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D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that...
AMP-activated protein kinase (AMPK) is a principal metabolic regulator affecting growth and response to cellular stress. Comprised of catalytic and regulatory subunits, each present in multiple forms, AMPK is best described as a family of related enzymes. In recent years, AMPK has emerged as a desirable target for modulation of numerous diseases, yet clinical therapies remain elusive. Challenges result,...
The 2013 Nobel Prize in Chemistry has been awarded to Martin Karplus, Michael Levitt, and Arieh Warshel for their work on developing computational methods to study complex chemical systems. Their work has led to mechanistic critical insights into chemical systems both large and small and has enabled progress in a number of different fields, including structural biology.
Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates ∼65°. Simultaneous with this “recovery stroke,” myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 Å-distant Switch-2 loop...
Sirtuins catalyze the NAD + -dependent protein deacetylation of lysine residues. In this issue of Structure, Hoff et al. (2006) report the structure of a sirtuin homolog with both substrates bound, providing new insight into the catalytic mechanism.
The mechanics of a protein joint, gluing two elastic titin molecules together in muscle, are explored using computer simulation in this issue of Structure by Lee et al. (2006). Maybe the glue itself also has another, more subtle, sensory role?
Aligned α helix peptide dipoles sum to a “macroscopic” dipole parallel to the helix axis that has been implicated in protein folding and function. However, in aqueous solution the dipole is counteracted by an electrostatic reaction field generated by the solvent, and the strength of the helix dipole may reduce drastically from its value in vacuum. Here, using atomic-detail helix models and Poisson-Boltzmann...
Halorhodopsin is a light-driven chloride anion pump in which the trans→cis photoisomerization of a retinal chromophore triggers a photocyle resulting in the translocation of chloride across the plasma membrane. The mechanism of chloride transfer past the cis retinal is determined here by computing multiple pathways for this process. The calculations reveal two conditions of the valve mechanism. First,...
Recent structures of putative intermediates in the bacteriorhodopsin photocycle have provided valuable snapshots of the mechanism by which protons are pumped across the membrane. However, key steps remain highly controversial, particularly the proton transfer occurring immediately after retinal trans→cis photoisomerization. The gradual release of stored energy is inherently nonequilibrium: which photocycle...
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