Fabrizio

Nature Biotechnology, Published online: 23 April 2024; doi:10.1038/s41587-024-02214-2

Metrics that predict the success of folding and the activity of designed protein sequences are developed and experimentally validated.

Nature Catalysis, Published online: 23 April 2024; doi:10.1038/s41929-024-01137-0

Synthetic methylotrophic organisms provide potential for valorization of greenhouse gas-derived methanol. Here an Escherichia coli strain is generated that reaches a similar growth rate on methanol to many natural methylotrophs and is capable of producing chemicals from this carbon source.

Publication date: 28 May 2024

Source: Cell Reports, Volume 43, Issue 5

Author(s): Guang Yang, Ognjen Pećanac, Hein J. Wijma, Henriëtte J. Rozeboom, Gonzalo de Gonzalo, Marco W. Fraaije, Maria Laura Mascotti

S-Adenosylmethionine assumes a crucial role in biocatalytic alkylation. To improve the catalytic ability of BxHMT towards methyl toluene sulfonate, a strategy named dynamic cross-correlation network analysis (DCCNA) was proposed for the identification of potential mutation sites, both distal and proximal. Experimental results proved the efficiency of the approach, which is expected to be a useful tool for other enzyme engineering studies.

Abstract

Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles, such as methyl iodide (MeI) and methyl toluene sulfonate (MeOTs). As compared with MeI, the cost-effective unnatural substrate MeOTs can be accessed directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. In this study, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the catalytic efficiency of the enzyme, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvement, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase as compared to the wild-type (WT) enzyme. Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes a promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.

Multiple enzymes catalyze the formation of pyrroloindoles from indoles, usually coupled with a functional group transfer in the 3-position. In this work, two high-throughput complementary absorbance-based assays were developed for the monitoring of substrate depletion (indole) and product formation (pyrroloindole). The assays were used successfully for enzymatic activity determination, but can be also used for the quantification of natural products.

Abstract

Indoles and pyrroloindoles are structural motifs present in many biologically active natural products. Multiple classes of enzymes catalyze the transformation of indoles into pyrroloindoles via group transfer followed by intramolecular cyclization, such as peroxydases, methyltransferases, and prenyltransferases. Due to the selective introduction of a stereogenic center, these enzymes receive increasing attention as catalytic tools for the production of pharmacologically relevant compounds. Two new colorimetric assays are described in this work, which allow for the quantification of such enzymatic reactions from the perspective of the substrate and the product. For the substrates, the indole assay is based on a modified version of the Ehrlich test, with the use of light as a driving force for color formation. The pyrroloindole assay uses cerium sulfate as a reagent for the colorimetric quantification of the enzymatic products. The assays are complementary and both were successfully utilized for enzymatic activity determination of a C3-indole methyltransferase. They can facilitate high-throughput screening of mutant libraries, offering support for the engineering of such enzymes, but can also be used as stand-alone methods for the detection and quantification of natural products.

Proteins and enzymes can be repurposed by the introduction of artificial cofactors or non-canonical amino acids (ncAAs). These artificial biocatalytic constructs turned into valuable tools to perform new-to-nature reactions with biocatalysts increasing their scope. This perspective focuses on the limitations and future application for in vivo biosynthetic pathways.

Abstract

Astonishing progress has been achieved in unlocking new-to-nature biocatalysis in the past decades. The progress in protein engineering enabled research to efficiently incorporate artificial structural elements into enzyme design. Recent trends include cofactor mimetics, artificial metalloenzymes and non-canonical amino acids. In this perspective article, we present the state-of-the-art, discuss recent examples and our view on what we call artificial biocatalysis. Although these artificial systems undoubtedly increase the scope of biocatalysis, their applicability remains challenging. Fundamental questions regarding the impact of this research field are addressed in this perspective.

An M9 minimum media based on ¹³C-depleted glucose and ¹⁵N-depleted salt dissolved in D,¹⁸O-depleted water (Depleted media) was formulated. E. coli bacteria grow faster in Depleted media compared with isotopically natural media (Normal media). In addition, four different enzymes recombinantly produced in Depleted media showed faster kinetics compared with the enzymes produced in Normal media.

Abstract

Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.

Nature Chemical Biology, Published online: 20 November 2023; doi:10.1038/s41589-023-01484-2

Oxygen sensitivity hampers applications of metal-dependent CO2 reductases. Here, Oliveira et al. describe how an allosteric disulfide bond controls the activity of a CO2 reductase, preventing its physiological reduction during transient O2 exposure and allowing aerobic handling of the enzyme.

