Magnesium induced structural reorganization in the active site of adenylate kinase

K Nam, ARA Thodika, S Tischlik, C Phoeurk… - Science …, 2024 - science.org
Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that
requires Mg2+ as an essential cofactor. While the primary function of Mg2+ is electrostatic …

[HTML][HTML] Protein dynamics: The future is bright and complicated!

K Nam, M Wolf-Watz - Structural Dynamics, 2023 - pubs.aip.org
Biological life depends on motion, and this manifests itself in proteins that display motion
over a formidable range of time scales spanning from femtoseconds vibrations of atoms at …

Dynamic connection between enzymatic catalysis and collective protein motions

P Ojeda-May, AUI Mushtaq, P Rogne, A Verma… - Biochemistry, 2021 - ACS Publications
Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical
reactions. While the role of collective protein motions in substrate binding, product release …

Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release

K Nam, AR Arattu Thodika… - Journal of Chemical …, 2023 - ACS Publications
This study explores ligand-driven conformational changes in adenylate kinase (AK), which is
known for its open-to-close conformational transitions upon ligand binding and release. By …

Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases

A Verma, E Åberg-Zingmark, T Sparrman… - Science …, 2022 - science.org
Enzymatic catalysis is critically dependent on selectivity, active site architecture, and
dynamics. To contribute insights into the interplay of these properties, we established an …

Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

P Rogne, M Rosselin, C Grundström… - Proceedings of the …, 2018 - National Acad Sciences
Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In
cases where chemically related substrates are present inside cells, robust mechanisms of …

Mechanistic basis for a connection between the catalytic step and slow opening dynamics of Adenylate Kinase

B Dulko-Smith, P Ojeda-May, J Ådén… - Journal of Chemical …, 2023 - ACS Publications
Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes
the catalytic step with the enzyme's conformational dynamics to optimize a phosphoryl …

Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus

K Ding, L Zhang, L Sun, C Lin, Q Feng, S Zhang… - … and Physiology Part D …, 2019 - Elsevier
The sea cucumber Apostichopus japonicus (Selenka) is a valuable economic species in
Southeast Asia. It has many fascinating behavioral characteristics, such as autolysis …

Cell cycle–dependent association of polo kinase Cdc5 with CENP-A contributes to faithful chromosome segregation in budding yeast

PK Mishra, G Olafsson, L Boeckmann… - Molecular Biology of …, 2019 - Am Soc Cell Biol
Evolutionarily conserved polo-like kinase, Cdc5 (Plk1 in humans), associates with
kinetochores during mitosis; however, the role of cell cycle–dependent centromeric (CEN) …

Nucleation of an Activating Conformational Change by a Cation− π Interaction

P Rogne, D Andersson, C Grundström… - Biochemistry, 2019 - ACS Publications
As a key molecule in biology, adenosine triphosphate (ATP) has numerous crucial functions
in, for instance, energetics, post-translational modifications, nucleotide biosynthesis, and …