Hydrogen/deuterium exchange on protein solutions containing nucleic acids: utility of protamine sulfate

Obtaining global hydrogen/deuterium (H/D) exchange data on proteins is an important first step in amide proton exchange experiments. Important information such as the mode of exchange, the cooperativity of folding/unfolding reactions, and the effects of ligand binding can be readily obtained in global exchange experiments. Many interesting biological systems are complexes containing both proteins and nucleic acids. The low pH conditions required to quench H/D exchange reactions result in the formation of stable protein/nucleic acid precipitates which interfere with the liquid chromatography step of the experiment and preclude obtaining mass spectrometric data. In this work we show that the precipitation of proteins and nucleic acids is electrostatic in nature and can be prevented by high ionic strength and by removing nucleic acids by protamine sulfate. Using protamine sulfate in quenching solution, we were able to obtain global H/D data with protein samples containing large amounts of DNA or RNA.     

Correlations between the quantum-chemical parameters of amino acids and regioselectivity of isotope exchange with the spillover hydrogen

The effective charges and the proton affinity of carbon atoms of α-amino acids were calculated by quantum-chemical methods. The relative reactivity of the C−H bonds of amino acids under conditions of high-temperature solid-state catalytic isotope exchange (HSCIE) was studied. Correlations between the electron structure of amino acids and the regioselectivity of the solid-state isotope exchange were established. The reactivity of the carbon atoms with high proton affinity increases under HSCIE conditions. An assumption was made that the interaction of a solid organic compound with the spillover hydrogen can be described as the electrophilic substitution at the saturated and aromatic carbon atoms. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1611–1617, September, 1997.     

Biosynthetic 13C labeling of aromatic side chains in proteins for NMR relaxation measurements

Site-specific 13C labeling offers a desirable means of eliminating unwanted relaxation pathways and coherent magnetization transfer in NMR relaxation experiments. Here we use [1-13C]-glucose as the sole carbon source in the growth media for protein overexpression in Escherichia coli. The approach results in specific incorporation of 13C at isolated positions in the side chains of aromatic amino acids, which greatly simplifies the measurements and interpretation of 13C relaxation rates in these spin systems. The method is well suited for characterization of chemical exchange by CPMG or spin-lock relaxation methods. We validated the method by acquiring 13C rotating-frame relaxation dispersion data on the E140Q mutant of the C-terminal domain of calmodulin, which reveal conformational exchange dynamics with a time constant of 71 mus for Y138.     

Modern Strategies for Carbon Isotope Exchange

In contrast to stable and natural abundant carbon-12, the synthesis of organic molecules with carbon (radio)isotopes must be conceived and optimized in order to navigate through the hurdles of radiochemical requirements, such as high costs of the starting materials, harsh conditions and radioactive waste generation. In addition, it must initiate from the small cohort of available C-labeled building blocks. For long time, multi-step approaches have represented the sole available patterns. On the other side, the development of chemical reactions based on the reversible cleavage of C−C bonds might offer new opportunities and reshape retrosynthetic analysis in radiosynthesis. This review aims to provide a short survey on the recently emerged carbon isotope exchange technologies that provide effective opportunity for late-stage labeling. At present, such strategies have relied on the use of primary and easily accessible radiolabeled C1-building blocks, such as carbon dioxide, carbon monoxide and cyanides, while the activation principles have been based on thermal, photocatalytic, metal-catalyzed and biocatalytic processes.     

Ligation-state hydrogen exchange: coupled binding and folding equilibria in ribonuclease P protein

Bacillus subtilis ribonuclease P protein (P protein) is predominantly unfolded (D) at physiological pH and low ionic strength; however, small molecule anionic ligands (e.g., sulfate) directly bind to and stabilize the folded state (NL2). Because the D + 2L <--> NL2 transition is experimentally two-state, high-energy states such as the singly bound, folded species (NL) and the unliganded folded species (N) are generally difficult to detect at equilibrium. To study the conformational properties of these ensembles, NMR-detected amide hydrogen exchange (HX) rates of P protein were measured at four sulfate (i.e., ligand) concentrations, a method we denote "ligation-state hydrogen exchange". The ligand concentration dependence of the HX rate of 47 residues was fit to a model with four possible HX pathways, corresponding to the local and/or global opening reactions from NL2 and NL, the local opening of N, and the global opening of N to D. Data analysis permits the calculation of the residue-specific free energy of opening from each ensemble as well as the fractional amide HX flux through each pathway. Results indicate that the predominant route of HX is through the NL and N states, which represent only 0.45% and 0.0005% of the total protein population in 20 mM sodium sulfate, respectively. Despite the low population of N, a region of protected amides was identified. Therefore, exchange through unliganded forms must be accounted for prior to the interpretation of HX-based protein-interaction studies. We offer a simple test to determine if HX occurs through the liganded or unliganded form.     

