Lack Of Catalytic Activity Research Articles

Anhydride Photolysis on a Semiconductor Surface

The on-surface synthesis (OSS) method has facilitated the growth of diverse carbon-based nanomaterials, with the goal of integrating them into electronic devices. However, the reliance on metallic substrates in OSS restricts these materials' applications, necessitating strategies for transferring these materials into technological relevant substrates or direct synthesis on non-metallic surfaces, where the low absorption energies and lack of catalytic activity from the substrate complicate this approach. Addressing these limitations, we explore on-surface photochemistry as an alternative to thermally induced reactions, enabling controlled chemical processes at lower temperatures. While prior works have demonstrated light-induced reactions on metallic surfaces, where the hot electrons photogenerated from the metallic surface play a crucial role, synthesizing nanostructures directly on semiconducting or insulating surfaces through a purely intramolecular energy absorption remains challenging.The photolysis and pyrolysis of anhydrides has proven to be a suitable approach for the formation of arynes, as schematically shown in the Figure. Our study focuses on the selective photodissociation of maleic anhydride-containing precursors on a semiconductor surface (SnSe), unveiling their distinct photochemical behaviors. Specifically, tetraphenylphthalic anhydride (TPPA) undergoes successful photolysis on SnSe, forming tetraphenyl benzyne (TPBY) intermediates, and eventually, tetraphenyl benzene (TPBE) products. Furthermore, TPPA photolysis occurs efficiently also at room temperature, leading to the direct formation of TPBE. Contrastingly, benzo[ghi]perylene-1,2-dicarboxylic anhydride (BPA) possesses an extended pi-conjugated backbone and exhibits no photoactivity upon irradiation on the same semiconductor surface. Our calculations of TPPA and BPA excited states predict different behaviors, demonstrating the relationship between molecular structure, pi-conjugation, and photochemical reactivity, offering insights into the design principles for light-induced reactions on inert surfaces. Figure 1

The Therapeutic Significance of HER3 in Non-small Cell Lung Cancer (NSCLC): A Review Study.

HER3 (Human Epidermal Growth Factor Receptor 3) is frequently overexpressed in various cancers, including non-small cell lung cancer (NSCLC), with a prevalence of 83% in primary tumors. Its involvement in tumorigenesis and resistance to targeted therapies makes HER3 a promising target for cancer treatment. Despite being initially considered "undruggable" due to its lack of catalytic activity, significant progress has been made in the development of anti-HER3 therapeutics. Monoclonal antibodies such as lumretuzumab, seribantumab, and patritumab have shown potential in targeting HER3 to overcome resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). Additionally, antibody-drug conjugates (ADCs) like HER3-DXd (patritumab deruxtecan) are new drug candidates that have demonstrated selective delivery of cytotoxic chemicals to NSCLC cells by exploiting HER3's widespread expression, minimizing cytotoxicity. This review aims to evaluate the efficacy of current HER3 therapeutics in development and their therapeutic potential in NSCLC, incorporating evidence from clinical trials.

A Novel Catalytically Inactive Construct of Botulinum Neurotoxin A (BoNT/A) Directly Inhibits Visceral Sensory Signalling.

Botulinum neurotoxin A (BoNT/A) is a potent neurotoxin that silences cholinergic neurotransmission through the cleavage of the synaptic protein SNAP-25. Previous studies have shown that, in addition to its paralytic effects, BoNT/A can inhibit sensory nerve activity. The aim of this study was to identify how BoNT/A inhibits afferent signalling from the bladder. To investigate the role of SNAP-25 cleavage in the previously reported BoNT/A-dependent inhibition of sensory signalling, we developed a recombinant form of BoNT/A with an inactive light chain, rBoNT/A (0), unable to paralyse muscle. We also developed recombinant light chain (LC)-domain-only proteins to better understand the entry mechanisms, as the heavy chain (HC) of the protein is responsible for the internalisation of the light chain. We found that, despite a lack of catalytic activity, rBoNT/A (0) potently inhibited the afferent responses to bladder distension to a greater degree than catalytically active rBoNT/A. This was also clear from the testing of the LC-only proteins, as the inactive rLC/A (0) protein inhibited afferent responses significantly more than the active rLC/A protein. Immunohistochemistry for cleaved SNAP-25 was negative, and purinergic and nitrergic antagonists partially and totally reversed the sensory inhibition, respectively. These data suggest that the BoNT/A inhibition of sensory nerve activity in this assay is not due to the classical well-characterised 'double-receptor' mechanism of BoNT/A, is independent of SNAP25 cleavage and involves nitrergic and purinergic signalling mechanisms.

