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Hydrogen-deuterium exchange mass spectrometry (HDX MS) has become an important technique for the analysis of protein structure and dynamics. Data analysis remains a bottleneck in the workflow. Sophisticated computer analysis is required to scan through the voluminous MS output in order to find, identify, and validate many partially deuterated peptides, elicit the HDX information, and extend the results to higher structural resolution. We previously made available two software suites, ExMS for identification and analysis of peptide isotopic envelopes in the HDX MS raw data and HDsite for residue-level resolution. Further experience has led to advances in the usability and performance of both programs. Also, newly added modules deal with ETD/ECD analysis, multimodal mass spectra analysis, and presentation options. These advances have been integrated into a stand-alone software solution named ExMS2. The package has been successfully tested by many workers in fine scale epitope mapping, in protein folding studies, and in dissecting structure and structure change of large protein complexes. A description and tutorial for this major upgrade are given here.

The analysis of many hydrogen exchange (HX) experiments depends on knowledge of exchange rates expected for the unstructured protein under the same conditions. We present here some minor adjustments to previously calibrated values and a stringent test of their accuracy. Graphical Abstract ᅟ.

The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by two-fold only reduced back-exchange by ~2 % (from ~30% to 28%), while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (< 20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90 ± 5%.

To promote studies of cytochrome c (Cyt c) ranging from apoptosis to protein folding, a system for facile mutagenesis and high-level expression is desirable. This work used a generally applicable strategy for improving yields of heterologously expressed protein in Escherichia coli. Starting with the yeast Cyt c plus heme lyase construct of Pollock et al. [Pollock, W. B., Rosell, F. I., Twitchett, M. B., Dumont, M. E., and Mauk, A. G. (1998) Biochemistry 37, 6124-6131], an E. coli-based system was designed that consistently produces high yields of recombinant eucaryotic (equine) Cyt c. Systematic changes to the ribosome binding site, plasmid sequence, E. coli strain, growth temperature, and growth duration increased yields from 2 to 3 mg/L to as much as 105 mg/L. Issues related to purification, fidelity of heme insertion, equilibrium stability, and introduction and analysis of mutant forms are described. As an example, variants tailored for folding studies are discussed. These remove known pH-dependent kinetic folding barriers (His26 and His33 and N-terminus), reveal an additional kinetic trap at higher pH due to some undetermined residue(s), and show how a new barrier can be placed at different points in the folding pathway in order to trap and characterize different folding intermediates. In addition, destabilizing glycine mutants in the N-terminal helix are shown to affect the fractional yield of a heme inverted Cyt c isoform.

[structure] C-Glycosides of N-acyl 2-amino-2-deoxygalactose (acyl = MeCO, CF(3)CO, t-BuOCO) are available in a stereoselective manner by trapping of an anomeric radical with an activated alkene. Using anomeric selenides, radical generation and trapping is carried out under conditions that avoid competitive reduction, and this chemistry has been applied to the synthesis of the novel C-glycoside analogue of O-benzyl alpha-D-GalNAc.

The synthesis of the Fmoc-protected C-glycosyl tyrosines 1 and 2, together with two other related C-glycosyl tyrosines, has been achieved. Key reactions involved (i) the reaction of a glycal with an organozinc reagent (carrying an aryl iodide function) in the presence of a Lewis acid to establish the C-glycosyl linkage and (ii) subsequent cross coupling of the aryl iodide to an alanyl zinc reagent (in the presence of a Pd(0) catalyst) to complete the construction of the alpha-amino acid moiety. Using solid-phase peptide synthesis methods, two units of the mannosyl derivative 1 (shown as L-Tyr[C-Ac(4)-alpha-D-Man]) have been incorporated (with four units of glycine) into the linear hexapeptide 3 which was then converted to the C(2)-symmetric cyclic oligopeptide 4.

