Residue proximities

However, diffusion of the reactive QM out of the enzyme active site is a major concern. For instance, a 2-acyloxy-5-nitrobenzylchloride does not modify any nucleophilic residue located within the enzyme active site but becomes attached to a tryptophan residue proximal to the active site of chymotrypsin or papain.23,24 The lack of inactivation could also be due to other factors the unmasked QM being poorly electrophilic, active site residues not being nucleophilic enough, or the covalent adduct being unstable. Cyclized acyloxybenzyl molecules of type a could well overcome the diffusion problem. They will retain both the electrophilic hydroxybenzyl species b, and then the tethered QM, in the active site throughout the lifetime of the acyl-enzyme (Scheme 11.1). This reasoning led us to synthesize functionalized... 

The QM/MM studies found a negligible effect of the protein environment. Nevertheless, theoretical DFT calculations that have included protein residues proximal to the active site in the cluster model have demonstrated the influence of near-neighbor residues in the calculation of the g-tensors for the Nir and Niu states.66 Those calculations have even associated the different behavior of Nir and Niu with different interactions with a nearby glutamic acid residue, which are originated in different orientations of a cysteine residue that bridges it to the active site. It has been... 

Markosyan RM, Leung MY, Cohen FS (2009) The six-helix bundle of human immunodeficiency virus env controls pore formation and enlargement and is initiated at residues proximal to the hairpin turn. J Virol 83 10048-10057... 

The stereochemical course of conversion from the adduct 150 into macrophomate 152 is shown in Scheme 27. Since inspection of the active site does not identify any basic residue proximal to the pro-R proton, the Cl-carboxylate may abstract the proton by ArglOl accepting the developing charge on the lactone oxygen. 

NOESY-HMQC (HSQC) double resonance experiments can provide unique and unambiguous indications of inter-residue proximities by through-space NOE correlations between pairs of IV H resonance signals. The appearance of symmetrical peaks (see triangulations above) occurs when NOEs are observed between NH systems of amino acid residues with essentially identical chemical shifts to each other (adapted from J. Am. Chem. Soc., 1990, 112, 9020-9022 fig. 2). 

Compare the spectra paying particular attention to tyrosine residues and residues proximal to tyrosines. Similarities in chemical shift correlate with the absence of sulfation while differences in chemical shift are indicative of tyrosine sulfation (see Fig. 4). 

Figure 5.15. Plot of T, as a function of log(calcium ion concentration), log[Ca ], which is proportional to chemical energy. Considering the biological transition zone of lowering T, from 37°C to 25°C, it is possible visually to gain a sense of how the amount of chemical energy differs as the composition of the model protein changes. Clearly, as the hydrophobicity increases per carboxylate, the chemical energy required to drive hydrophobic association decreases, and it further decreases by having the carboxylates of the Glu (E) residues proximal for bidentate interaction with the doubly charged calcium ion. (D. Urry and C.-H. Luan, unpublished results.)...

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