From Bioorganic Models to Cells.

I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.

RNA Splicing by the Spliceosome.

The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5' splice site (5'SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5'SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5'SS, producing a free 5' exon. Removal of the BP adenosine from the active site allows the 3'SS to bind, so that the 5' exon attacks the 3'SS to produce mature mRNA and an excised lariat intron.

Moving Through Barriers in Science and Life.

This first serious attempt at an autobiographical accounting has forced me to sit still long enough to compile my thoughts about a long personal and scientific journey. I especially hope that my trajectory will be of interest and perhaps beneficial to much younger women who are just getting started in their careers. To paraphrase from Virginia Woolf's writings in A Room of One's Own at the beginning of the 20th century, "for most of history Anonymous was a Woman." However, Ms. Woolf is also quoted as saying "nothing has really happened until it has been described," a harbinger of the enormous historical changes that were about to be enacted and recorded by women in the sciences and other disciplines. The progress in my chosen field of study-the chemical basis of enzyme action-has also been remarkable, from the first description of an enzyme's 3D structure to a growing and deep understanding of the origins of enzyme catalysis.

Directed Evolution of Protein Catalysts.

Directed evolution is a powerful technique for generating tailor-made enzymes for a wide range of biocatalytic applications. Following the principles of natural evolution, iterative cycles of mutagenesis and screening or selection are applied to modify protein properties, enhance catalytic activities, or develop completely new protein catalysts for non-natural chemical transformations. This review briefly surveys the experimental methods used to generate genetic diversity and screen or select for improved enzyme variants. Emphasis is placed on a key challenge, namely how to generate novel catalytic activities that expand the scope of natural reactions. Two particularly effective strategies, exploiting catalytic promiscuity and rational design, are illustrated by representative examples of successfully evolved enzymes. Opportunities for extending these approaches to more complex biocatalytic systems are also considered.

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.

Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.

Mechanisms of Deubiquitinase Specificity and Regulation.

Protein ubiquitination is one of the most powerful posttranslational modifications of proteins, as it regulates a plethora of cellular processes in distinct manners. Simple monoubiquitination events coexist with more complex forms of polyubiquitination, the latter featuring many different chain architectures. Ubiquitin can be subjected to further posttranslational modifications (e.g., phosphorylation and acetylation) and can also be part of mixed polymers with ubiquitin-like modifiers such as SUMO (small ubiquitin-related modifier) or NEDD8 (neural precursor cell expressed, developmentally downregulated 8). Together, cellular ubiquitination events form a sophisticated and versatile ubiquitin code. Deubiquitinases (DUBs) reverse ubiquitin signals with equally high sophistication. In this review, we conceptualize the many layers of specificity that DUBs encompass to control the ubiquitin code and discuss examples in which DUB specificity has been understood at the molecular level. We further discuss the many mechanisms of DUB regulation with a focus on those that modulate catalytic activity. Our review provides a framework to tackle lingering questions in DUB biology.

Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads to Mutations and Creates Sequence Diversity.

Self-catalyzed DNA depurination is a sequence-specific physiological mechanism mediated by spontaneous extrusion of a stem-loop catalytic intermediate. Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue of the 5'GAGA loop, together with particular first stem base pairs, specifies their hydrolysis without involving protein, cofactor, or cation. As such, this mechanism is the only known DNA catalytic activity exploited by nature. The consensus sequences for self-depurination of such G- and A-loop residues occur in all genomes examined across the phyla, averaging one site every 2,000-4,000 base pairs. Because apurinic sites are subject to error-prone repair, leading to substitution and short frameshift mutations, they are both a source of genome damage and a means for creating sequence diversity. Their marked overrepresentation in genomes, and largely unchanging density from the lowest to the highest organisms, indicate their selection over the course of evolution. The mutagenicity at such sites in many human genes is associated with loss of function of key proteins responsible for diverse diseases.

Hierarchy of RNA functional dynamics.

RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.

Double-duty isomerases: a case study of isomerization-coupled enzymatic catalysis.

Enzymes can usually be unambiguously assigned to one of seven classes specifying the basic chemistry of their catalyzed reactions. Less frequently, two or more reaction classes are catalyzed by a single enzyme within one active site. Two examples are an isomerohydrolase and an isomero-oxygenase that catalyze isomerization-coupled reactions crucial for production of vision-supporting 11-cis-retinoids. In these enzymes, isomerization is obligately paired and mechanistically intertwined with a second reaction class. A handful of other enzymes carrying out similarly coupled isomerization reactions have been described, some of which have been subjected to detailed structure-function analyses. Herein we review these rarefied enzymes, focusing on the mechanistic and structural basis of their reaction coupling with the goal of revealing catalytic commonalities.