Summary. Following early suggestions, 25,26 a role fornucleation has more recently been proposed on the basisof simulated model folding 15,16 and experiment. 1,17,18,27 Cyt c results 1,27 demonstrate the uphill nature of thenucleated transition state, its massively collapsed condi-tion, and the significant time requirement for its formationand imply a long-range search for a nativelike transitionstate topology. The nucleation barrier occurs at the verybeginning of the cyt c folding process. When subsequentlarger barriers (misfold-reorganization barriers) are notencountered, the initial nucleation becomes the rate-limiting step for native state acquisition, subsequentintermediates are kinetically invisible, and folding appearsto be a two-state process. Misfold - Reorganization Barriers Many proteins including cyt c at neutral pH fold on a ˘1s time scale in a multistate way. Until recently this ratewas considered to be extraordinarily fast and was thoughtto be limited by a late intrinsic on-pathway barrier,perhaps the final molten globule to native state transition.A study of cyt

Many authors have described naphthalene disulphonic acid formation by sulphonation of naphthalene with sulphuric acid: the proportions of the different isomers in this reaction are discussed under several sets of experimental conditions. On the contrary, little data is available concerning the use of oleum as a sulphonation medium. The use of oleum as a sulphonating medium is interesting from an industrial point of view for monosulphonic acid preparation, since it results in fast reaction rates and yields a minimum of water. However, since polysulphonic acid formation is enhanced in this way, it is important to know how much of these unwanted products are formed. The proportion of the different isomers of the obtained naphthalenedisulphonic acids is strongly dependent on reaction conditions. This work deals with the influence of reaction time and temperature on the reaction yields. HPLC is used for diacid separation and determination.

A previous paper considered the problems that presently limit the hydrogen exchange - mass spectrometry (HX-MS) method for studying the biophysical and functional properties of proteins. Many of these problems can be overcome by obtaining and analyzing hundreds of sequentially overlapping peptide fragments that cover the protein many times over (Mayne et al. J. Am. Soc. Mass Spectrom. 2011: 10.1007/s13361-011-0235-4). This paper describes a computer program called ExMS that furthers this advance by making it possible to efficiently process crowded mass spectra and definitively identify and characterize these many peptide fragments. ExMS automatically scans through high resolution MS data to find the individual isotopic peaks and isotopic envelopes of a list of peptides previously identified by MS/MS. It performs a number of tests to ensure correct identification in spite of peptide overlap in both chromatographic and mass spectrometric dimensions and possible multi-modal envelopes due to static or dynamic structural heterogeneity or HX EX1 behavior. The program can automatically process data from many sequential HX time points with no operator intervention at the rate of ~2 sec per peptide per HX time point using desktop computer equipment, but it also provides for rapid manual checking and decision when ambiguity exists. Additional subroutines can provide a step by step report of performance at each test along the way and parameter adjustment, deconvolute isotopic envelopes, and plot the time course of single and multi-modal H-D exchange. The program will be available on an open source basis at: http://HX2.med.upenn.edu/download.html

Measurement of the naturally occurring hydrogen exchange (HX) behavior of proteins can in principle provide highly resolved thermodynamic and kinetic information on protein structure, dynamics, and interactions. The HX fragment separation-mass spectrometry method (HX-MS) is able to measure hydrogen exchange in biologically important protein systems that are not accessible to NMR methods. In order to achieve high structural resolution in HX-MS experiments, it will be necessary to obtain many sequentially overlapping peptide fragments and be able to identify and analyze them efficiently and accurately by mass spectrometry. This paper describes operations which, when applied to four different proteins ranging in size from 140 to 908 residues, routinely provides hundreds of useful unique peptides, covering the entire protein length many times over. Coverage in terms of the average number of peptide fragments that span each amino acid exceeds 10. The ability to achieve these results required the integrated application of experimental methods that are described here and a computer analysis program, called ExMS, described in a following paper.

We have used hydrogen-exchange labeling detected by 2D NMR to study antibody-protein interactions for two monoclonal antibodies raised against horse cytochrome c. The data show that these antibodies bind mainly to the large 37-59 omega-loop of the cytochrome c molecule. In addition, the results provide some suggestive evidence concerning units of local structural flexibility in cytochrome c.

