Conformation barrel

In all jelly roll barrels the polypeptide chain enters and leaves the barrel at the same end, the base of the barrel. In the viral coat proteins a fairly large number of amino acids at the termini of the polypeptide chain usually lie outside the actual barrel structure. These regions vary considerably both in size and conformation between different coat proteins. In addition, there are three loop regions at this end of the barrel that usually are quite long and that also show considerable variation in size in the plant viruses and the... 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

Figure 13-7. A snapshot of the MD simulation of the Orf2 ternary complex looking down the PT-barrel. The protein backbone is shown as ribbons (red) superimposed on top of the crystal conformation (gray). GPP and the magnesium ion are shown as licorice as well as 1,6-DHN, proximal protein side chains (within 3 A) and 4 Mg-coordinating solvent molecules...

Three patents (MacLean, et al., 1982) assigned to Texaco filed in the latter half of 1980 resulted from an in-house review of all observed instances of erosion of cyclones in Texaco s FCC units. The patents specify that to minimize erosion and maximize collection efficiency, the length of the cyclone relative to its barrel diameter is to conform to the relationship ... 

In summary, we can expect that most disulfides will have Cat separations of less than 6.5 A unless they are stretched across a 0 barrel or perhaps a short loop. The majority will have either the left-handed spiral conformation or the right-handed hook conformation. 

The crystal structure of a pentamer of GlcNAc residues, representing the chitin polymer (poly-/l-(l-4)-GlcNAc), boimd to the chitinase enzyme ChiB from Serratia marcescens, revealed a narrow, timnel-like active site in the center of the TIM barrel fold [167]. Several conserved residues near the center of the site, which are important in catalysis, interact with the substrate via hydrogen bonds, while interactions farther from the center depend on van der Waals interactions. The sugar in the - 1 subsite adopts a boat conformation, presumably due to interactions with these critical active-site residues. 

Another significant difference between the large- and small-subunit enzymes lies in the fact that the heme d of HPII and PVC is flipped 180° relative to the heme b moiety of BLC, MLC, SCC-A, and PMC (Fig. 13). This is clearly a function of the residues that form the heme pocket, although attempts to force a change in heme orientation in HPII by mutating residues that interact with the heme were imsuccessful. The heme is situated in the (3-barrel and has interactions with the wrapping domain and with the amino-terminal arm of the R-related subunit. The dimensions of the pocket demand that heme bind in its final conformation and that flipping once inside the pocket not be possible. 

We have completed several structures each of NPl, NP2, and NP4 (31, 46 9, 110). These structures reveal the Rhodnius nitrophorins to have a fold dominated by an eight-stranded antiparallel beta-barrel, as shown in Fig. 15, and to rely on a remarkable ligand-induced conformational change for NO transport, described later. The structures confirm that the nitrophorins are completely unrelated to the globins, the only other heme-based gas transport proteins whose structures are known. Rather, their fold places them in the lipocalin family, for which several other examples are known (111-113). Our initial nitrophorin structure was of NPl and was determined using standard MIR and... 

ATP synthesis takes place by conformational changes at the catalytic binding sites. Recent structural [21, 27], biochemical [13, 28, 31], spectroscopic [32, 33] and microscopic [34, 35] studies indicate that these conformational changes arise from rotation of the y- subunit in a static barrel of agPj subunits in ATP synthase, making it the world s smallest molecular machine with a rotor radius of 1 nm (Fig. 1). 

The NADPH cofactor is bound in an extended conformation across the C-terminal end of the 3 barrel. The catalytically active nicotinamide moiety is located... 

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