Olesia V. Moroz

Short peptides self-assemble to produce catalytic amyloids

Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (> 10,000 Dalton). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of 7-residue peptides that act as Zn2+-dependent esterases. Zn2+ helps stabilize the fibril formation, while also acting as a cofactor to catalyze acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyze their own formation – they also can catalyze chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and nonbiological metal ions.

New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities

Design of a new catalytic function in proteins, apart from its inherent practical value, is important for fundamental understanding of enzymatic activity. Using a computationally inexpensive, minimalistic approach that focuses on introducing a single highly reactive residue into proteins to achieve catalysis we converted a 74-residue-long C-terminal domain of calmodulin into an efficient esterase. The catalytic efficiency of the resulting stereoselective, allosterically regulated catalyst, nicknamed AlleyCatE, is higher than that of any previously reported de novo designed esterases. The simplicity of our design protocol should complement and expand the capabilities of current state-of-art approaches to protein design. These results show that even a small nonenzymatic protein can efficiently attain catalytic activities in various reactions (Kemp elimination, ester hydrolysis, retroaldol reaction) as a result of a single mutation. In other words, proteins can be just one mutation away from becoming entry points for subsequent evolution.

A Single Mutation in a Regulatory Protein Produces Evolvable Allosterically Regulated Catalyst of Nonnatural Reaction

It only takes one mutation: a strategically placed single mutation in a non-enzymatic protein scaffold produced AlleyCat, a small, allosterically regulated catalyst of Kemp elimination. In only 7 rounds of directed evolution enzymatic efficiency of the original 74 amino acid residue catalyst was improved more than 220-fold to achieve kcat value higher than that of catalytic antibodies for the same reaction, still preserving allosteric regulation.

Design of an allosterically regulated retroaldolase

We employed a minimalist approach for design of an allosterically controlled retroaldolase. Introduction of a single lysine residue into the nonenzymatic protein calmodulin led to a 15,000‐fold increase in the second order rate constant for retroaldol reaction with methodol as a substrate. The resulting catalyst AlleyCatR is active enough for subsequent directed evolution in crude cell bacterial lysates. AlleyCatRs activity is allosterically regulated by Ca2+ ions. No catalysis is observed in the absence of the metal ion. The increase in catalytic activity originates from the hydrophobic interaction of the substrate (∼2000‐fold) and the change in the apparent pKa of the active lysine residue.

N-[Bis(dimethyl­amino)phosphinoyl]-2,2,2-trichloro­acetamide

In the title compound, C6H13Cl3N3O2P or CCl3C(O)NHP(O)(N(CH3)2), the phosphinoyl group is synclinal to the carbonyl group and acts as an acceptor for an intermolecular N—H⋯O hydrogen bond from the amide group as the donor.

Bis{N-[bis­(pyrrolidin-1-yl)phosphor­yl]-2,2,2-trichloro­acetamide}di­nitrato­dioxidouranium(VI)

The crystal structure of the title compound, [U(NO3)2O2(C10H17Cl3N3O2P)2], is composed of centrosymmetric [UO2(L)2(NO3)2] molecules {L is N-[bis(pyrrolidin-1-yl)phosphoryl]-2,2,2-trichloroacetamide, C10H17Cl3N3O2P}. The UVI ion, located on an inversion center, is eight-coordinated with axial oxido ligands and six equatorial oxygen atoms of the phosphoryl and nitrate groups in a slightly distorted hexagonal-bipyramidal geometry. One of the pyrrolidine fragments in the ligand is disordered over two conformation (occupancy ratio 0.58:0.42). Intramolecular N—H⋯O hydrogen bonds between the amine and nitrate groups are found.

Crystal structure of {μ-6,6′-dimeth­oxy-2,2′-[ethane-1,2-diylbis(nitrilo­methanylyl­idene)]diphenolato}(meth­anol)(nitrato)nickel(II)sodium

Two phenolate O atoms provided by a Schiff base ligand create a double bridge between Ni2+ and Na+ ions. The coordination environment of the Ni2+ ion is square-planar and it has an unusual seven-coordinated geometry: four atoms from the Schiff base ligand, two from a nitrate anion, which coordinates in a bidentate chelating mode, and one O atom from the coordinated methanol molecule. C—H⋯O weak hydrogen-bond interactions result in the formation of chains along the b-axis direction which are further assembled by bifurcated O—H⋯O hydrogen bonds and π-stacking interactions.

{Dimeth­yl [(phenyl­sulfon­yl)amido­]phosphato-κ2O,O′}bis­(tri­phenylphosphane-κP)copper(I)

In the title complex, [Cu(C8H11NO5PS)(C18H15P)2], the CuI ion is coordinated by two triphenylphosphane molecules and two O atoms of the chelating dimethyl(phenylsulfonyl)amidophosphate anion, generating a squashed CuO2P2 tetrahedron. In the six-membered chelate ring, the Cu, P and O atoms are almost coplanar (r.m.s. deviation = 0.024 Å), with the N and S atoms displaced in the same direction, by 0.708 (5) and 0.429 (2) Å, respectively.

Tris{N-[bis-(dimethyl-amino)phosphino-yl]-2,2,2-trichloro-acetamido}(triphenyl-phosphine oxide)holmium(III).

In the title compound, [Ho(C6H12Cl3N3O2P)3(C18H15OP)], the HoIII ion is surrounded by six O atoms from the three bidentate N-[bis(dimethylamino)phosphinoyl]-2,2,2-trichloroacetamido ligands (L −) and by one O atom from the triphenylphosphine oxide ligand, with the formation of a distorted monocapped octahedron. In one ligand L −, the trichloromethyl group is rotationally disordered between two orientations in a 1:1 ratio, while two dimethylamino groups in another ligand L − are disordered between two conformations, each with the same 1:1 ratio.