Whence cometh the allosterome?

Abstract

Regulation of cellular functions can be accomplished by many mechanisms, including transcriptional regulation, alternative splicing, translational regulation, phosphorylation and other posttranslational covalent modifications, degradation, localization, proteinprotein interactions, and small-molecule allosteric effectors. Largely because of advances in the techniques of molecular biology in the past few decades, our knowledge of regulation by most of these mechanisms has expanded enormously. Regulation by smallmolecule, allosteric interactions is an exception. Many of the best-known allosteric regulators were discovered decades ago, when we knew little about all of these other forms of regulation. Allostery is the most direct, rapid, and efficient regulatory mechanism to sense changes in the concentration of small molecules and alter cellular responses to maintain homeostasis. In this perspective, we present the argument that allosteric regulation is underappreciated in the systems biology world and that many allosteric effectors remain to be discovered.

Metal‐Ion‐Regulated Miniature DNA‐Binding Proteins Based on GCN4 and Non‐native Regulation Sites

“…[37] This is consistent with a shorter peptide design and previous reports indicating that truncation of the hinge area of GCN4, results in a decrease in the stability of the peptide-DNA complex, preventing successful separation under electrophoresis conditions. [11, 12a, 13] The CD spectrum of a 5 mm solution of (GCN4bd) 2 , lacking the chelating polypyridyl dimerisation unit, in 10 mm phosphate buffer pH 7.4 is consistent with a random coil structure. On addition of 1 equivalent of non-specific (NS) DNA, there was a small increase in the negative signal (V 222 À3.…”

“…The linkers, 5,5'-dibromomethyl-2,2'-bipyridine and 6,6''-dibromomethyl-2,2':6',2''-terpyridine, were successfully coupled to the Cys side-chain to generate GCN4 peptide dimers (bipy-(GCN4bd) 2 and terpy(GCN4bd) 2 ) which contain a metal-ion chelation site in place of the leucine zipper dimerisation domain. Though 5,5'-disubstituted-2,2'-bipyridine compounds have previously been introduced into peptides, [14c, 26, 41, 42] this and our recently reported model compounds with glutathione [27] constitute, to the best of our knowledge, the first describing the insertion of a disubstituted terpyridine unit as a linker between two peptide strands.…”

“…A control peptide dimer, which lacks a metal chelating unit (bipyridine or terpyridine), was prepared by dimerising two equivalents of GCN4bd by formation of a disulfide bond to generate (GCN4bd) 2 .…”

“…[1] Transcription factors are activated and regulated through various allosteric mechanisms. [2] Notable examples which are relevant to this work are metal-sensing transcriptional regulators which trigger expression of the machinery required for heavy metal detoxification or regulation, in response to accumulation of specific metal ions. For example, SmtB and ArsR are bound to gene promoter sites in the absence of Zn II and As III , respectively, but a conformational change is triggered on metal-ion coordination resulting in dissociation from DNA and expression of metallothioneins.…”

NMR reveals novel mechanisms of protein activity regulation

“…[1][2][3][4][5] The cornerstone of this mechanism is the intrinsic capacity of proteins to switch functional states as a response to signal, which is typically triggered by small effector or other protein or nucleic acid binding and posttranslational modifications. Over the recent years, the view and understanding of the fundamental principles underlying allostery have been enriched and often utterly reshaped as techniques such as NMR spectroscopy has been offering insights complementary to those provided by static structures.…”