The Biotin Repressor: Modulation of Allostery by Corepressor Analogs

Brown, Patrick H.; Cronan, John E.; Grøtli, Morten; Beckett, Dorothy

doi:10.1016/j.jmb.2004.01.041

Cited by 53 publications

(76 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The quality of each fit was assessed from the magnitude of the square root of the variance of the fit and the residual plots. The dimerization free energy of the wild-type repressor bound to each of the adenylates is in excellent agreement with previously reported values (17,23). Results obtained with the ABL variants indicate in all cases defects in dimerization relative to the wild type repressor.…”

Section: Dimerization Of Adenylate-bound Repressor Variant Proteinssupporting

confidence: 89%

“…High-resolution structures are available for the apoBirA monomer and two dimers in which the repressor is complexed with biotin or an analogue of bio-5'-AMP, btnOH-AMP (15,22). While enhancement of dimerization energetics upon biotin binding is in effect zero, binding of btnOH-AMP results in an enhancement nearly as large as that associated with physiological corepressor binding (23). Comparison of the apoBirA monomer with the two ligand-bound dimer structures reveals that three loops, which are disordered in the unliganded protein, are ordered and participate directly in the intersubunit interface of each ligand-bound structure.…”

Section: Discussionmentioning

confidence: 99%

“…However, while biotin is a weak allosteric activator, btnOH-AMP is nearly equivalent to bio-5'-AMP in its ability to drive repressor dimerization. For the wild type repressor dimerization of the btnOH-AMP complex is energetically more favorable than that of the biotin complex by approximately -3 kcal/mole (23). Indeed, the energetic enhancement of dimerization associated with biotin binding is, within error, zero.…”

Section: Dimerization Of Adenylate-bound Repressor Variant Proteinsmentioning

confidence: 93%

See 2 more Smart Citations

Nucleation of an Allosteric Response via Ligand-induced Loop Folding

Naganathan

Beckett

2007

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

The Escherichia coli biotin repressor, BirA, is an allosteric transcription regulatory protein to which binding of the small ligand corepressor, biotinyl-5'-AMP, promotes homodimerization and subsequent DNA binding. Structural data indicate that the apo-or unliganded repressor is characterized by four partially disordered loops that are ordered in the ligand-bound dimer. While three of these loops participate directly in the dimerization, the fourth, consisting of residues 212-234 is distal to the interface. This loop, which is ordered around the adenine ring of the adenylate in the BirA adenylate structure, is referred to as the adenylate binding loop or ABL. Although residues in the loop do not directly interact with the ligand, a hydrophobic cluster consisting of a tryptophan and two valine side chains assembles over the adenine base. Results of previous measurements suggest that folding of the ABL is integral to the allosteric response. This idea and the role of the hydrophobic cluster in the process were investigated by systematic replacement of each side chain in the cluster with alanine and analysis of the variant proteins for small ligand binding and dimerization. Isothermal titration calorimetry measurements indicate defects in adenylate binding for all ABL variants. Additionally, sedimentation equilibrium measurements reveal that coupling between adenylate binding and dimerization is compromised in each mutant. Partial proteolysis measurements indicate that the mutants are defective in ligand-linked folding of the ABL. These results indicate that the hydrophobic cluster is critical to the ligand-induced disorder-to-order transition in the ABL and that this transition is integral to the allosteric response in the biotin repressor.

show abstract

Section: Dimerization Of Adenylate-bound Repressor Variant Proteinssupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Dimerization Of Adenylate-bound Repressor Variant Proteinsmentioning

confidence: 93%

See 1 more Smart Citation

Nucleation of an Allosteric Response via Ligand-induced Loop Folding

Naganathan

Beckett

2007

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Four biotin analogs have been subjected to analysis with respect to effects of their binding on energetics of both repressor dimerization and total assembly of the repressor:operator complex (18). As shown in Figure 1, total assembly refers to combined dimerization and site-specific DNA binding of the dimer.…”

Section: The Biotin Repressor: An Allosteric Site-specific Dna Bindinmentioning

confidence: 99%

Allosteric Signaling in the Biotin Repressor Occurs via Local Folding Coupled to Global Dampening of Protein Dynamics

Laine

Streaker

Nabavi

et al. 2008

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

SummaryThe biotin repressor is an allosterically regulated site-specific DNA binding protein. Binding of the small ligand, bio-5'-AMP, activates repressor dimerization, which is a prerequisite to DNA binding. Multiple disorder-to-order transitions, some of which are known to be important for the functional allosteric response, occur in the vicinity of the ligand binding site concomitant with effector binding to the repressor monomer. In this work the extent to which these local changes are coupled to additional changes in the structure/dynamics of the repressor was investigated using HydrogenDeuterium exchange coupled to Mass Spectrometry. Measurements were performed on the apoprotein and on complexes of the protein bound to four different effectors that elicit a range of thermodynamic responses in the repressor. Global exchange measurements indicate that binding of any effector to the intact protein is accompanied by protection from exchange. Mass spectrometric analysis of pepsin-cleavage products generated from the exchanged complexes reveals that the protection is distributed throughout the protein. Furthermore, the magnitude of the level of protection in each peptide from H-D exchange correlates with the magnitude of the functional allosteric response elicited by a ligand. These results indicate that local structural changes in the binding site that occur concomitant with effector binding nucleate global dampening of dynamics. Moreover, the magnitude of dampening of repressor dynamics tracks with magnitude of the functional response to effector binding.