Low-field 2D NMR relaxation and DRIFTS studies of glucose isomerization in zeolite Y: New insights into adsorption effects on catalytic performance

Sn and Ga doped zeolite Y catalysts were tested for the isomerization of glucose to fructose carried out in different solvents (water, methanol and ethanol). Therein, ethanol favoured a Lewis acid site catalyzed pathway that promotes glucose isomerization to fructose, whereas methanol resulted in an equal distribution of products (mannose, fructose and alkyl fructoside). In contrast, the catalysts were totally inactive in water solvent. NMR relaxation measurements, including solvent displacement experiments, suggested that the lack of catalytic activity in water is due to the strong adsorption of this solvent within the zeolite pores blocking reactants from the Lewis acid sites active for the sugar isomerization. In comparison, ethanol adsorbs relatively more strongly than methanol, hence is retained in the pores where solvated fructose is preferentially prevented from the further reaction on Brønsted acid sites situated outside of the pore space. NMR relaxation measurements using pyridine and tetrahydrofuran (THF) and pyridine-DRIFTS measurements suggest metal doping had little effect on the overall relative acid strength of the zeolites but resulted in zeolites with increased Lewis acid strength relative to the non-doped zeolites. The results reported provide direct experimental evidence on the importance of adsorption properties of solvents within zeolites used for glucose to fructose isomerization and may serve as a starting point for a new approach towards designing and optimizing such catalytic systems.

On the use of 17O NMR for understanding molecular and silica-grafted tungsten oxo siloxide complexes.

17O-labelled tungsten siloxide complexes [WOCl2(OSitBu3)2] (1-Cl) and [WOMe2(OSitBu3)2] (1-Me) were prepared and characterized by 17O MAS NMR, with input from theoretical calculations of NMR parameters. Guidelines linking 17O NMR parameters and the coordination sphere of molecular and silica-grafted tungsten oxo species are proposed. The grafting of 1-Me on SiO2-700 afforded material 2, with surface species [(SiO)WOMe2(OSitBu3)] as shown by elemental analysis, IR and 1H and 13C MAS NMR. The DFT calculations of the grafting mechanism are in line with the observed reactivity. They indicate the occurrence of several isomeric species of close energy for the grafted W centers, precluding efficient 17O MAS NMR studies. The lack of catalytic activity in olefin metathesis and ring-opening olefin metathesis polymerization indicates that initiation by α-H elimination is not operative in 2, contrary to related tungsten surface species, which illustrates the crucial influence of the nature of the metal coordination sphere.

Role of introduced Se element and induced anion vacancies in Mo(SSe)2-x/G van der Waals heterostructure for enhanced hydrogen evolution reaction

The Gibbs free energy of hydrogen adsorption at the edge of molybdenum disulfide (MoS2) is close to that of Pt, meaning that MoS2 is the best candidate to replace Pt-based materials. However, easy agglomeration between layers to mask active sites, lack of catalytic activity in the basal planes, and poor electronic conductivity make MoS2 exhibit dissatisfactory hydrogen evolution reaction (HER) catalytic performance. Here, we successfully construct a van der Waals heterostructure stacked alternately with Mo(SSe)2-x and graphene (Mo(SSe)2-x/G) to enhance its catalytic ability. The introduction of Se into MoS2 and the thermal treatment induce the sample to generate more anion vacancies. Theoretical and experimental results demonstrate the constructed van der Waals heterostructure, the introduced Se element, and the increased anion vacancies are in favor of promoting the number of active sites and improving the electronic conductivity of the catalyst. Therefore, Mo(SSe)2-x/G exhibits superior HER catalytic performance (the overpotentials of 137 mV and 136 mV at a current of 10 mA cm−2) and long-term stabilities (>90 h and 140 h at a current density of 20 mA cm−2) in both acidic and alkaline media.

