An artificial protein cage made from a 12-membered ring

Stupka, Izabela; Biela, Artur P.; Piette, Bernard; Kowalczyk, Agnieszka; Majsterkiewicz, Karolina; Borzęcka-Solarz, Kinga; Naskalska, Antonina; Heddle, Jonathan G.

doi:10.1039/d3tb01659e

Cited by 3 publications

(2 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Comparison of the crystal structure coordinates and optimized model for holo dTRAP revealed a 6% expansion in the diameter of the TRAP ring, as measured by the change in distance between corresponding atoms on opposite sides of the ring (e.g., Lys37 C α ). Because the template was obtained from crystals of Aha TRAP, we also compared the cryo-EM electron potential map of holo dTRAP with that of a point mutant of Aha TRAP modified to form protein cages via interaction with gold nanoparticles [18]. The potential map obtained for dTRAP with its twelve effective protomers (six dTRAP chains) appears expanded by ~6% compared to that of Aha TRAP dodecamers (Figure S 18).…”

Section: Cryo-em Single Particle Reconstruction Of Dtrap Wt-wt and Wt...mentioning

confidence: 99%

“…The RNA structures that are formed upon TRAP binding play roles in down-regulating expression of the Trp biosynthesis machinery by promoting both transcription attenuation and translational repression [1]. Because of these properties TRAP has served as a paradigm for understanding ligand-modulated gene expression [1][2][3], ligand-coupled protein folding [4,5], protein-mediated RNA remodeling [6][7][8], and homotropic and heterotropic cooperativity [9][10][11][12][13][14][15][16], and as a tool for nanotechnology [17,18]. As a highly specific ligand-activated gene regulatory protein [12,[19][20][21], TRAP also has potential as a template for systems biology applications [22].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Li,

Yang,

Stachowski

et al. 2024

Preprint

View full text Add to dashboard Cite

Homotropic cooperativity is widespread in biological regulation. The homo-oligomeric ring-shaped trp RNA binding attenuation protein (TRAP) from bacillus binds multiple tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5' leader region of the trp operon mRNA. Ligand-activated binding to this specific RNA sequence regulates downstream biosynthesis of Trp in a feedback loop. Characterized TRAP variants form 11- or 12-mer rings and bind Trp at the interface between adjacent subunits. Various studies have shown that a pair of loops that gate each Trp binding site is flexible in the absence of the ligand and become ordered upon ligand binding. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity we engineered dodecameric (12-mer) TRAP variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated one of the protomers such that only every other site was competent for Trp binding. Thermodynamic and structural studies using native mass spectrometry, NMR spectroscopy, and cryo-EM provided unprecedented detail into the thermodynamic and structural basis for the observed ligand binding cooperativity. Such insights can be useful for understanding allosteric control networks and for the development of new ones with defined ligand sensitivity and regulatory control.

show abstract

Section: Cryo-em Single Particle Reconstruction Of Dtrap Wt-wt and Wt...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Li,

Yang,

Stachowski

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Li,

Yang,

Stachowski

et al. 2024

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

View full text Add to dashboard Cite

The homo-dodecameric ring-shaped trp RNA binding attenuation protein (TRAP) from Alkalihalobacillus halodurans (Aha) binds up to twelve tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5’ leader region of the trp operon mRNA, thereby downregulating biosynthesis of Trp. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity in TRAP, we engineered variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated the binding sites of alternating protomers such that only every other site was competent for Trp binding (WT-Mut dTRAP). Ligand binding monitored by NMR, calorimetry, and native mass spectrometry revealed strong cooperativity in dTRAP containing adjacent binding-competent sites, but a severe binding defect when the wild-type sites were separated by mutated sites. Cryo-EM experiments of dTRAP in its ligand-free apo state, and both dTRAP and WT-Mut dTRAP in the presence of Trp, revealed progressive stabilization of loops that gate the Trp binding site and participate in RNA binding. These studies provide important insights into the thermodynamic and structural basis for the observed ligand binding cooperativity in TRAP. Such insights can be useful for understanding allosteric control networks and for the development of those with defined ligand sensitivity and regulatory control.

show abstract

Biequivalent Planar Graphs

Piette

2024

Axioms

View full text Add to dashboard Cite

We define biequivalent planar graphs, which are a generalisation of the uniform polyhedron graphs, as planar graphs made out of two families of equivalent nodes. Such graphs are required to identify polyhedral cages with geometries suitable for artificial protein cages. We use an algebraic method, which is followed by an algorithmic method, to determine all such graphs with up to 300 nodes each with valencies ranging between three and six. We also present a graphic representation of every graph found.

show abstract

An artificial protein cage made from a 12-membered ring

Abstract: Changing the symmetry of the constituent ring-shaped building block of an artificial cage.

Cited by 3 publications

References 22 publications

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Biequivalent Planar Graphs

Contact Info

Product

Resources

About