Functional site residues

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

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... 

Hasslacher, M., Schall, M., Hayn, M. et al. (1996) Molecular cloning of the full-length cDNA of (5)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue. The Journal of Biological Chemistry, 271, 5884-5891. 

From 13 completed amino-acid sequences and 54 partial sequences (>40 residues) of plastocyanins from higher plants it appears that sixty residues are invariant and 7 are conservatively substituted 02,7). With three algal plastocyanins included there are 39 invariant or conservatively substituted groups. It is believed that the same structural features apply to the whole family, and that highly conserved residues are an indication of functional sites on the protein surface. The upper hydrophobic and right-hand-side surfaces are believed to be particularly relevant in this context, the latter including four consecutive... 

A number of 7V-carboxyalkyl and A-phosphonoalkyl substituted substrate analogue inhibitors have been examined [161,204-208]. These derivatives contain both the acidic carboxylate (or phosphonate) and basic amine functionalities in the vicinity of the scissile bond. Thus, they are capable both of electrostatic interaction with the active site Zn(II) and hydrogen bonding interactions with other active site residues. They are, however, only moderately potent collagenase inhibitors Table 8.18). The stereochemistry at the carbon atom to which the carboxylate moiety is bonded markedly influences the inhibitory potency of these derivatives ((197) vs. (198)). The phosphonate analogues of this class of derivatives have also been evaluated Table 8.18), but are not substantially better inhibitors than the carboxyl-ates. 

Kalinina OV, Gelfand MS, RusseU RB (2009) Combining specificity determining and conserved residues improves functional site prediction. Bioinformatics. doi 10.1186/1471-... 

Extensive mutagenesis studies have provided information related to the structural integrity, receptor binding region, and residues that are important for IL-1 function. Site-directed mutagenesis (SDM) can create a single-site mutant and its receptor binding and bioactivity values can be calculated. The results... 

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