New insights into the molecular mechanisms of ROR1, ROR2, and PTK7 signaling from the proteomics and pharmacological modulation of ROR1 interactome

ROR1, ROR2, and PTK7 are Wnt ligand-binding members of the receptor tyrosine kinase family. Despite their lack of catalytic activity, these receptors regulate skeletal, cardiorespiratory, and neurological development during embryonic and fetal stages. However, their overexpression in adult tissue is strongly connected to tumor development and metastasis, suggesting a strong pharmacological potential for these molecules. Wnt5a ligand can activate these receptors, but lead to divergent signaling and functional outcomes through mechanisms that remain largely unknown. Here, we developed a cellular model by stably expressing ROR1, ROR2, and PTK7 in BaF3 cells that allowed us to readily investigate side-by-side their signaling capability and functional outcome. We applied proteomic profiling to BaF3 clones and identified distinctive roles for ROR1, ROR2, and PTK7 pseudokinases in modulating the expression of proteins involved in cytoskeleton dynamics, apoptotic, and metabolic signaling. Functionally, we show that ROR1 expression enhances cell survival and Wnt-mediated cell proliferation, while ROR2 and PTK7 expression is linked to cell migration. We also demonstrate that the distal C-terminal regions of ROR1 and ROR2 are required for receptors stability and downstream signaling. To probe the pharmacological modulation of ROR1 oncogenic signaling, we used affinity purification coupled to mass spectrometry (AP-MS) and proximity-dependent biotin identification (BioID) to map its interactome before and after binding of GZD824, a small molecule inhibitor previously shown to bind to the ROR1 pseudokinase domain. Our findings bring new insight into the molecular mechanisms of ROR1, ROR2, and PTK7, and highlight the therapeutic potential of targeting ROR1 with small molecule inhibitors binding to its vestigial ATP-binding site.

Structural basis for signaling by the HER3 pseudokinase receptor

The Human Epidermal Growth Factor Receptor 3 (HER3) is a pseudokinase receptor which contains a catalytically inactive kinase domain in its intracellular region. Despite lack of catalytic activity, HER3 is an essential signaling receptor serving as an allosteric activator of other HER receptors (EGFR and HER2), and a potent scaffold for recruitment an activation of PI3K. To form an active complex, HER3 and the orphan receptor HER2 assemble into a singly liganded, pro‐oncogenic heterocomplex upon binding to the HER3 ligand neuregulin‐1b (NRG1b). In the absence of structures of the HER2/HER3 heterodimer, the mechanism by which HER2 and HER3 interact upon ligand binding remains unknown. We isolated the near full‐length HER2/HER3 heterocomplex with their growth factor neuregulin (NRG) and obtained a 2.9Å cryo‐EM reconstruction of the extracellular domain module. We discovered an unexpected dynamics at the HER2/HER3 dimerization interface, which is exploited by oncogenic mutations and known therapeutics targeting HER2 – such as trastuzumab. The unique features of the NRG‐bound HER2/HER3 heterodimer underscore an allosteric connection between the ligand‐binding pocket and the dimerization interface, and explain why extracellular domains of unliganded HER2 do not homo‐associate via canonical active dimer interfaces.

CRISPR deletions in cell lines for reconstitution studies of pseudokinase function.

The non-catalytic cousins of protein kinases, the pseudokinases, have grown to prominence as indispensable signaling entities over the past decade, despite their lack of catalytic activity. Because their importance has only been fully embraced recently, many of the 10% of the human kinome categorized as pseudokinases are yet to be attributed biological functions. The advent of CRISPR-Cas9 editing to genetically delete pseudokinases in a cell line of interest has proven invaluable to dissecting many functions and remains the method of choice for gene knockout. Here, using the terminal effector pseudokinase in the necroptosis cell death pathway, MLKL, as an exemplar, we describe a method for genetic knockout of pseudokinases in cultured cells. This method does not retain the CRISPR guide sequence in the edited cells, which eliminates possible interference in subsequent reconstitution studies where mutant forms of the pseudokinase can be reintroduced into cells exogenously for detailed mechanistic characterization.

Catalytic activity of Co(II) Salen@KCC-1 on the synthesis of 2,4,5-triphenyl-1H-imidazoles and benzimidazoles

The synthesis, reactions and biological properties of imidazoles and benzimidazole make up the bulk of the ring chemistry. In this study, the reaction between different types of aromatic aldehydes and ammonium acetate with diphenylethanedione, in ethanol solvent, using the Co(II) Salen complex@KCC-1 catalyst which is produced from Co (II) complex which is supported onto the KCC-1 was studied. The results showed that the products were synthesized in good to excellent yields. The products were identified with IR and NMR spectroscopy. Also, the catalyst was identified by FT-IR, TGA, TEM, and XRD. Finally, the catalyst was reused several times without lack of catalytic activity.

Characterization and assembly of the Pseudomonas aeruginosa aspartate transcarbamoylase-pseudo dihydroorotase complex.