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

Thermo-photo catalytic anode process for carbonate-superstructured solid fuel cells.

Converting hydrocarbons and greenhouse gases (i.e., carbon dioxide, CO2) directly into electricity through fuel cells at intermediate temperatures (450 to 550 °C) remains a significant challenge, primarily due to the sluggish activation of C-H and C=O bonds. Here, we demonstrated a unique strategy to address this issue, in which light illumination was introduced into the thermal catalytic CO2 reforming of ethane in the anode as a unique thermo-photo anode process for carbonate-superstructured solid fuel cells. The light-enhanced fuel activation led to excellent cell performance with a record-high peak power density of 168 mW cm-2 at an intermediate temperature of 550 °C. Furthermore, no degradation was observed during ~50 h operation. Such a successful integration of photo energy into the fuel cell system provides a new direction for the development of efficient fuel cells.

Demystifying group-4 polyolefin hydrogenolysis catalysis. Gaseous propane hydrogenolysis mechanism over the same catalysts.

A kinetic/mechanistic investigation of gaseous propane hydrogenolysis over the single-site heterogeneous polyolefin depolymerization catalysts AlS/ZrNp2 and AlS/HfNp2 (AlS = sulfated alumina, Np = neopentyl), is use to probe intrinsic catalyst properties without the complexities introduced by time- and viscosity-dependent polymer medium effects. In a polymer-free automated plug-flow catalytic reactor, propane hydrogenolysis turnover frequencies approach 3,000 h-1 at 150 °C. Both catalysts exhibit approximately linear relationships between rate and [H2] at substoichiometric [H2] with rate law orders of 0.66 ± 0.09 and 0.48 ± 0.07 for Hf and Zr, respectively; at higher [H2], the rates approach zero-order in [H2]. Reaction orders in [C3H8] and [catalyst] are essentially zero-order under all conditions, with the former implying rapid, irreversible alkane binding/activation. This rate law, activation parameter, and DFT energy span analysis support a scenario in which [H2] is pivotal in one of two plausible and competing rate-determining transition states-bimolecular metal-alkyl bond hydrogenolysis vs. unimolecular ß-alkyl elimination. The Zr and Hf catalyst activation parameters, ΔH‡ = 16.8 ± 0.2 kcal mol-1 and 18.2 ± 0.6 kcal mol-1, respectively, track the relative turnover frequencies, while ΔS‡ = -19.1 ± 0.8 and -16.7 ± 1.4 cal mol-1 K-1, respectively, imply highly organized transition states. These catalysts maintain activity up to 200 °C, while time-on-stream data indicate multiday activities with an extrapolated turnover number ~92,000 at 150 °C for the Zr catalyst. This methodology is attractive for depolymerization catalyst discovery and process optimization.

Catalysis driven by an amyloid-substrate complex.

Amine modification through nucleophilic attack of the amine functionality is a very common chemical transformation. Under biorelevant conditions using acidic-to-neutral pH buffer, however, the nucleophilic reaction of alkyl amines (pKa ≈ 10) is not facile due to the generation of ammonium ions lacking nucleophilicity. Here, we disclose a unique molecular transformation system, catalysis driven by amyloid-substrate complex (CASL), that promotes amine modifications in acidic buffer. Ammonium ions attached to molecules with amyloid-binding capability were activated through deprotonation due to the close proximity to the amyloid catalyst formed by Ac-Asn-Phe-Gly-Ala-Ile-Leu-NH2 (NL6), derived from islet amyloid polypeptide (IAPP). Under the CASL conditions, alkyl amines underwent various modifications, i.e., acylation, arylation, cyclization, and alkylation, in acidic buffer. Crystallographic analysis and chemical modification studies of the amyloid catalysts suggested that the carbonyl oxygen of the Phe-Gly amide bond of NL6 plays a key role in activating the substrate amine by forming a hydrogen bond. Using CASL, selective conversion of substrates possessing equivalently reactive amine functionalities was achieved in catalytic reactions using amyloids. CASL provides a unique method for applying nucleophilic conversion reactions of amines in diverse fields of chemistry and biology.

Long-lasting organics removal via •OH adsorbed transition metal flocs: Electron transfer-mediated H-bond and van der Waals force.