Regional stability changes in oxidized and reduced cytochrome c located by hydrogen exchange and mass spectrometry

Amide hydrogen exchange rates are highly sensitive to protein structure and may, therefore, be used to detect and characterize structural changes in proteins. Specific regions within folded proteins undergoing structural change can often be identified if localized amide hydrogen exchange rates are determined by nuclear magnetic resonance (NMR). The ability to measure localized amide hydrogen exchange rates by proteolytic fragmentation followed by mass spectrometric analysis opens the possibility to also identify localized structural changes in proteins by mass spectrometry. If successful, this approach offers considerable advantage over NMR in speed, sensitivity, protein solubility, and ability to study large proteins. This possibility has been investigated by determining the amide hydrogen exchange rates in oxidized and reduced cytochrome c by protein fragmentation/mass spectrometry. The fundamental difference in these forms of cytochrome c is the oxidation state of the iron, which other studies have shown results in only minor structural changes in the protein. In the present study, the largest differences in hydrogen exchange rates were found for peptide amide hydrogens located distant from the Nand C-termini, indicating that the structure in these regions is most affected by the oxidation state of the iron. These results are consistent with previous studies of oxidized and reduced cytochrome c, suggesting that hydrogen exchange and mass spectrometry may be generally useful for locating subtle changes in protein structure.     

Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic studies of proteins

Solid-state 31P NMR spectroscopy was applied to measure the isotropic chemical shifts, chemical shift anisotropies and asymmetry parameters of three phosphorylated amino acids, O-phospho-L-serine, O-phospho-L-threonine and O-phospho-L-tyrosine. The cross-polarization buildup rates and longitudinal relaxation times of 31P and 1H were-determined and compared with the values measured for a triphosphate (GppCH2p) bound to a crystalline protein (Ras). It is shown that the phosphorylated amino acids are well-suited model compounds, e.g. for the optimization of experiments on crystalline proteins. Two-dimensional exchange experiments on O-phospho-L-tyrosine indicate the existence of an exchange between the two different conformations of the molecule.     

Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry

One advantage of detecting amide H/2H exchange by mass spectrometry instead of NMR is that the more rapidly exchanging surface amides are still detectable. In this study, we present quench-flow amide H/2H exchange experiments to probe how rapidly the surfaces of two different proteins exchange. We compared the amide H/2H exchange behavior of thrombin, a globular protein, and IkappaBalpha, a nonglobular protein, to explore any differences in the determinants of amide H/2H exchange rates for each class of protein. The rates of exchange of only a few of the surface amides were as rapid as the "intrinsic" exchange rates measured for amides in unstructured peptides. Most of the surface amides exchanged at a slower rate, despite the fact that they were not seen to be hydrogen bonded to another protein group in the crystal structure. To elucidate the influence of the surface environment on amide H/2H exchange, we compared exchange data with the number of amides participating in hydrogen bonds with other protein groups and with the solvent accessible surface area. The best correlation with amide H/2H exchange was found with the total solvent accessible surface area, including side chains. In the case of the globular protein, the correlation was modest, whereas it was well correlated for the nonglobular protein. The nonglobular protein also showed a correlation between amide exchange and hydrogen bonding. These data suggest that other factors, such as complex dynamic behavior and surface burial, may alter the expected exchange rates in globular proteins more than in nonglobular proteins where all of the residues are near the surface.     

Coordination properties of zinc finger peptides revisited: ligand competition studies reveal higher affinities for zinc and cobalt

Zinc fingers are ubiquitous small protein domains which have a Zn(Cys)(4-x)(His)(x) site. They possess great diversity in their structure and amino acid composition. Using a family of six peptides, it was possible to assess the influence of hydrophobic amino acids on the metal-peptide affinities and on the rates of metal association and dissociation. A model of a treble-clef zinc finger, a model of the zinc finger site of a redox-switch protein, and four variants of the classical ββα zinc finger were used. They differ in their coordination set, their sequence length, and their hydrophobic amino acid content. The speciation, metal binding constants, and structure of these peptides have been investigated as a function of pH. The zinc binding constants of peptides, which adopt a well-defined structure, were found to be around 10(15) at pH 7.0. The rates of zinc exchange between EDTA and the peptides were also assessed. We evidenced that the packing of hydrophobic amino acids into a well-defined hydrophobic core can have a drastic influence on both the binding constant and the kinetics of metal exchange. Notably, well-packed hydrophobic amino acids can increase the stability constant by 4 orders of magnitude. The half-life of zinc exchange was also seen to vary significantly depending on the sequence of the zinc finger. The possible causes for this behavior are discussed. This work will help in understanding the dynamics of zinc exchange in zinc-containing proteins.     