Pseudomonas aeruginosa is a virulent pathogen that has become more threatening with the emergence of multidrug resistance. The aspartate transcarbamoylase (ATCase) of this organism is a dodecamer comprised of six 37 kDa catalytic chains and six 45 kDa chains homologous to dihydroorotase (pDHO). The pDHO chain is inactive but is necessary for ATCase activity. A stoichiometric mixture of the subunits associates into a dodecamer with full ATCase activity. Unlike other known ATCases, the P. aeruginosa catalytic chain does not spontaneously assemble into a trimer. Chemical-crosslinking and size-exclusion chromatography showed that P. aeruginosa ATCase is monomeric which accounts for its lack of catalytic activity since the active site is a composite comprised of residues from adjacent monomers in the trimer. Circular dichroism spectroscopy indicated that the ATCase chain adopts a structure that contains secondary structure elements although neither the ATCase nor the pDHO subunits are very stable as determined by a thermal shift assay. Formation of the complex increases the melting temperature by about 30°C. The ATCase is strongly inhibited by all nucleotide di- and triphosphates and exhibits extreme cooperativity. Previous studies suggested that the regulatory site is located in an 11-residue extension of the amino end of the catalytic chain. However, deletion of the extensions did not affect catalytic activity, nucleotide inhibition or the assembly of the dodecamer. Nucleotides destabilized the dodecamer which probably accounts for the inhibition and apparent cooperativity of the substrate saturation curves. Contrary to previous interpretations, these results suggest that P. aeruginosa ATCase is not allosterically regulated by nucleotides.

Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach.

The universal protein knowledgebase (UniProtKB) collects and centralises functional information on proteins across a wide range of species. In addition to the functional information added to all protein entries, for enzymes, which represent 20-40% of most proteomes, UniProtKB provides additional information about Enzyme Commission classification, catalytic activity, cofactors, enzyme regulation, kinetics and pathways, all based on critical assessment of published experimental data. Computer-based analysis and structural data are used to enrich the annotation of the sequence through the identification of active sites and binding sites. While the annotation of enzymes is well-defined, the curation of pseudoenzymes in UniProtKB has highlighted some challenges: how to identify them, how to assess their lack of catalytic activity, how to annotate their lack of catalytic activity in a consistent way and how much can be inferred and propagated from experimental data obtained from other species. Through various examples, we illustrate some of these issues and discuss some of the changes we propose to enhance the annotation and discovery of pseudoenzymes. Ultimately, improving the curation of pseudoenzymes will provide the scientific community with a comprehensive resource for pseudoenzymes, which in turn will lead to a better understanding of the evolution of these molecules, the aetiology of related diseases and the development of drugs.

PARP inhibition causes premature loss of cohesion in cancer cells.

Poly(ADP-ribose) polymerases (PARPs) regulate various aspects of cellular function including mitotic progression. Although PARP inhibitors have been undergoing various clinical trials and the PARP1/2 inhibitor olaparib was approved as monotherapy for BRCA-mutated ovarian cancer, their mode of action in killing tumour cells is not fully understood. We investigated the effect of PARP inhibition on mitosis in cancerous (cervical, ovary, breast and osteosarcoma) and non-cancerous cells by live-cell imaging. The clinically relevant inhibitor olaparib induced strong perturbations in mitosis, including problems with chromosome alignment at the metaphase plate, anaphase delay, and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest, resulting in sister chromatid scattering. PARP1 and PARP2 depletion suppressed the phenotype while PARP2 overexpression enhanced it, suggesting that olaparib-bound PARP1 and PARP2 rather than the lack of catalytic activity causes this phenotype. Olaparib-induced mitotic chromatid scattering was observed in various cancer cell lines with increased protein levels of PARP1 and PARP2, but not in non-cancer or cancer cell lines that expressed lower levels of PARP1 or PARP2. Interestingly, the sister chromatid scattering phenotype occurred only when olaparib was added during the S-phase preceding mitosis, suggesting that PARP1 and PARP2 entrapment at replication forks impairs sister chromatid cohesion. Clinically relevant DNA-damaging agents that impair replication progression such as topoisomerase inhibitors and cisplatin were also found to induce sister chromatid scattering and metaphase plate alignment problems, suggesting that these mitotic phenotypes are a common outcome of replication perturbation.

Expression of inactive glutathione peroxidase 4 leads to embryonic lethality, and inactivation of the Alox15 gene does not rescue such knock-in mice.