Homogenous advanced oxidation processes (AOPs) based on transition metal catalysts toward the activation of H2O2 to hydroxyl radical (•OH) have been widely applied to organic pollutants removal, such as Fenton and Fenton-like processes. These transition metal catalysts mostly flocculate as the pH increases. It's worth noting that the formed transition metal flocs are complex heterogeneous aggregations with active substances, providing diverse reaction spaces and interfaces. However, it is a challenge to distinguish the roles of transition metal flocs in the organic pollutants removal from homogeneous catalytic reactions. Herein, we unveiled a pathway for the long-lasting removal of organic pollutants via Cr flocs adsorbed with •OH (HO•-Cr flocs) using a stepwise method. First, adsorbed •OH (•OHads) within the HO•-Cr flocs was proved to be the active site forming hydrogen bond (H-bond) and van der Waals force with organic pollutants. Then, the presence of switchable electron transfer between Cr and OH groups within the HO•-Cr flocs was revealed, contributing to the persistent existence of •OHads and consequently ensuring the long-lasting organics removal. Further, this removal pathway of organic pollutants was confirmed during the leather wastewater treatment. These findings will complement a different pathway for organic pollutants removal via transition metal flocs and extend the lifetime of homogeneous AOPs based on transition metal catalysts, providing significant implications for their design and optimization.

Achieving metal-like catalysis from semiconductor for on-surface synthesis.

Free of posttransfer, on-surface synthesis (OSS) of single-atomic-layer nanostructures directly on semiconductors holds considerable potential for next-generation devices. However, due to the high diffusion barrier and abundant defects on semiconductor surfaces, extended and well-defined OSS on semiconductors has major difficulty. Furthermore, given semiconductors' limited thermal catalytic activity, initiating high-barrier reactions remains a significant challenge. Herein, using TiO2(011) as a prototype, we present an effective strategy for steering the molecule adsorption and reaction processes on semiconductors, delivering lengthy graphene nanoribbons with extendable widths. By introducing interstitial titanium (Tiint) and oxygen vacancies (Ov), we convert TiO2(011) from a passive supporting template into a metal-like catalytic platform. This regulation shifts electron density and surface dipoles, resulting in tunable catalytic activity together with varied molecule adsorption and diffusion. Cyclodehydrogenation, which is inefficient on pristine TiO2(011), is markedly improved on Tiint/Ov-doped TiO2. Even interribbon cyclodehydrogenation is achieved. The final product's dimensions, quality, and coverage are all controllable. Tiint doping outperforms Ov in producing regular and prolonged products, whereas excessive Tiint compromises molecule landing and coupling. This work demonstrates the crucial role of semiconductor substrates in OSS and advances OSS on semiconductors from an empirical trial-and-error methodology to a systematic and controllable paradigm.

Capturing the catalytic intermediates of parkin ubiquitination.

Parkin is an E3 ubiquitin ligase implicated in early-onset forms of Parkinson's disease. It catalyzes a transthiolation reaction by accepting ubiquitin (Ub) from an E2 conjugating enzyme, forming a short-lived thioester intermediate, and transfers Ub to mitochondrial membrane substrates to signal mitophagy. A major impediment to the development of Parkinsonism therapeutics is the lack of structural and mechanistic detail for the essential, short-lived transthiolation intermediate. It is not known how Ub is recognized by the catalytic Rcat domain in parkin that enables Ub transfer from an E2~Ub conjugate to the catalytic site and the structure of the transthiolation complex is undetermined. Here, we capture the catalytic intermediate for the Rcat domain of parkin in complex with ubiquitin (Rcat-Ub) and determine its structure using NMR-based chemical shift perturbation experiments. We show that a previously unidentified α-helical region near the Rcat domain is unmasked as a recognition motif for Ub and guides the C-terminus of Ub toward the parkin catalytic site. Further, we apply a combination of guided AlphaFold modeling, chemical cross-linking, and single turnover assays to establish and validate a model of full-length parkin in complex with UbcH7, its donor Ub, and phosphoubiquitin, trapped in the process of transthiolation. Identification of this catalytic intermediate and orientation of Ub with respect to the Rcat domain provides important structural insights into Ub transfer by this E3 ligase and explains how the previously enigmatic Parkinson's pathogenic mutation T415N alters parkin activity.

Site-selective peptide bond hydrolysis and ligation in water by short peptide-based assemblies.

