Daniel Lundin

Mutational and bioinformatic analysis of the binding site for the ribonucleotide reductase-specific transcriptional repressor NrdR

The paper tests the conservation requirements of NrdR binding site basepairs using synthetic DNA fragments and assesses binding affinity of NrdR proteins from different bacteria.

The Mycobacterium smegmatis bd-II terminal oxidase employs a 1 carboxylate shift mechanism

This study characterizes the Mycobacterium smegmatis bd-II terminal oxidase using biochemical and structural methods, revealing a 1 carboxylate shift mechanism for oxygen reduction.

nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

The path to dependence: stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses

This study examines genome evolution in diatom-Richelia symbioses, showing genome reduction and increased host dependency in endobionts compared to periplasmic and epibionts.

Bacterial transcriptional repressor NrdR - a flexiblemultifactorial nucleotide sensor

This study characterizes the structure and nucleotide-dependent binding mechanism of E. coli NrdR, revealing its flexibility in adapting to different promoter configurations.

Strong conservation of spacer lengths in NrdR repressor DNA binding sites

The paper investigates NrdR repressor DNA binding preferences across species, finding optimal spacer lengths between NrdR boxes for efficient binding.

Temperature and dissolved organic matter shape marine prokaryotic activity and gene expression in a sub-arctic sea

This study investigates how temperature and dissolved organic matter affect prokaryotic activity and gene expression in a sub-arctic sea using mesocosm experiments and metatranscriptomic analysis.

Fusion of a functional glutaredoxin to the radical-generating subunit of ribonucleotide reductase

This paper demonstrates that a fused glutaredoxin domain in F. ignava NrdB functions as a reductant for RNR via both dithiol and monothiol mechanisms, and shows the ATP-cone's role in regulating enzyme activity through dATP binding.

Unique ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit

The paper identifies an ATP-cone in the radical-generating subunit of RNRs, showing it regulates enzyme activity through quaternary structure changes and dATP-induced tetramer formation.