The free energy contribution of salt bridges to protein stability remains a controversial issue. The role of single salt bridges has been investigated in protein and peptide studies; there is no reported value of a multiple salt bridge employing peptide models. We have designed a de novo peptide model to evaluate the strength of a multiple salt bridge. Measurement of the rate of hydrogen exchange (HX) of the backbone NH groups in α-helical peptides allows determination of the absolute free energy of individual interactions that participate in helix stabilization. We apply this procedure here to evaluate the stabilizing contribution of a multiple salt bridge involving Glu3, Asp4, and Arg7 in an 11-mer peptide. The peptide is prenucleated by a lactam bridge connecting two side chains spaced four residues apart. Measurement of the HX rates of each NH group in this peptide as a function of pH, together with the pH independent rate of a Gln3 and Asn4 analogue, reveals a substantial favorable contribution to th...

Two-dimensional nuclear magnetic resonance techniques were used to assign the NH, C alpha H, and C beta H protons of over 60 of the 104 amino acid residues in the 1H NMR spectrum of horse ferrocytochrome c. The majority of these amino acids were completely assigned. Assignments were based on the analysis of two-dimensional J-correlated (COSY), nuclear Overhauser effect (NOESY), and relayed COSY spectra and on comparisons of the J-correlated spectra of various cytochrome c species. Spin diffusion is not a problem with monomeric proteins the size of cytochrome c. Here these advances are illustrated with data that lead to the assignment of the heme-associated residues cysteine-14 and tryptophan-59, the axial ligands methionine-80 and histidine-18, the entire N-terminal helix, and several other amino acid spin systems. With these approaches, structure, structure change, the internal dynamics of cytochrome c, and the interaction of these with function are being studied, especially by observation of the hydrogen exchange behavior of essentially all the H-bonded amides and some side chain protons in both the reduced and oxidized proteins.

The synthesis and anticonvulsant activity of a number of 2-aryl-5-guanidino-1,3,4 thiadiazoles are described. The unsubstituted guanidine 2a was found to possess potent anticonvulsant properties; considerable reduction or loss of activity however was observed with the majority of the substituted guanidines. Incorporation of the guanidine group into an imidazoline ring also resulted in a loss of activity. Secondary pharmacological evaluation confirmed the anticonvulsant properties of 2a but also revealed that the compound exhibited a considerable degree of sedative activity.

This paper describes the synthesis and pharmacological evaluation of a number evaluation of a number of substituted 1,3,4-thiadiazoles. The first member of the series, 2-(aminomethyl)-5-(2-biphenylyl)-1,3,4-thiadiazole (7) was found to possess potent anticonvulsant properties in rats and mice and compared favorably with the standard anticonvulsant drugs phenytoin, phenobarbital, and carbamazepine in a number of test situations. The potency of compound 7 was maintained on alkylation of the side-chain nitrogen atom; however, aryl substitution or chain lengthening caused a drop in potency. Replacement of the 2-biphenylyl group by phenyl or benzyl also lead to inactive compounds.

The ability of a variety of phenyl derivatives to inhibit sickle cell hemoglobin gelation was placed on a quantitative scale by parallel equilibrium and kinetic assays. Modifications of the phenyl ring studied include polar, nonpolar, and charged substituents, added aromatic rings, and loss of aromaticity. Other noncovalent inhibitors previously reported to have high potency were measured and placed on the same quantitative scale. Some phenyl derivatives were found to be as effective an any other known noncovalent antigelling agent. The phenyl compounds penetrate easily into red cells, and their potency is tolerant to chemical modification, which holds out the possibility of designing low-toxicity derivatives. On the negative side, the level of potency obtainable appears to be inadequate for clinical use. The best phenyl inhibitors display a functionally defined inhibitory constant (K1) of 75 mM, and it can be estimated that inhibitor concentrations over 20 mM would be necessary to obtain minimal clinically significant benefit. Furthermore, with the variety of modifications tested here, no impressive increase in activity could be achieved over that found in the simplest phenyl compounds.