Glutathione peroxidases (Gpx) and lipoxygenases (Alox) are functional counterplayers in the metabolism of hydroperoxy lipids that regulate cellular redox homeostasis. Gpx4 is a moonlighting protein that has been implicated not only as an enzyme in anti-oxidative defense, gene expression regulation, and programmed cell death, but also as a structural protein in spermatogenesis. Homozygous Gpx4 knock-out mice are not viable, but molecular reasons for intrauterine lethality are not completely understood. This study was aimed at investigating whether the lack of catalytic activity or the impaired function as structural protein is the dominant reason for embryonic lethality. We further explored whether the pro-oxidative enzyme mouse 12/15 lipoxygenase (Alox15) plays a major role in embryonic lethality of Gpx4-deficient mice. To achieve these goals, we first created knock-in mice, which express a catalytically inactive Gpx4 mutant (Sec46Ala). As homozygous Gpx4-knock-out mice Sec46Ala-Gpx4(+/+) knock-in animals are not viable but undergo intrauterine resorption between embryonic day 6 and 7 (E6-7). In contrast, heterozygous knock-in mice (Sec46Ala-Gpx4(-/+)) are viable, fertile and do not show major phenotypic alterations. Interestingly, homozygous Alox15 deficiency did not rescue the U46A-Gpx4(+/+) mice from embryonic lethality. In fact, when heterozygous U46A-Gpx4(-/+) mice were stepwise crossed into an Alox15-deficent background, no viable U46A-Gpx4(+/+)+Alox15(-/-) individuals were obtained. However, we were able to identify U46A-Gpx4(+/+)+Alox15(-/-) embryos in the state of resorption around E7. These data suggest that the lack of catalytic activity is the major reason for the embryonic lethality of Gpx4(-/-) mice and that systemic inactivation of the Alox15 gene does not rescue homozygous knock-in mice expressing catalytically silent Gpx4.

Membrane Association of the PTEN Tumor Suppressor: Molecular Details of the Protein-Membrane Complex from SPR Binding Studies and Neutron Reflection

The structure and function of the PTEN phosphatase is investigated by studying its membrane affinity and localization on in-plane fluid, thermally disordered synthetic membrane models. The membrane association of the protein depends strongly on membrane composition, where phosphatidylserine (PS) and phosphatidylinositol diphosphate (PI(4,5)P2) act pronouncedly synergistic in pulling the enzyme to the membrane surface. The equilibrium dissociation constants for the binding of wild type (wt) PTEN to PS and PI(4,5)P2 were determined to be Kd∼12 µM and 0.4 µM, respectively, and Kd∼50 nM if both lipids are present. Membrane affinities depend critically on membrane fluidity, which suggests multiple binding sites on the protein for PI(4,5)P2. The PTEN mutations C124S and H93R show binding affinities that deviate strongly from those measured for the wt protein. Both mutants bind PS more strongly than wt PTEN. While C124S PTEN has at least the same affinity to PI(4,5)P2 and an increased apparent affinity to PI(3,4,5)P3, due to its lack of catalytic activity, H93R PTEN shows a decreased affinity to PI(4,5)P2 and no synergy in its binding with PS and PI(4,5)P2. Neutron reflection measurements show that the PTEN phosphatase “scoots" along the membrane surface (penetration <5 Å) but binds the membrane tightly with its two major domains, the C2 and phosphatase domains, as suggested by the crystal structure. The regulatory C-terminal tail is most likely displaced from the membrane and organized on the far side of the protein, ∼60 Å away from the bilayer surface, in a rather compact structure. The combination of binding studies and neutron reflection allows us to distinguish between PTEN mutant proteins and ultimately may identify the structural features required for membrane binding and activation of PTEN.

Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases

Prolyl-tRNA synthetases (ProRSs) have been shown to activate both cognate and some noncognate amino acids and attach them to specific tRNA(Pro) substrates. For example, alanine, which is smaller than cognate proline, is misactivated by Escherichia coli ProRS. Mischarged Ala-tRNA(Pro) is hydrolyzed by an editing domain (INS) that is distinct from the activation domain. It was previously shown that deletion of the INS greatly reduced cognate proline activation efficiency. In this study, experimental and computational approaches were used to test the hypothesis that deletion of the INS alters the internal protein dynamics leading to reduced catalytic function. Kinetic studies with two ProRS variants, G217A and E218A, revealed decreased amino acid activation efficiency. Molecular dynamics studies showed motional coupling between the INS and protein segments containing the catalytically important proline-binding loop (PBL, residues 199-206). In particular, the complete deletion of INS, as well as mutation of G217 or E218 to alanine, exhibited significant effects on the motion of the PBL. The presence of coupled dynamics between neighboring protein segments was also observed through in silico mutations and essential dynamics analysis. Altogether, this study demonstrates that structural elements at the editing domain-activation domain interface participate in coupled motions that facilitate amino acid binding and catalysis by bacterial ProRSs, which may explain why truncated or defunct editing domains have been maintained in some systems, despite the lack of catalytic activity.