Abstract

Synthetic binding proteins have emerged as modulators of protein functions through protein–protein interactions (PPIs). Because PPIs are influenced by the structural dynamics of targeted proteins, investigating whether the synthetic-binders-based strategy is applicable for proteins with large conformational changes is important. This study demonstrates the applicability of monobodies (fibronectin type-III domain-based synthetic binding proteins) in regulating the functions of proteins that undergo tens-of-angstroms-scale conformational changes, using an example of the A55C/C77S/V169C triple mutant (Adk_tm; a phosphoryl transfer-catalyzing enzyme with a conformational change between OPEN/CLOSED forms). Phage display successfully developed monobodies that recognize the OPEN form (substrate-unbound form), but not the CLOSED form of Adk_tm. Two OPEN form-specific clones (OP-2 and OP-4) inhibited Adk_tm kinase activity. Epitope mapping with a yeast-surface display/flow cytometry indicated that OP-2 binds to the substrate-entry side of Adk_tm, whereas OP-4 binding occurs at another site. Small angle X-ray scattering  coupled with size-exclusion chromatography (SEC-SAXS) indicated that OP-4 binds to the hinge side opposite to the substrate-binding site of Adk_tm, retaining the whole OPEN-form structure of Adk_tm. Titration of the OP-4–Adk_tm complex with Ap₅A, a transition-state analog of Adk_tm, showed that the conformational shift to the CLOSED form was suppressed although Adk_tm retained the OPEN-form (i.e., substrate-binding ready form). These results show that OP-4 captures and stabilizes the OPEN-form state, thereby affecting the hinge motion. These experimental results indicate that monobody-based modulators can regulate the functions of proteins that show tens-of-angstroms-scale conformational changes, by trapping specific conformational states generated during large conformational change process that is essential for function exertion.

An aqueous Pictet-Spengler annulation has been interfaced with whole-cell alcohol oxidation. This one-pot cascade reaction converts aliphatic alcohols and tyramines or tryptamines into alkaloid heterocycles under mild, aqueous conditions, delivering tetrahydroisouinolines and tryptolines in >90 % and >40 % isolated yield, respectively, with excellent regioselectivity.

Abstract

Biocatalytic processes are highly selective and specific. However, their utility is limited by the comparatively narrow scope of enzyme-catalysed transformations. To expand product scope, we are developing biocompatible processes that combine biocatalytic reactions with chemo-catalysis in single-flask processes. Here, we show that a chemocatalysed Pictet-Spengler annulation can be interfaced with biocatalysed alcohol oxidation. This two-step, one-pot cascade reaction converts tyramine and aliphatic alcohols to tetrahydroisoquinoline alkaloids in aqueous buffer at mild pH. Tryptamine derivatives are also efficiently converted to tryptolines. Optimization of stoichiometry, pH, reaction time, and whole-cell catalyst deliver the tetrahydroisouinolines and tryptolines in >90 % and >40 % isolated yield, respectively, with excellent regioselectivity.

Abstract

G protein-coupled receptors (GPCRs) are medically important membrane proteins that sample inactive, intermediate, and active conformational states characterized by relatively slow interconversions (~μs–ms). On a faster timescale (~ps–ns), the conformational landscape of GPCRs is governed by the rapid dynamics of amino acid side chains. Such dynamics are essential for protein functions such as ligand recognition and allostery. Unfortunately, technical challenges have almost entirely precluded the study of side-chain dynamics for GPCRs. Here, we investigate the rapid side-chain dynamics of a thermostabilized α_1B-adrenergic receptor (α_1B-AR) as probed by methyl relaxation. We determined order parameters for Ile, Leu, and Val methyl groups in the presence of inverse agonists that bind orthosterically (prazosin, tamsulosin) or allosterically (conopeptide ρ-TIA). Despite the differences in the ligands, the receptor's overall side-chain dynamics are very similar, including those of the apo form. However, ρ-TIA increases the flexibility of Ile176^4×56 and possibly of Ile214^5×49, adjacent to Pro215^5×50 of the highly conserved P^5×50I^3×40F^6×44 motif crucial for receptor activation, suggesting differences in the mechanisms for orthosteric and allosteric receptor inactivation. Overall, increased Ile side-chain rigidity was found for residues closer to the center of the membrane bilayer, correlating with denser packing and lower protein surface exposure. In contrast to two microbial membrane proteins, in α_1B-AR Leu exhibited higher flexibility than Ile side chains on average, correlating with the presence of Leu in less densely packed areas and with higher protein-surface exposure than Ile. Our findings demonstrate the feasibility of studying receptor-wide side-chain dynamics in GPCRs to gain functional insights.