Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

Hydrogen–deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Cyclodimerization versus Polymerization of Methyl Methacrylate Induced by N‐Heterocyclic Carbenes: A Combined Experimental and Theoretical Study

The activation behavior of two N‐heterocyclic carbenes (NHCs), namely, 1,3‐bis(isopropyl)imidazol‐2‐ylidene(NHCiPr) and 1,3‐bis(tert‐butyl) imidazol‐2‐ylidene (NHCtBu), as organic nucleophiles in the reaction with methyl methacrylate (MMA) is described. NHCtBu allows the polymerization of MMA in DMF at room temperature and in toluene at 50 °C, whereas NHCiPr reacts with two molecules of MMA, forming an unprecedented imidazolium–enolate cyclodimer (NHCiPr/MMA=1:2). It is proposed that the reaction mechanism occurs by initial 1,4‐nucleophilic addition of NHCiPr to MMA, generating a zwitterionic enolate 2 , followed by addition of 2 to a second MMA molecule, forming a linear imidazolium–enolate 3 (NHCiPr/MMA=1:2). Proton transfer, generating intermediate 5 , followed by cyclization and release of methanol yielded the aforementioned zwitterionic cyclodimer 1:2 adduct 7 , the molecular structure of which has been established by NMR spectroscopy, X‐ray diffraction, and mass spectrometry. This unexpected difference between NHCtBu and NHCiPr in the reaction with MMA (polymerization and cyclodimerization, respectively) can be rationalized by using DFT calculations. In particular, the nature of the NHC strongly influences the cyclodimerization pathway, the cyclization of 5 and the release of methanol are the discriminating step and limiting step, respectively. In the case of NHCtBu, both steps are strongly disfavoured compared with that of NHCiPr (energetic difference of around 14 and 9 kcal mol^?1, respectively), preventing the cyclization mechanism from a kinetic viewpoint. Moreover, addition of a third molecule of MMA in the polymerization pathway results in a lower activation barrier than that of the limiting step in the cyclodimerization pathway (difference of around 14 kcal mol^?1), in agreement with the formation of polymethyl methacrylate (PMMA) by using NHCtBu as nucleophile.     

Initiation of Protein Synthesis with Non-Canonical Amino Acids In Vivo

By transplanting identity elements into E. coli tRNA^fMet, we have engineered an orthogonal initiator tRNA (itRNA^Ty2) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNA^Ty2 can initiate translation in vivo with aromatic non-canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNA^fMet from the genome afforded an E. coli strain in which the efficiency of non-canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo.     

Initiation of Protein Synthesis with Non‐Canonical Amino Acids In Vivo

By transplanting identity elements into E. coli tRNA^fMet, we have engineered an orthogonal initiator tRNA (itRNA^Ty2) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNA^Ty2 can initiate translation in vivo with aromatic non‐canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNA^fMet from the genome afforded an E. coli strain in which the efficiency of non‐canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo.     

Thiaminase I (42 kDa) heterogeneity,sequence refinement,and active site location from high-resolution tandem mass spectrometry

Thiaminase I (E.C. 2.5. 1.2) from Bacillus thiaminolyticus catalyzes the degradation of thiamin (vitamin B₁). Unexpected mass heterogeneity (MW 42,127, 42,197, and 42,254; 1:2:1) in recombinant thiaminase I from Escherichia coli was detected by electrospray ionization Fourier-transform mass spectrometry, resolving power 7×10⁴. Nozzle-skimmer fragmentation data reveal an extra Ala (+71.02; 71.04=theory) and GlyAla (+128.04; 128.06=theory) on the N-terminus, in addition to the fully processed enzyme. However, the fragment ion masses were consistent only with this sequence through 330 N-terminal residues; resequencing of the last 150 bps of the thiaminase I gene yields a sequence consistent with the molecular weight values and all 61 fragment ion masses. Covalently labeling the active site with a 108-Da pyrimidine moiety via mechanism-based inhibition produces a corresponding molecular weight increase in all three thiaminase I components, which indicates that they are all enzymatically active. Inspection of the fragment ions that do and do not increase by 108 Da indicates that the active site nucleophile is located between Pro⁷⁹ and Thr¹⁷⁷ in the 379 amino acid enzyme.     

Early gas chromatography/mass spectrometry

Spectroscopy Laboratory, The Dow Chemical Company, Midland, Michigan, USA In December 1955 or thereabouts, the authors coupled a homemade gas chromatograph to a research time-of-flight mass spectrometer constructed by W. C. Wiley, I. H. McLaren, and D. B. Harrington. This unique gas chromatography/mass spectrometry (GC/MS) instrument generated mass spectra at a lo-kHz rate for display on an oscilloscope; eluted gas chromate graphic components, such as methanol, acetone, benzene, toluene, and carbon tetrachloride, could be visually identified immediately from the oscilloscope display. Many years of further research and development in many laboratories worldwide were necessary, however, to make continuous on-line GC/MS the uniquely valuable analytical tool that it is today.     

Selective detection of sulfur-containing compounds by gas chromatography/chemical reaction interface mass spectrometry

Addition of a reactant gas to a low pressure microwave-induced plasma creates a reaction interface in which complex molecules are converted into small polyatomic neutral species. For a given reactant gas the array of these small molecules reflect s the elemental composition of the original analyte. In this study HCI has been found highly effective as a reactant gas for selective detection of sulfur-eontaining compounds using capillary gas chromatography/ chernical reaction interface mass spectrometry. Detection limits as low as 30 pg of a sulfur-containing compound and a dynamic range of two orders of magnitude were achieved.     

A novel approach to combinatorial library design

We address the problem of designing a general-purpose combinatorial library to screen for pharmaceutical leads. Conventional approaches focus on diversity as the primary factor in designing such libraries. We suggest making screening libraries out of a set of pharmaceutically relevant scaffolds, with multiple analogs per scaffold. The rationale for this rests on the fact that even though the hit-rate in active series is much higher than in the database as a whole, often a large fraction of the compounds in active series are inactive. This is especially true when the series has not been optimized for the target under study. We introduce the concept of hit-rate within a series and use historic screening data to arrive at a crude estimate for it. We then use simple probability arguments to show that 50-100 compounds are required in each series in order to be nearly certain of finding at least one active compound in each true active series for any given target.     

Prevalence of unstable attractors in networks of pulse-coupled oscillators

We present and analyze the first example of a dynamical system that naturally exhibits attracting periodic orbits that are unstable. These unstable attractors occur in networks of pulse-coupled oscillators, and become prevalent with increasing network size for a wide range of parameters. They are enclosed by basins of attraction of other attractors but are remote from their own basin volume such that arbitrarily small noise leads to a switching among attractors.     

Long-term neprilysin gene transfer is associated with reduced levels of intracellular Abeta and behavioral improvement in APP transgenic mice

Background  

Proteolytic degradation has emerged as a key pathway involved in controlling levels of the Alzheimer's disease (AD)-associated amyloid-β (Aβ) peptide in the brain. The endopeptidase, neprilysin, has been implicated as a major Aβ degrading enzyme in mice and humans. Previous short and intermediate term studies have shown the potential therapeutic application of neprilysin by delivering this enzyme into the brain of APP transgenic mice using gene transfer with viral vectors. However the effects of long-term neprilysin gene transfer on other aspects of Aβ associated pathology have not been explored yet in APP transgenic mice.