Alterations at Dispersed Sites Cause Phosphorylation and Activation of SNF1 Protein Kinase during Growth on High Glucose

The SNF1/AMP-activated protein kinases are central energy regulators in eukaryotes. SNF1 of Saccharomyces cerevisiae is inhibited during growth on high levels of glucose and is activated in response to glucose depletion and other stresses. Activation entails phosphorylation of Thr(210) on the activation loop of the catalytic subunit Snf1 by Snf1-activating kinases. We have used mutational analysis to identify Snf1 residues that are important for regulation. Alteration of Tyr(106) in the αC helix or Leu(198) adjacent to the Asp-Phe-Gly motif on the activation loop relieved glucose inhibition of phosphorylation, resulting in phosphorylation of Thr(210) during growth on high levels of glucose. Substitution of Arg for Gly(53), at the N terminus of the kinase domain, increased activation on both high and low glucose. Alteration of the ubiquitin-associated domain revealed a modest autoinhibitory effect. Previous studies identified alterations of the Gal83 (β) and Snf4 (γ) subunits that relieve glucose inhibition, and we have here identified a distinct set of Gal83 residues that are required. Together, these results indicate that alterations at dispersed sites within each subunit of SNF1 cause phosphorylation of the kinase during growth on high levels of glucose. These findings suggest that the conformation of the SNF1 complex is crucial to maintenance of the inactive state during growth on high glucose and that the default state for SNF1 is one in which Thr(210) is phosphorylated and the kinase is active.

Poly(ADP-Ribose) Regulates Stress Responses and MicroRNA Activity in the Cytoplasm

Poly(ADP-ribose) is a major regulatory macromolecule in the nucleus, where it regulates transcription, chromosome structure, and DNA damage repair. Functions in the interphase cytoplasm are less understood. Here, we identify a requirement for poly(ADP-ribose) in the assembly of cytoplasmic stress granules, which accumulate RNA-binding proteins that regulate the translation and stability of mRNAs upon stress. We show that poly(ADP-ribose), six specific poly(ADP-ribose) polymerases, and two poly(ADP-ribose) glycohydrolase isoforms are stress granule components. A subset of stress granule proteins, including microRNA-binding Argonaute family members Ago1-4, are modified by poly(ADP-ribose), and such modification increases upon stress, a condition when both microRNA-mediated translational repression and microRNA-directed mRNA cleavage are relieved. Similar relief of repression is also observed upon overexpression of specific poly(ADP-ribose) polymerases or, conversely, upon knockdown of glycohydrolase. We conclude that poly(ADP-ribose) is a key regulator of posttranscriptional gene expression in the cytoplasm.

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems

The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts. The RNA world hypothesis, however, posits that, at the earlier stages of evolution, RNA acted as both template and catalyst. Why would such division of labor evolve in the RNA world? We investigated the evolution of DNA-like molecules, i.e. molecules that can function only as template, in minimal computational models of RNA replicator systems. In the models, RNA can function as both template-directed polymerase and template, whereas DNA can function only as template. Two classes of models were explored. In the surface models, replicators are attached to surfaces with finite diffusion. In the compartment models, replicators are compartmentalized by vesicle-like boundaries. Both models displayed the evolution of DNA and the ensuing division of labor between templates and catalysts. In the surface model, DNA provides the advantage of greater resistance against parasitic templates. However, this advantage is at least partially offset by the disadvantage of slower multiplication due to the increased complexity of the replication cycle. In the compartment model, DNA can significantly delay the intra-compartment evolution of RNA towards catalytic deterioration. These results are explained in terms of the trade-off between template and catalyst that is inherent in RNA-only replication cycles: DNA releases RNA from this trade-off by making it unnecessary for RNA to serve as template and so rendering the system more resistant against evolving parasitism. Our analysis of these simple models suggests that the lack of catalytic activity in DNA by itself can generate a sufficient selective advantage for RNA replicator systems to produce DNA. Given the widespread notion that DNA evolved owing to its superior chemical properties as a template, this study offers a novel insight into the evolutionary origin of DNA.

Mechanism of substrate specificity in 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases

5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.