Side chains, proteins

The Fe-N mode is at 222 in the R state and 207 cnY in the T state for the a subunits, but only shifted to 218 T state for the (3 subunits. This is consistent with the interpretation that the Fe-imidazole interations are weakened more in the T state of the a subunits than p subunits. Time-resolved resonance Raman studies have shown that the R T switch is complete on a 10 ps tuuescale [38]. Finally, UV excitation of the aromatic protein side chains yields... 

MJ Bower, FE Cohen, RL Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library A new homology modeling tool. J Mol Biol 267 1268-1282, 1997. 

RL Dunbrack, M Karplus. Pi ediction of protein side-chain conformations from a backbone conformation dependent rotamer library. J Mol Biol 230 543-571, 1993. 

P Koehl, M Delarue. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 239 249-275, 1994. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

The GAL4 recognition module therefore contains only one protein side chain, Lys 18, that provides specific interactions with the DNA. The remaining specific interactions with DNA are from main-chain atoms and depend critically on the correct conformation of the protein. The correct positioning of the C-terminus of the a helix is particularly important for recognition. This is to date the only example of a protein-DNA interaction in which... 

Scheme 10.31 Reaction cycle of KG-dependent (KG = a-keto-glutarate) enzymes. Metal ligands from protein side chains and water are omitted for clarity. One of the oxygens of O2 is incorporated into succinate. The other oxygen is either incorporated into the product or reduced to water depending on the nature of the reaction.

In the M. trichosporium OB3b system, a third intermediate, T, with kmax at 325 nm (e = 6000 M-1cm 1) was observed in the presence of the substrate nitrobenzene (70). This species was assigned as the product, 4-nitrophenol, bound to the dinuclear iron site, and its absorption was attributed primarily to the 4-nitrophenol moiety. No analogous intermediate was found with the M. capsulatus (Bath) system in the presence of nitrobenzene. For both systems, addition of methane accelerated the rate of disappearance of the optical spectrum of Q (k > 0.065 s-1) without appreciatively affecting its formation rate constant (51, 70). In the absence of substrate, Q decayed slowly (k 0.065 s-1). This decay may be accompanied by oxidation of a protein side chain. 

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...

Mineralisation Especially internal bone containing oxidised protein side chains... 

In contrast, with penicillins, cephalosporins, and monobactams where the substituents are cis to each other across the C3 - C4 bond, clockwise rotation can occur without conflict with protein side chains, and will leave the path open for the water molecule to attack and hydrolyze the ester group in B (Scheme 10). Thus, czs-substituted monobactam, as well as penicillins and cephalosporins are rapidly hydrolyzed by class C enzymes (Scheme 10). If this rotation could be prevented by a suitable structural modification, the access of the water molecule to the ester bond will be blocked, which would result in increased stability of the acyl-enzyme complex. 

Harry B. Gray and Walther Ellis,13 writing in Chapter 6 of reference 13, describe three types of oxidation-reduction centers found in biological systems. The first of these, protein side chains, may undergo oxidation-reduction reactions such as the transformation of two cysteine residues to form the cystine dimer as shown in equation 1.28 ... 

Metal bound 02 stoichiometry (ligands) Fe 02 (heme, histidine) Fe 02 (heme, histidine) 2 Fe 02 (nonheme, protein side chains) 2 Cu 02 (nonheme, protein side chains)... 

A solution structure of French Bean plastocyanin has been reported by Wright and co-workers,19 using nuclear magnetic resonance techniques described in Section 3.5 of Chapter 3. The structure, determined from a plastocyanin molecule in solution rather than in a solid-state crystal, agrees well with that of reduced poplar plastocyanin X-ray crystallographic structure reported above. Conformations of protein side chains constituting the hydrophobic core of the French bean plastocyanin are well-defined by the NMR technique. Surface side chains show... 

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