Structure and function of haemoglobins

Blood Cells Molecules and Diseases, Journal Year: 2017, Volume and Issue: 70, P. 13 - 42

Published: Oct. 31, 2017

Language: Английский

---

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

Nature Methods, Journal Year: 2017, Volume and Issue: 14(4), P. 443 - 449

Published: Feb. 27, 2017

Language: Английский

---

Archaeal phospholipids: Structural properties and biosynthesis

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Journal Year: 2016, Volume and Issue: 1862(11), P. 1325 - 1339

Published: Dec. 20, 2016

Language: Английский

---

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Science Advances, Journal Year: 2022, Volume and Issue: 8(2)

Published: Jan. 14, 2022

[Figure: see text].

Language: Английский

---

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 21, 2023

Abstract Recent advances in AI-based protein structure modeling have yielded remarkable progress predicting structures. Since structures are constrained by their biological function, geometry tends to evolve more slowly than the underlying amino acids sequences. This feature of could principle be used reconstruct phylogenetic trees over longer evolutionary timescales sequence-based approaches, but until now a reliable structure-based tree building method has been elusive. Here, we demonstrate that structure-informed phylogenies can outperform sequence-only ones not only for distantly related proteins also, remarkably, closely ones. is achieved inferring from using local structural alphabet, an approach robust conformational changes confound traditional distance measures. As illustration, decipher diversification particularly challenging family: fast-evolving RRNPPA quorum sensing receptors enabling gram-positive bacteria, plasmids and bacteriophages communicate coordinate key behaviors such as sporulation, virulence, antibiotic resistance, conjugation or phage lysis/lysogeny decision. The advent high-accuracy phylogenetics enables myriad applications across biology, uncovering deeper relationships, elucidating unknown functions, refining design bioengineered molecules.

Language: Английский

---

Chlorophyll Degradation and its Physiological Function

Plant and Cell Physiology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 22, 2024

Research on chlorophyll degradation has progressed significantly in recent decades. In the 1990s, structure of linear tetrapyrrole, which is unambiguously a product, was determined. From 2000s until 2010s, major enzymes involved were identified, and pheophorbide oxygenase/phyllobilin pathway established. This encompasses several steps: (1) initial conversion b to 7-hydroxymethyl a; (2) (3) dechelation pheophytin (4) dephytylation (5) opening macrocycle yield red catabolite; (6) catabolite phyllobilins. converts potentially harmful into safe molecules phyllobilins, are stored central vacuole terrestrial plants. The expression chlorophyll-degrading mediated by various transcription factors influenced light conditions, stress, plant hormones. Chlorophyll differently regulated different organs developmental stages initiation induces further enzymes, resulting acceleration degradation. initially considered last reaction senescence; however, plays crucial roles enhancing senescence, degrading chlorophyll-protein complexes, forming photosystem II, maintaining seed quality. Therefore, controlling important agricultural applications.

Language: Английский

---

NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor

Molecular Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 18, 2025

ABSTRACT NrdR is a universal transcriptional repressor of bacterial genes coding for ribonucleotide reductases (RNRs), essential enzymes that provide DNA building blocks in all living cells. Despite its prevalence, the mechanism has been scarcely studied. We report biochemical, biophysical, and bioinformatical characterization binding sites from two major pathogens phylum Bacillota Listeria monocytogenes Streptococcus pneumoniae . consists Zn‐ribbon domain followed by an ATP‐cone domain. show it forms tetramers bind to when loaded with ATP dATP, but if only ATP, various oligomeric complexes unable DNA. The DNA‐binding site L. pair boxes separated 15–16 bp, whereas S. , are unusually long spacers 25–26 bp. This observation triggered comprehensive study four NrdRs Escherichia coli Streptomyces coelicolor series dsDNA fragments where were 12–27 vitro results confirmed vivo E. revealed binds most efficiently there integer number turns between center boxes. facilitates prediction genomes suggests conserved throughout It sheds light on RNR regulation since does not occur eukaryotes, opens way development novel antibiotics.

Language: Английский

---

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

Molecular Cell, Journal Year: 2017, Volume and Issue: 66(2), P. 206 - 220.e9

Published: April 1, 2017

Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis deoxyribonucleotide triphosphates (dNTPs). However, oxygen an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us question source dNTPs in hypoxia. Here, we show that RRM1/RRM2B retaining activity therefore favored over RRM1/RRM2 order preserve ongoing avoid accumulation damage. We found two distinct mechanisms by which RRM2B maintains hypoxic identified responsible residues RRM2B. The importance response tumor further illustrated correlation its expression with a signature patient samples roles growth radioresistance. Our data provide mechanistic insight into biology, highlighting as hypoxic-specific, anti-cancer therapeutic target.

Language: Английский

---

New tricks for the glycyl radical enzyme family

Critical Reviews in Biochemistry and Molecular Biology, Journal Year: 2017, Volume and Issue: 52(6), P. 674 - 695

Published: Sept. 13, 2017

Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles the human microbiota environment. GREs contain a backbone glycyl that is post-translationally installed, enabling radical-based mechanisms. function several metabolic pathways including mixed acid fermentation, ribonucleotide reduction anaerobic breakdown of nutrient choline pollutant toluene. By generating substrate-based species within active site, enable C-C, C-O C-N bond breaking formation steps otherwise challenging for nonradical enzymes. Identification previously unknown family members from genomic data determination structures well-characterized have expanded scope GRE-catalyzed reactions as well defined features catalysis. Here, we review mechanisms characterized GREs, classifying into five categories. We consider open questions about each GRE classes evaluate tools available to interrogate uncharacterized GREs.

Language: Английский

---

The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism

Journal of Molecular Evolution, Journal Year: 2016, Volume and Issue: 82(1), P. 17 - 26

Published: Jan. 1, 2016

The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive architecture that present in approximately 10 % of all enzymes. It generally assumed this ubiquity modern proteomes reflects an essential historical role early protein-mediated metabolism. Here, we provide quantitative and comparative analyses to support several hypotheses about the importance TIM architecture. An information theoretical analysis structures supports hypothesis could arise more easily by duplication recombination compared other mixed α/β structures. We show enzymes corresponding most taxonomically broad superfamilies also have broadest range functions, often aided metal nucleotide-derived cofactors are thought reflect earlier stage metabolic evolution. By comparison putatively ancient architectures, find functional diversity proteins cannot be explained simply their antiquity. Instead, breadth functions can explained, part, incorporation cofactors, trend does not appear shared general. These results simple functionally general may arisen evolution biosynthesis provided ideal scaffold facilitate transition from ribozymes, peptides, geochemical catalysts

Language: Английский

---