LC-mass spectrometry analysis of N- and C-terminal boundary sequences of polypeptide fragments by limited proteolysis

Limited proteolysis is an important and widely used method for analyzing the tertiary structure and determining the domain boundaries of proteins. Here we describe a novel method for determining the N- and C-terminal boundary amino acid sequences of products derived from limited proteolysis using semi-specific and/or non-specific enzymes, with mass spectrometry as the only analytical tool. The core of this method is founded on the recognition that cleavage of proteins with non-specific proteases is not random, but patterned. Based on this recognition, we have the ability to determine the sequence of each proteolytic fragment by extracting a common association between data sets containing multiple potential sequences derived from two or more different mass spectral molecular weight measurements. Proteolytic product sequences derived from specific and non-specific enzymes can be accurately determined without resorting to the conventional time-consuming and laborious methods of SDS-PAGE and N-terminal sequencing analysis. Because of the sensitivity of mass spectrometry, multiple transient proteolysis intermediates can also be identified and analyzed by this method, which allows the ability to monitor the progression of proteolysis and thereby gain insight into protein structures.     

DNA recognition interfaces: the influence of interfacial design on the efficiency and kinetics of hybridization

The effect of the surface chemistry of DNA recognition interfaces on DNA hybridization at a gold surface was investigated using both electrochemistry and the quartz crystal microbalance (QCM) technique. Different DNA recognition interfaces were prepared using a two-component self-assembled monolayer consisting of thiolated 20-mer probe single-stranded DNA (ss-DNA) containing either a 3'-mercaptopropyl or a 3'-mercaptohexyl linker group and an alcohol-terminated diluent layer with 2-, 6-, or 11-carbon length. The influence of the interfacial design on the hybridization efficiency, the affinity constant (Ka) describing hybridization, and the kinetics of hybridization was assessed. It was found that the further the DNA was above the surface defined by the diluent layer the higher the hybridization efficiency and Ka. The kinetics of DNA hybridization was assessed using both a QCM and an electrochemical approach to ascertain the influence of the interface on both the initial binding of target DNA to the surface and the formation of a complete duplex. These measurements showed that the length of the diluent layer has a large impact on the time taken to form a perfect duplex but no impact on the initial recognition of the target DNA by the immobilized probe DNA.     

Synthesis and protein degradation capacity of photoactivated enediynes

[structure: see text] The viability of proteins as targets of thermally and photoactivated enediynes has been confirmed at the molecular level. Model studies using a labeled substrate confirmed the efficacy of atom transfer from diyl radicals produced from enediynes to form captodatively stabilized carbon centered aminoacyl radicals, which then undergo either fragmentation or dimerization. To exploit this finding, a family of enediynes was developed using an intramolecular coupling strategy. Derivatives were prepared and used to target specific proteins, showing good correlation between affinity and photoinduced protein degrading activity. The findings have potential applications in the design of artificial chemical proteases and add to our understanding of the mechanism of action of the clinically important enediyne antitumor antibiotics.     

Blind prediction of HIV integrase binding from the SAMPL4 challenge

Here, we give an overview of the protein-ligand binding portion of the Statistical Assessment of Modeling of Proteins and Ligands 4 (SAMPL4) challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components—a small “virtual screening” challenge, a binding mode prediction component, and a small affinity prediction component. Here, we give summary results and statistics concerning the performance of all submissions at each of these challenges. Virtual screening was particularly challenging here in part because, in contrast to more typical virtual screening test sets, the inactive compounds were tested because they were thought to be likely binders, so only the very top predictions performed significantly better than random. Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging. Still, the best methods managed low root mean squared deviation predictions in many cases. Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details.     

A convergent approach to batzelladine alkaloids. Total syntheses of (+)-batzelladine E, (−)-dehydrobatzelladine C,and (+)-batzelladine K

We recently reported a convergent strategy to access the polycyclic guanidinium alkaloid (+)-batzelladine B via an aldol addition–retro-aldol–aza-Michael addition cascade. Here we describe the application of this approach toward the total syntheses of (+)-batzelladine E, (?)-dehydrobatzelladine C, and (+)-batzelladine K. The identification of suitable methods to functionalize a common tropane core by electrophilic alkynylation and nucleophilic 1,2-addition were essential to generalizing this approach. We provide evidence for the intermediacy of an acylallene species in the cascade reaction.     

Utilization of the p-nitrobenzyloxycarbonyl (pNZ) amine protecting group and pentafluorophenyl (Pfp) esters for the solid phase synthesis of spiroligomers

Spiroligomers are a class of peptidomimetics that connect interchangeable, stereochemically pure, cyclic monomers through pairs of amide bonds to form diketopiperazines between the monomers. This enables them to adopt predictable and programmable structure due to the rigidity of the final molecule. We present a new method for the solid phase synthesis of highly functionalized spiroligomers that incorporates the use of the p-nitrobenzyloxycarbonyl (pNZ) as a temporary amine protecting group and the pentafluorophenyl ester for monomer activation. This new method allows for the synthesis of spiroligomers with higher purity and increased yields when compared to previous methods. This improved method of synthesis of functionalized spiroligomers will facilitate the development of applications as catalysts, therapeutics and membrane channels.     

Effect of Mo–Fe substitution on glass forming ability and thermal stability of Fe–C–B–Mo–Cr–W bulk amorphous alloys

Amorphous Fe_67?xC₁₀B₉Mo_7+xCr₄W₃ (x = 1–7 at.%) plates with 0.64 mm thickness were prepared by copper mold casting. The thermal properties and microstructural development during heat treatments were investigated by a combination of differential scanning calorimetry, differential thermal analysis, and X-ray diffraction. The glass forming ability (GFA) and activation energy for crystallization have a distinct dependence on Mo content. Fe₆₂C₁₀B₉Mo₁₂Cr₄W₃ was the best glass former in this study, demonstrating a supercooled liquid region, ΔT_x = 51 K, and an activation energy for crystallization, Q = 453 kJ/mol. The GFA of alloys in this system was governed by elastic strain optimization resulting directly from the variation in Mo content. Heat treatments were performed to demonstrate resistance to crystallization under typical processing conditions. Alloys in this system exhibited a three phased evolution during crystallization. A second set of heat treatments was performed to identify each phase. An analysis of phase evolution revealed a distinct dependence of phase evolution with stepwise substitution of Mo for Fe in this system.