Evolution of Allosteric Control in Glycogen Phosphorylase

Hudson, John W.; Golding, G. Brian; Crerar, Michael M.

doi:10.1006/jmbi.1993.1621

Cited by 116 publications

(116 citation statements)

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“…Our expectation is that orthologs (e.g., human and mouse CDK2) will share similar regulatory mechanisms. We do not expect such regulatory mechanisms to be as strongly conserved among paralogs (e.g., human CDK2 and human P38) (36,37). For a protein site with no biological function, we would expect the sequence conservation of pocket residues between the human and an orthologous protein to be similar to the overall sequence conservation between the two proteins.…”

Section: Resultsmentioning

confidence: 96%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

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Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.protein structure | protein function | X-ray crystallography | fragment-based drug design

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Section: Resultsmentioning

confidence: 96%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

View full text Add to dashboard Cite

show abstract

“…The p.A365V missense mutation disrupts a high conserved buried site localized near various residues involved in glycogen storage (Hudson et al 1993).The p.G174D missense mutation modifies a buried conserved site that lies close to two clusters of aminoacid residues that are important in dimerization (Hudson et al 1993). The p.R490W missense mutation alters a buried conserved site that lies next to a piridoxal-5'-phosphate (PLP) binding site (Hudson et al 1993). The p.I83F mutation disrupts a conserved buried site that resides in a fragment of the protein important for dimerization and, binding to PLP and AMP (Hudson et al 1993).…”

Section: Discussionmentioning

confidence: 99%

“…The p.R490W missense mutation alters a buried conserved site that lies next to a piridoxal-5'-phosphate (PLP) binding site (Hudson et al 1993). The p.I83F mutation disrupts a conserved buried site that resides in a fragment of the protein important for dimerization and, binding to PLP and AMP (Hudson et al 1993). The p.Q577R missense mutation modifies a strictly conserved buried site that is located in clusters of aminoacid residues that are related to active site, glucose-binding, PLPbinding, and purine nucleoside-inhibitor sites (Hudson et al 1993).…”

Section: Discussionmentioning

confidence: 99%

“…The p.I83F mutation disrupts a conserved buried site that resides in a fragment of the protein important for dimerization and, binding to PLP and AMP (Hudson et al 1993). The p.Q577R missense mutation modifies a strictly conserved buried site that is located in clusters of aminoacid residues that are related to active site, glucose-binding, PLPbinding, and purine nucleoside-inhibitor sites (Hudson et al 1993). Therefore, these missense mutations would presumably affect protein sites that are important for the enzyme activity.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, these missense mutations would presumably affect protein sites that are important for the enzyme activity. In addition, they are likely to be the cause of myophosphorylase deficiency, because (a) they were the only nucleotide alteration in the coding region and adjacent exon/intron boundaries of the PYGM gene; (b) they lead to the replacement of amino acid residues that are identical not only in the glycogen phosphorylase of various species but also in the three human isoforms of this enzyme (Hudson et al 1993) which is consistent with a crucial role of these amino acids in the normal function of myophosphorylase; and 100 normal controls and 50 disease controls did not have any of these mutations in their alleles.…”

Section: Discussionmentioning

confidence: 99%

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