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Journal article

How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-form Trypanosoma brucei cell

Authors : Nascimento, Janaina F. (2023)

ATP hydrolysis is required for the synthesis, transport and polymerization of monomers for 25 macromolecules as well as for the assembly of the latter into cellular structures. Other 26 cellular processes not directly related to synthesis of biomass, such as maintenance of 27 membrane potential and cellular shape, also require ATP. The unicellular flagellated 28 parasite Trypanosoma brucei has a complex digenetic life cycle. The primary...

Journal article

An intramolecular bivalent degrader glues an intrinsic BRD4-DCAF16 interaction

Authors : Hsia, Oliver (2023)

Targeted protein degradation is a drug modality represented by compounds that recruit a target to an E3 ubiquitin ligase to promote target ubiquitination and proteasomal degradation. Historically, the field distinguishes monovalent degraders from bifunctional degraders (PROTACs) that connect target and ligase via separate binding ligands joined via a linker1-4. Here, we elucidate the mechanism of action of a PROTAC-like degrader of the transcription...

Journal article

Nanocontainer derived from silkworm carotenoprotein for carotenoid extraction and presentation in biotechnology and biomedical applications

Authors : Sluchanko, Nikolai N. (2023)

Found in many organisms, soluble carotenoproteins are considered as antioxidant 29 nanocarriers for biomedical applications, although the structural basis for their carotenoid 30 transfer function, a prerequisite for rational bioengineering, is largely unknown. We report 31 crystal structures of the Carotenoid-Binding Protein from Bombyx mori (BmCBP) in apo- and 32 zeaxanthin (ZEA)-bound forms. We use spectroscopy and calorimetry to characterize how 33&#...

Journal article

Studies in CRISPR-generated Mediterranean G6PD variant rats reveal G6PD orchestrates genome-wide DNA methylation and gene expression in vascular wall

Authors : Signoretti, Christina (2023)

Recent advances have revealed the importance of epigenetic modifications to gene regulation and transcriptional activity. DNA methylation, a determinant of genetic imprinting and de novo silencing of genes genome-wide, is known to be controlled by DNA methyltransferases (DNMT) and demethylases (TET) under disease conditions. However, the mechanism(s)/factor(s) influencing the expression and activity of DNMTs and TETs, and thus DNA methylation, in he...

Journal article

Mouse tissue harvest-induced hypoxia rapidly alters the in vivo metabolome, between-genotype metabolite level differences, and 13C-tracing enrichments

Authors : Rauckhorst, Adam J. (2023)

Metabolism is potently regulated by oxygen as the terminal acceptor of the electron transport chain. Thus, a challenge for capturing the in vivo metabolome of animal tissues is to achieve rapid freezing after dissection-induced loss of perfusion before the onset of hypoxia-driven metabolomic remodeling. However, the timing of the metabolomic changes elicited by post-dissection freezing delays are not well described. We addressed this problem by&...

Journal article

Beyond the Active Site: The addition of a remote loop reveals a new complex biological function for chitinase enzymes

Authors : Kozome, Dan (2023)

Loops are small secondary structural elements that play a crucial role in the emergence of new 14 enzyme functions. However, our understanding of loop functions is mainly limited to the 15 catalytic loops. To understand the function of remote loops in enzymes, we studied Glycoside 16 hydrolase family 19 (GH19) chitinase - an essential enzyme family for pathogen degradation 17 in plants. By revealing the evolutionary history and loops appearance...

Journal article

Neural coding of temperature with a DNA-based spiking chemical neuron

Authors : Dauzier, N. Lobato- (2023)

Complex organisms perceive their surroundings with sensory neurons which encode physical stimuli into spikes of electrical activities. The past decade has seen reports of DNA-based chemical neurons that mimic artificial neural networks with chemical reactions. Yet, they lack the physical sensing and temporal coding of sensory biological neurons. Here we report a thermosensory chemical neuron based on DNA and enzymes that spikes with chemical act...

Journal article

Nucleic acid quantification with amplicon yield in recombinase polymerase amplification

Authors : Roy, Rahul (2023)

Amplification-based qPCR provides accurate and sensitive nucleic acid quantification. However, the requirement of temperature cycling and real-time monitoring limits its translation to different settings. Here, we adapted isothermal Recombinase Polymerase Amplification (RPA) reaction to develop a semi-quantitative method that relies on final amplicon yield to estimate initial target nucleic acid copy number. To achieve this, we developed a phenomenological model&#...

Journal article

Diverse Phosphoserine Phosphatases Exhibit Maximum Activity at an Intermediate Binding Affinity in Accord with the Sabatier Principle of Catalysis

Authors : Chiba, Yoko (2023)

A unified framework to rationalize enzymatic activity is essential to understand cellular function and metabolic evolution. Recent studies have shown that the activity of several hydrolases is maximized when the substrate binding affinity (Michaelis-Menten constant:) is neither too strong nor too weak. This is because an intermediate resolves the trade-off between, in accord with the Sabatier principle of artificial catalysis. However, it remains unc...

Journal Article

Site-Specific Introduction of Alanines for the NMR Investigation of Low-Complexity Regions and Large Biomolecular Assemblies

Authors : Elena-Real, Carlos A. (2023)

NMR studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning signals to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. We have d...

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