Health Benefits of Cereal Grain- and Pulse-Derived Proteins

Pulses and whole grains are considered staple foods that provide a significant amount of calories, fibre and protein, making them key food sources in a nutritionally balanced diet. Additionally, pulses and whole grains contain many bioactive compounds such as dietary fibre, resistant starch, phenolic compounds and mono- and polyunsaturated fatty acids that are known to combat chronic disease. Notably, recent research has demonstrated that protein derived from pulse and whole grain sources contains bioactive peptides that also possess disease-fighting properties. Mechanisms of action include inhibition or alteration of enzyme activities, vasodilatation, modulation of lipid metabolism and gut microbiome and oxidative stress reduction. Consumer demand for plant-based proteins has skyrocketed primarily based on the perceived health benefits and lower carbon footprint of consuming foods from plant sources versus animal. Therefore, more research should be invested in discovering the health-promoting effects that pulse and whole grain proteins have to offer.     

Semi-Synthesis and Analysis of Chemically Modified Zif268 Zinc-Finger Domains

Total synthesis of proteins can be challenging despite assembling techniques, such as native chemical ligation (NCL) and expressed protein ligation (EPL). Especially, the combination of recombinant protein expression and chemically addressable solid-phase peptide synthesis (SPPS) is well suited for the redesign of native protein structures. Incorporation of analytical probes and artificial amino acids into full-length natural protein domains, such as the sequence-specific DNA binding zinc-finger motifs, are of interest combining selective DNA recognition and artificial function. The semi-synthesis of the natural 90 amino acid long sequence of the zinc-finger domain of Zif268 is described including various chemically modified constructs. Our approach offers the possibility to exchange any amino acid within the third zinc finger. The realized modifications of the natural sequence include point mutations, attachment of a fluorophore, and the exchange of amino acids at different positions in the zinc finger by artificial amino acids to create additional metal binding sites. The individual constructs were analyzed by circular dichroism (CD) spectroscopy with respect to the integrity of the zinc-finger fold and DNA binding.     

Synthesis of polyesters from active diesters

Ester-exchange and polycondensation reactions of active diesters such as diphenyl, dithiophenyl, or dipyridinyl esters of adipic or terephthalic acids with glycols were carried out in order to investigate the reactivity of these active diesters toward nucleophilic replacement. Catalysts such as potassium carbonate were required for the esterexchange of these active diesters. Comparison of the reactivity of these active diesters with that of ordinary diesters in the presence of potassium carbonate as a catalyst indicates the rates or the equilibrium constants of the exchange reactions of these active diesters were much larger than those of ordinary diesters, indicating that polyesterification reactions favorably occur. Polyesters were obtained in good yield either by solution or bulk methods in mild conditions.     

Utilisation de membranes echangeuses d'ions en electrosynthese organique. : V. Additions de michael induites par des bases électrogénérées au contact d'un électrolyte solide.

The addition of carbon acids to acrylonitrile or methyl acylate can be initiated by means of bases electrogenerated in aprotic media in the absence of supporting-electrolyte, at the interface between a porous cathode and a solid polymer electrolyte. The consumption of electricity is below 10^-2 faraday per mole. Putting to the test donors with decreasing acidity (2-nitropropane, malononitrile, diethyl malonate, ethyl cyanacetate, 2-methylcyclohexanone, fluorene) allows to estimate the basicity level that can be reached at such an interface. The influence of different factors (such as the nature of the ion exchange membrane, the basicity of the second side of the membrane, the presence of a probase) on the rates and yields of the reactions has been investigated.     

Transition-Metal-Free Carbon Isotope Exchange of Phenyl Acetic Acids

A transition-metal-free carbon isotope exchange procedure on phenyl acetic acids is described. Utilizing the universal precursor CO₂, this protocol allows the carbon isotope to be inserted into the carboxylic acid position, with no need of precursor synthesis. This procedure enabled the labeling of 15 pharmaceuticals and was compatible with carbon isotopes [¹⁴C] and [¹³C]. A proof of concept with [¹¹C] was also obtained with low molar activity valuable for distribution studies.     

Investigation of methods suitable for the matrix-assisted laser desorption/ionization mass spectrometric analysis of proteins from ribonucleoprotein complexes

A variety of protein isolation and purification techniques for ribonucleoprotein (RNP) complexes were investigated for their compatibility with downstream analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Ribosomal proteins from Escherichia coli 70S ribosomes were obtained using methods such as phenol extraction and precipitation by organic solvents or acids. Under optimal conditions, more than 90% of the expected ribosomal proteins were detected in a single MALDI-MS experiment. The most effective approach combined ribosome denaturation by buffer exchange with acid precipitation of the ribosomal ribonucleic acids. An improved acid precipitation approach, involving the sequential additions of acetic and trifluoroacetic acid, yielded more complete protein coverage while minimizing loss of ion signal from lower molecular weight proteins. With phenol extraction, substantial gains in ion abundance of higher molecular weight proteins are noted, although some of the lower molecular weight proteins were not efficiently extracted. These results illustrate several effective approaches for protein isolation from protein complexes such as RNPs that are MALDI-MS compatible, and these approaches should extend the use of MALDI-MS for proteomics-based analyses of other protein-nucleic acid complexes.     