show abstract

“…5,6 An important approach to these inhibitors involves replacing the hydrolytically unstable acyl phosphate linker of 1 with a more stable bioisostere, as in biotinol-5′-AMP 2. 6,7 This phosphodiester mimic is a potent inhibitor of BPLs from S. aureus, Escherichia coli, and Homo sapiens. 6,8 However, its antibacterial properties have not been investigated.…”

mentioning

confidence: 99%

Improved Synthesis of Biotinol-5′-AMP: Implications for Antibacterial Discovery

Tieu

Polyak

Paparella

et al. 2014

ACS Med. Chem. Lett.

View full text Add to dashboard Cite

An improved synthesis of biotinol-5′-AMP, an acyl-AMP mimic of the natural reaction intermediate of biotin protein ligase (BPL), is reported. This compound was shown to be a pan inhibitor of BPLs from a series of clinically important bacteria, particularly Staphylococcus aureus and Mycobacterium tuberculosis, and kinetic analysis revealed it to be competitive against the substrate biotin. Biotinol-5′-AMP also exhibits antibacterial activity against a panel of clinical isolates of S. aureus and M. tuberculosis with MIC values of 1−8 and 0.5−2.5 μg/mL, respectively, while being devoid of cytotoxicity to human HepG2 cells. KEYWORDS: Antibiotics, enzyme inhibitors, biotin protein ligase, chemical synthesis, drug design A denylate-forming enzymes play a central role in many key metabolic pathways such as ribosomal and nonribosomal peptide synthesis, fatty acid synthesis, and enzyme regulation. As such they are of significant interest as potential drug targets. 1,2 These enzymes function by activating a carboxylate metabolite on reaction with ATP to form an acyl-AMP intermediate, which then reacts with a nucleophile to generate the desired product ( Figure 1). The acyl-AMP reaction intermediates possess a high binding affinity for the enzyme, often 2−3 orders of magnitude greater than the carboxylic acid or ATP substrates. 3,4 The inhibition of biotinyl-5′-AMP 1, one such intermediate produced by the biotin protein ligase (BPL) catalyzed reaction of biotin and ATP, has attracted recent interest as a potential new class of antibiotic. 5,6 An important approach to these inhibitors involves replacing the hydrolytically unstable acyl phosphate linker of 1 with a more stable bioisostere, as in biotinol-5′-AMP 2. 6,7 This phosphodiester mimic is a potent inhibitor of BPLs from S. aureus, Escherichia coli, and Homo sapiens. 6,8 However, its antibacterial properties have not been investigated. Other acyl phosphate bioisosteres used in this context include, sulfonyl and 1,2,3-triazole groups, among others. 5,6,9−25 Importantly, acyl-AMP mimics (containing sulfonmyl and 1,2,3-triazole isosteres, see 3 and 4 in Figure 1) have been shown to be potent agents against M. tuberculosis and S. aureus, respectively. 26 Given the central importance of biotinol-5′-AMP 2 as a BPL inhibitor, we now report an expedient method for its synthesis and an investigation of its activity profile against clinically significant bacteria.Biotinol-5′-AMP 2 is reportedly prepared according to a modified "phosphodiester" procedure as shown in Scheme 1. 7 However, in our hands this procedure gave an unsatisfactory overall yield of 9% from adenosine 5. The key limitation with this procedure was a DCC mediated coupling of 6 and 8 to give phosphodiester 9, with subsequent in situ deprotection of the acetonide group to give 2. An overall yield of 15% was obtained over these two steps. Attempts to optimize the DCC coupling step using other solvents, particularly pyridine or DMF, or longer reaction times (up to 48 h) failed to improve the yield. The u...

show abstract

The Biotin Repressor: Modulation of Allostery by Corepressor Analogs

Cited by 53 publications

References 43 publications

Nucleation of an Allosteric Response via Ligand-induced Loop Folding

Nucleation of an Allosteric Response via Ligand-induced Loop Folding

Allosteric Signaling in the Biotin Repressor Occurs via Local Folding Coupled to Global Dampening of Protein Dynamics

Improved Synthesis of Biotinol-5′-AMP: Implications for Antibacterial Discovery

Contact Info

Product

Resources

About