Bond PJ
Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein
Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation.
ReadA second shell residue modulates a conserved ATP-binding site with radically different affinities for ATP
Prediction of ligand binding and design of new function in enzymes is a time-consuming and expensive process. Crystallography gives the impression that proteins adopt a fixed shape, yet enzymes are functionally dynamic. Molecular dynamics offers the possibility of probing protein movement while predicting ligand binding. Accordingly, we choose the bacterial F1Fo ATP synthase ε subunit to unravel why ATP affinity by ε subunits from Bacillus subtilis and Bacillus PS3 differs ~500-fold, despite sharing identical sequences at the ATP-binding site.
ReadCharacterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species.
The membrane-embedded domain of ATP synthases contains the c-ring, which translocates ions across the membrane, and its resultant rotation is coupled to ATP synthesis in the extramembranous domain. During rotation, the c-ring becomes accessible on both sides of the lipid bilayer to solvent via channels connected to the other membrane-embedded component, the a subunit, and thereby allows the ion to be released into the solvent environment.
ReadMolecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?
The outer membrane of Gram-negative bacteria is almost exclusively composed of lipopolysaccharide in its outer leaflet, whereas the inner leaflet contains a mixture of phospholipids. Lipopolysaccharide diffuses at least an order of magnitude slower than phospholipids, which can cause issues for molecular dynamics simulations in terms of adequate sampling.
ReadThe Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit
The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non‐inhibitory down‐state to an extended up‐state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain.
Read3D reconstruction and flexibility of the hybrid engine Acetobacterium woodii F-ATP synthase
The Na+-translocating F1FO ATP synthase from Acetobacterium woodii (AwF-ATP synthase) with a subunit stoichiometry of α3:β3:γ:δ:ε:a:b2:(c2/3)9:c1 represents an evolutionary path between ATP-synthases and vacuolar ATPases, by containing a heteromeric rotor c-ring, composed of subunits c1, c2 and c3, and an extra loop (γ195-211) within the rotary γ subunit.
ReadComputational modelling of flavivirus dynamics: The ins and outs
- Computational methods integrating experimental data help elucidate viral life cycle. - Viruses are dynamic and have complex interactions with a variety of host factors. - We can now model the complex interplay of proteomic and genomic components. - Molecular biology, genomics, and computation complement structural methods.
ReadComputational modelling of flavivirus dynamics: The ins and outs
Enveloped viruses such as the flaviviruses represent a significant burden to human health around the world, with hundreds of millions of people each year affected by dengue alone. In an effort to improve our understanding of the molecular basis for the infective mechanisms of these viruses, extensive computational modelling approaches have been applied to elucidate their conformational dynamics.
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