The evolution of complex chemical inventory from Darwin's nutrient-rich warm pond necessitated rudimentary yet efficient catalytic folds. Short peptides and their self-organized microstructures, ranging from spherical colloids to amyloidogenic aggregates might have played a crucial role in the emergence of contemporary catalytic entities. However, the question of how short peptide fragments had functions akin to contemporary complex enzymes to catalyze cleavage and formation of highly stable peptide bonds that constitute the backbone of all proteins remains an unresolved yet fundamentally important question in terms of the origins of enzymes. We report short-peptide-based spherical assemblies that demonstrated residue-specific cleavage and formation of peptide bonds of diverse peptide-based substrates under aqueous environment. Despite the short sequence length, the assemblies utilized the synergistic collaboration of four residues which included the catalytic triad of extant serine proteases with a nonproteinogenic amino acid (quinone moiety), to facilitate proteolysis, ligation, and a three-step (hydrolysis-ligation-hydrolysis) cascade. Such short-peptide-based catalytic assemblies argue for their candidacy as the earliest protein folds and open up avenues for biotechnological applications.

Lutetium texaphyrin: A photocatalyst that triggers pyroptosis via biomolecular photoredox catalysis.

Photon-controlled pyroptosis activation (PhotoPyro) is a promising technique for cancer immunotherapy due to its noninvasive nature, precise control, and ease of operation. Here, we report that biomolecular photoredox catalysis in cells might be an important mechanism underlying PhotoPyro. Our findings reveal that the photocatalyst lutetium texaphyrin (MLu) facilitates rapid and direct photoredox oxidation of nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and various amino acids, thereby triggering pyroptosis through the caspase 3/GSDME pathway. This mechanism is distinct from the well-established role of MLu as a photodynamic therapy sensitizer in cells. Two analogs of MLu, bearing different coordinated central metal cations, were also explored as controls. The first control, gadolinium texaphyrin (MGd), is a weak photocatalyst but generates reactive oxygen species (ROS) efficiently. The second control, manganese texaphyrin (MMn), is ineffective as both a photocatalyst and a ROS generator. Neither MGd nor MMn was found to trigger pyroptosis under the conditions where MLu was active. Even in the presence of a ROS scavenger, treating MDA-MB-231 cells with MLu at concentrations as low as 50 nM still allows for pyroptosis photo-activation. The present findings highlight how biomolecular photoredox catalysis could contribute to pyroptosis activation by mechanisms largely independent of ROS.

The smallest electrochemical bubbles.

Many of the relevant electrochemical processes in the context of catalysis or energy conversion and storage, entail the production of gases. This often implicates the nucleation of bubbles at the interface, with the concomitant blockage of the electroactive area leading to overpotentials and Ohmic drop. Nanoelectrodes have been envisioned as assets to revert this effect, by inhibiting bubble formation. Experiments show, however, that nanobubbles nucleate and attach to nanoscale electrodes, imposing a limit to the current, which turns out to be independent of size and applied potential in a wide range from 3 nm to tenths of microns. Here we investigate the potential-current response for disk electrodes of diameters down to a single-atom, employing molecular simulations including electrochemical generation of gas. Our analysis reveals that nanoelectrodes of 1 nm can offer twice as much current as that delivered by electrodes with areas four orders of magnitude larger at the same bias. This boost in the extracted current is a consequence of the destabilization of the gas phase. The grand potential of surface nanobubbles shows they can not reach a thermodynamically stable state on supports below 2 nm. As a result, the electroactive area becomes accessible to the solution and the current turns out to be sensitive to the electrode radius. In this way, our simulations establish that there is an optimal size for the nanoelectrodes, in between the single-atom and ∼3 nm, that optimizes the gas production.

Switching of electrochemical selectivity due to plasmonic field-induced dissociation.

Electrochemical reactivity is known to be dictated by the structure and composition of the electrocatalyst-electrolyte interface. Here, we show that optically generated electric fields at this interface can influence electrochemical reactivity insofar as to completely switch reaction selectivity. We study an electrocatalyst composed of gold-copper alloy nanoparticles known to be active toward the reduction of CO2 to CO. However, under the action of highly localized electric fields generated by plasmonic excitation of the gold-copper alloy nanoparticles, water splitting becomes favored at the expense of CO2 reduction. Real-time time-dependent density functional tight binding calculations indicate that optically generated electric fields promote transient-hole-transfer-driven dissociation of the O─H bond of water preferentially over transient-electron-driven dissociation of the C─O bond of CO2. These results highlight the potential of optically generated electric fields for modulating pathways, switching reactivity on/off, and even directing outcomes.