Expansion of time window for mass spectrometric measurement of amide hydrogen/deuterium exchange reactions

Backbone amide hydrogen exchange rates can be used to describe the dynamic properties of a protein. Amide hydrogen exchange rates in a native protein may vary from milliseconds (ms) to several years. Ideally, the rates of all amide hydrogens of the analyte protein can be determined individually. To achieve this goal, monitoring of a wider time window is critical, in addition to high sequence coverage and high sequence resolution. Significant improvements have been made to hydrogen/deuterium exchange mass spectrometry methods in the past decade for better sequence coverage and higher sequence resolution. On the other hand, little effort has been made to expand the experimental time window to accurately determine exchange rates of amide hydrogens. Many fast exchanging amide hydrogens are completely exchanged before completion of a typical short exchange time point (10–30 s) and many slow exchanging amide hydrogens do not start exchanging before a typical long exchanging time point (1–3 h). Here various experimental conditions, as well as a quenched‐flow apparatus, are utilized to monitor cytochrome c amide hydrogen exchange behaviors over more than eight orders of magnitude (0.0044–1 000 000 s), when converted into the standard exchange condition (pH 7 and 23°C). Copyright © 2010 John Wiley & Sons, Ltd.     

The complexation of protonated peptides with saccharides in the gas phase decreases the rates of hydrogen/deuterium exchange reactions

Gas-phase noncovalently bound complexes are probed by hydrogen/deuterium exchange. The complexes, composed of a protonated amino acid and a monosaccharide, are investigated to observe the effects of complexation on the rates of exchange. Rate constants are determined and compared for complexed and uncomplexed amino acids. The overall rate constant, which corresponds to exchange of a specific number of hydrogens, is deconvoluted to yield site-specific rate constants. Complexation of amino acids with saccharides significantly decreases the rate constants of the exchange. Results of molecular orbital calculations are provided to explain the decrease in the rates.     

Carbonylverbindungen als Kohlenstoffsäuren

Proton transfer to carbon bases (enols) and from carbon acids (ketones) determines the rate of ketonization and enolization reactions, respectively. Kinetic studies performed over the last two decades have provided absolute rate constants and reliable equilibrium constants for a broad range of prototropic reactions. Structure-reactivity and free energy relationships now form a reliable framework to predict the reactivity of the transient species involved in these fundamental reactions. Comparison of reaction rates in aqueous solution with rates achieved by enzymes reveals the striking efficiency of the latter.     

UV effects on marine planktonic food webs: A synthesis of results from mesocosm studies

UV irradiance has a broad range of effects on marine planktonic organisms. Direct and indirect effects on individual organisms have complex impacts on food-web structure and dynamics, with implications for carbon and nutrient cycling. Mesocosm experiments are well suited for the study of such complex interrelationships. Mesocosms offer the possibility to conduct well-controlled experiments with intact planktonic communities in physical, chemical and light conditions mimicking those of the natural environment. In allowing the manipulation of UV intensities and light spectral composition, the experimental mesocosm approach has proven to be especially useful in assessing the impacts at the community level. This review of mesocosm studies shows that, although a UV increase even well above natural intensities often has subtle effects on bulk biomass (carbon and chlorophyll), it can significantly impact the food-web structure because of different sensitivity to UV among planktonic organisms. Given the complexity of UV impacts, as evidenced by results of mesocosm studies, interactions between UV and changing environmental conditions (e.g. eutrophication and climate change) are likely to have significant effects on the function of marine ecosystems.     

Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions

Solvent exchange properties of protein backbone amide protons provide valuable residue‐specific information on protein solvent accessibility, structure stability and flexibility and hence are of significant interest in structural biology. NMR has served as a unique means for the characterization of chemical exchange including proton amide exchange with solvent water at residue‐specific levels across a broad range of exchange rates. One of the methods used for the characterization of protein backbone amide exchange by NMR involves the use of progressive selective irradiation of the water resonance. Here, we report the experimental observation of the nutation frequency (strength of RF field used for the irradiation of water resonance) modulation on amide proton signals for those in exchange with the solvent water under the band‐selective excitation short transient (BEST) conditions. Compared with conventional saturation transfer of water magnetization experiments, this nutation frequency modulation observed on signal of nuclear spins under the BEST conditions potentially offers a quick identification of protein backbone amides in rapid exchange with solvent water. Copyright © 2014 John Wiley & Sons, Ltd.