A unifying mechanism for protein transport through the core bacterial Sec machinery
WJ Allen, I Collinson - Open Biology, 2023 - royalsocietypublishing.org
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but
they also pose a challenge: how to partition the molecules that perform biological functions …
they also pose a challenge: how to partition the molecules that perform biological functions …
Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins
M Siemers, M Lazaratos, K Karathanou… - Journal of chemical …, 2019 - ACS Publications
Membrane proteins that function as transporters or receptors must communicate with both
sides of the lipid bilayer in which they sit. This long distance communication enables …
sides of the lipid bilayer in which they sit. This long distance communication enables …
Dynamic correlations: exact and approximate methods for mutual information
K Demirtaş, B Erman, T Haliloğlu - Bioinformatics, 2024 - academic.oup.com
Motivation Proteins are dynamic entities that undergo conformational changes critical for
their functions. Understanding the communication pathways and information transfer within …
their functions. Understanding the communication pathways and information transfer within …
Dynamic water hydrogen-bond networks at the interface of a lipid membrane containing palmitoyl-oleoyl phosphatidylglycerol
K Karathanou, AN Bondar - The Journal of Membrane Biology, 2018 - Springer
Lipid membrane interfaces are complex environments that host essential cellular processes
such as binding of proteins or drug molecules. A key open question is how water molecules …
such as binding of proteins or drug molecules. A key open question is how water molecules …
The mechanism and energetics of a ligand-controlled hydrophobic gate in a mammalian two pore channel
In the last decade two-pore intracellular channels (TPCs) attracted the interest of
researchers, still some key questions remain open. Their importance for vacuolar (plants) …
researchers, still some key questions remain open. Their importance for vacuolar (plants) …
The rational modification of the secretion pathway: the bidirectional grinding strategy on signal peptide and SecA in Bacillus subtilis
Z Jiang, L Zhang, W Zhou, H Li, Y Li, W Qin… - Biochemical …, 2023 - Elsevier
The secretory (Sec) pathway is essential for protein translocation in Bacillus subtilis. In
contrast to signal peptides (SPs), the key components of the Sec pathway lack excessive …
contrast to signal peptides (SPs), the key components of the Sec pathway lack excessive …
Using graphs of dynamic hydrogen-bond networks to dissect conformational coupling in a protein motor
K Karathanou, AN Bondar - Journal of Chemical Information and …, 2019 - ACS Publications
DExD/H-box proteins are soluble enzymes that couple binding and hydrolysis of adenosine
triphosphate (ATP) with reactions involving RNA metabolism or bind and push newly …
triphosphate (ATP) with reactions involving RNA metabolism or bind and push newly …
Dynamic hydrogen-bond networks in bacterial protein secretion
K Karathanou, AN Bondar - FEMS microbiology letters, 2018 - academic.oup.com
The Sec protein secretion machinery includes proteins whose reaction coordinates involve
large-scale conformational changes. Dynamic hydrogen-bond networks can provide …
large-scale conformational changes. Dynamic hydrogen-bond networks can provide …
Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines
Disaggregation and microtubule-severing nanomachines from the AAA+ (ATPases
associated with various cellular activities) superfamily assemble into ring-shaped hexamers …
associated with various cellular activities) superfamily assemble into ring-shaped hexamers …
Molecular dynamics of DNA translocation by FtsK
The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA
during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA …
during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA …