Flexing and stretching in nonribosomal Peptide synthetases

Re-engineering of nonribosomal peptide synthetase molecular assembly lines has been hampered by a lack of detailed knowledge concerning inter-domain substrate transfer. Recent structural studies of catalytically relevant domain-domain interactions provide valuable insights into this problem (Liu et?al., 2011; Sundlov et?al., 2012 [in this issue of Chemistry & Biology]).     

High-throughput interrogation of ligand binding mode using a fluorescence-based assay

Probing the pocket: A high-throughput fluorescence-based thermal shift (FTS) assay utilized different forms of a protein (in gray) to establish the binding mode of a ligand (see picture). The assay serves in the rapid evaluation of structure-activity binding-mode relationships for a series of ligands of Plk1, an important target of anticancer therapy.     

Gaining insight into the inhibition of glycoside hydrolase family 20 exo-β-N-acetylhexosaminidases using a structural approach

One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray structural analysis of a representative family 20 exo-β-N-acetylhexosaminidase in complex with various known classes of inhibitor of these types of enzymes, which highlights how different inhibitor classes can inhibit the same enzyme. This study will aid in the future development of inhibitors of not only exo-β-N-acetylhexosaminidases but also other types of glycoside hydrolases.     

Relaxation studies in magnetic resonance spectroscopy

The electron spin and nuclear spin relaxation in liquid solution arising from the electron-nuclear interaction is determined for the general case when the g-tensor may be anisotropic and the nine hyperfine interaction tensor components may be all different. The theoretical expressions are used in an attempt to interpret the relaxation times T ₁ and T ₂ for the various nuclei in the complex ruthenium acetylacetonate.     

Fluorescence techniques for probing water penetration into lipid bilayers

Fluorescence spectroscopy can be used as a highly sensitive and localized probe for hydration in lipid bilayers. Water associates with the head-group region, where it participates in an interlipid network of hydrogen bonds. Deeper in the bilayer, water is contained within acyl-chain packing defects. Fluorescence methodology is available to probe both the interstitial and head-group hydration in lipid bilayers, and results are in good agreement with other techniques. Using fluorescence spectroscopic approaches, cholesterol is shown to dehydrate the acyl-chain region, while hydrating the head-group region. Membrane proteins appear to increase acyl-chain hydration at the protein-lipid interface. Overall fluorescence spectroscopic techniques may be most effective in studying the water content of lipid bilayers and especially of biological membranes.     

Structural comparisons of the aggregates of tobacco mosaic virus protein

The coat protein of tobacco mosaic virus forms numerous aggregates, including the small A-protein, the disk, and two helical forms. The structures of the disk, the helical protein forms, and the virus are compared. Most of the differences are in the conformation of the chain between residues 89 and 113, which lies in the region of protein at the center of the virus, inside the RNA. It is disordered in the disk, but has a fixed conformation in the virus and the protein helices. The differences between the virus and the two helical protein forms are largely in the conformations of arginines and carboxylic acids in this region.     

O-GlcNAcase catalyzes cleavage of thioglycosides without general acid catalysis

O-GlcNAcase catalyzes the removal of N-acetylglucosamine residues from serine and threonine residues of post-translationally modified proteins using a catalytic mechanism involving substrate-assisted catalysis and general acid/base catalysis. Since thioglycosides are widely perceived as resistant to hydrolysis by glycosidases, it was surprising to find that O-GlcNAcase also catalyzes the efficient hydrolysis of S-glycosides. Br?nsted analyses and pH-activity studies of the O-GlcNAcase-catalyzed hydrolysis of a series of aryl S- and O-glycosides reveal that O-GlcNAcase effects hydrolysis of thioglycosides without the assistance of general acid catalysis. alpha-Deuterium kinetic isotope effects for O- and S-glycosides, as well as Taft-like analyses using N-fluoroacetyl-beta-glycosides, suggest that O-GlcNAcase accomplishes hydrolysis of thioglycosides by stabilizing late transition states. For S-glycosides this transition state shows greater nucleophilic participation from the 2-acetamido group than for O-glycosides. The rate constants governing the O-GlcNAcase-catalyzed hydrolysis of O- and S-glycosides as compared to those previously determined for the spontaneous hydrolysis of structurally similar O,O- and O,S-acetals show a similar ratio. O-GlcNAcase therefore demonstrates similar catalytic proficiency toward both O- and S-glycosides. We conclude that O-GlcNAcase is a bifunctional catalyst capable of efficiently cleaving thioglycosides without general acid catalysis, an observation that may have biological implications.     

Azasteroids. Reaction of Chiral N,N-Maleoyl Amino Acids with 1-(1-Trimethylsiloxyvinyl)-3,4-dihydronaphthalene

The cycloaddition between N,N-maleoyl amino acid esters and 1-(1-trimethylsiloxyvinyl)-3,4-dihydronaphthalene gave 11-(trimethylsiloxy) derivatives of 16-azaestra-1,3,5(10)-trienes. These were transformed by desilylation into the parent 11-oxo-derivatives, which reacted with hydroxylamines to 11-hydroxyimino derivatives. The stereochemistry of the products was elucidated using different NMR methods, HPLC, CD, X-ray structure analysis, and calculations. It was found that mixtures of diastereoisomers were obtained from these cycloadditions. Reactions using chiral maleoyl amino acid derivatves did not change this result. The chiral center did not provoke stereoselectivity, probably caused by the flexibility of the chiral side chain. A directing influence of the side chain was found only in reactions with derivatives of phenylalanine. This might be explained as an interaction between the aromatic system and the carbonyl groups of the imide moiety. This interaction kept the aromatic ring in its position in the final product, and was found in the X-ray crystallographic analysis, and agreed with results of calculations.     

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.