A fundamental problem in computational biophysics is to deduce the function of a protein
from the structure. Many biological macromolecules such as enzymes, molecular motors or …

Enzymatic mechanisms are typically inferred from structural data. However, understanding
enzymes require unravelling the intricate dynamic interplay between dynamics …

There has been an explosive growth in the applications of AlphaFold2, and other structure
prediction platforms, to accurately predict protein structures from a multiple sequence …

The histidine-phosphorylatable phosphocarrier protein (HPr) is an essential component of
the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent …

Motivation Molecular dynamics (MD) simulations have become routine tools for the study of
protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse …

Molecular dynamics (MD) simulations are frequently used to elucidate the molecular
mechanisms underlying protein behavior. Based on a conformational search with MD …

Macromolecular crowding, inside the physiological interior, modulates the energy landscape
of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special …

Adenylate kinase (AK, EC 2.7. 4.3) is a ubiquitous phosphotransferase which catalyzes the
reversible transfer of high-energy β-and γ-phosphate groups between nucleotides. All …

The enzyme adenylate kinase (ADK) features two substrate binding domains that undergo
large-scale motions during catalysis. In the apo state, the enzyme preferentially adopts a …

Adenylate kinase (ADK) catalyzes the reversible Mg2+‐dependent phosphoryl transfer
reaction Mg2++ 2ADP↔ Mg2++ ATP+ AMP in essential cellular systems. This reaction is a …