Allosteric Coupling via Distant Disorder-to-Order Transitions

Eginton, Christopher; Cressman, William J.; Bachas, Sharrol; Wade, Herschel; Beckett, Dorothy

doi:10.1016/j.jmb.2015.02.021

Cited by 28 publications

(36 citation statements)

References 38 publications

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“…Previous studies indicate that any perturbation of ABL folding, either through direct alanine substitution of loop residues or through the G142A substitution, is accompanied by a 3.0−4.0 kcal/mol penalty to bio-5′-AMP binding. 13,15,18 Consequently, the absence of effects of alanine substitutions on the bio-5′-AMP binding free energy at 20°C for the remaining dimerization surface variants provides strong evidence of the preservation of the ABL disorder-to-order transition in these proteins. Structural data indicate that the G142A substitution is also accompanied by disruption of a coilto-helix transition in residues 143−146 that occurs in wtBirA ( Figure 1).…”

Section: ■ Discussionmentioning

confidence: 97%

“…Consistent with this observation, the holoBirAG142A structure indicates that 20 of the 29 residues that fold upon binding of bio-5′-AMP to wtBirA remain disordered in the variant. 18 The well-characterized wtBirA and BirAG142A can serve as a reference in proposing the structural origins of heat capacity changes associated with binding of bio-5′-AMP to the remaining variants. First, heat capacity changes for binding of bio-5′-AMP to variants E140A, G196A, and K283A are similar in magnitude to that measured for wtBirA (Table 5).…”

Section: ■ Discussionmentioning

confidence: 99%

“…11 The structure of the holoBirAG142A variant indicates that the disorder-to-order transitions in the 140−146 and 193−199 loops are perturbed, consistent with a functional role for these transitions in activation of dimerization. 18 Furthermore, 33 Å from the alanine substitution, the disorderto-order transition in the effector binding site ABL is also disrupted. 18 The energetic penalty to bio-5′-AMP binding to the variant is 2.9 kcal/mol.…”

mentioning

confidence: 99%

“…18 Furthermore, 33 Å from the alanine substitution, the disorderto-order transition in the effector binding site ABL is also disrupted. 18 The energetic penalty to bio-5′-AMP binding to the variant is 2.9 kcal/mol. The combined results indicate that folding events at the two distant functional surfaces are required to obtain the full −4 kcal/mol coupling between corepressor binding and dimerization.…”

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confidence: 99%

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Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Cressman

Beckett

2015

Biochemistry

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Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.

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Section: ■ Discussionmentioning

confidence: 97%

Section: ■ Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Cressman

Beckett

2015

Biochemistry

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“…BirA belongs to biotin protein ligases which are the enzymes existing in many organisms and can attach biotin to a specific lysine of some target proteins. BirA is only 35.5 kDa and several studies have resolved the crystal structure of this protein . BirA contains three main domains: an N‐terminal DNA‐binding domain (residues 1–60), the central catalytic domain (residues 80–269), and a C‐terminal domain (residues 271–320) which is important for binding ATP and interacting with the target protein .…”

Section: Bioid: a Pdl Methods Undergoing Upgradationmentioning

confidence: 99%

Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

Wang

et al. 2017

Proteomics

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Proteins perform biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches such as phage display, yeast hybridization, etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity-dependent labeling (PDL) of interacting proteins has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently. Among the PDL methods, BioID is the earliest and the most widely used one and has been upgraded from its prototype, making it an extremely convenient research tool. In this review, we describe the BioID technology development, its potential applications according to the nature of the target protein, and some recent efforts to circumvent the technical limitations. Moreover, some comparable PDL methods are introduced, including selective proteomic proximity labeling assay using tyramide, enzyme-mediated activation of radical sources, Proximity Labeling with Ascorbate Peroxidase, in vivo proximal labeling, etc., and we propose that systematic comparison of the working radius of these methods may be helpful to develop a tool box, from which the right method can be selected for a given target protein for PPI research.

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A conserved regulatory mechanism in bifunctional biotin protein ligases

Wang

Beckett

2017

Protein Science

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Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms.

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Allosteric Coupling via Distant Disorder-to-Order Transitions

Cited by 28 publications

References 38 publications

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

A conserved regulatory mechanism in bifunctional biotin protein ligases

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