajectories are from the first milestone, the second 100 are from the second milestone, and so on. Note the significant large fluctuations in all torsions around milestone 30. A total of 5000 trajectories are summarized in this plot. 

Figure 19 the carbon-13 chemical shifts for a number of nitrogen heterocycles and their anions and cations are plotted against the proton shifts at the same positions. The scatter is excessive, and is not restricted to positions alpha to nitrogen (open circles). In Figure... 

In order to get information on iiltramicropores, detailed measurements of the amount of adsorption under a relative pressure of 10" are required in other words, measurements in a very low relative pressure range are necessary. In Fig. 9b), the adsorbed amount of nitrt en is plotted against the logarithm of P/Pg for the same three activated carbon fibers to highlight the differences in adsorption at low relative pressures. To get a quantitative evaluation of micropores, the so-called alpha plot is often employed (Fig. 9c), which compares the isotherm with that one for an equivalent material having a flat surface (data fijr a carbon black are usually employed as reference). 

Figure 2.7 Robeson plot illustrating the tradeoff between selectivity (a, ALPHA) and permeability (P) for the separation of carbon dioxide from nitrogen with polymer membranes [47]. The circles indicate all literature data considered relevant. The upper bound line is an empirical judgment of the outermost range of reliable data. Reprinted from Robeson IM. The upper bound revisited. J Membr Sci 2008 320(1—2) 390—400. Copyright (2008), with permission from Elsevier.

Selles-Perez, M.J., and Martin-Martinez, J.M., Classification of alpha plots obtained from nitrogen/77K adsorption isotherms of activated carbons. Fuel. 70(7). 877-882 (1991). 

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