Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR.

Fold-switch pathways remodel the secondary structure topology of proteins in response to the cellular environment. It is a major challenge to understand the dynamics of these folding processes. Here, we conducted an in-depth analysis of the α-helix-to-ß-strand and ß-strand-to-α-helix transitions and domain motions displayed by the essential mannosyltransferase PimA from mycobacteria. Using 19F NMR, we identified four functionally relevant states of PimA that coexist in dynamic equilibria on millisecond-to-second timescales in solution. We discovered that fold-switching is a slow process, on the order of seconds, whereas domain motions occur simultaneously but are substantially faster, on the order of milliseconds. Strikingly, the addition of substrate accelerated the fold-switching dynamics of PimA. We propose a model in which the fold-switching dynamics constitute a mechanism for PimA activation.

Insight into Functional Membrane Proteins by Solution NMR: The Human Bcl-2 Protein-A Promising Cancer Drug Target.

Evasion from programmed cell death (apoptosis) is the main hallmark of cancer and a major cause of resistance to therapy. Many tumors simply ensure survival by over-expressing the cell-protecting (anti-apoptotic) Bcl-2 membrane protein involved in apoptotic regulation. However, the molecular mechanism by which Bcl-2 protein in its mitochondrial outer membrane location protects cells remains elusive due to the absence of structural insight; and current strategies to therapeutically interfere with these Bcl-2 sensitive cancers are limited. Here, we present an NMR-based approach to enable structural insight into Bcl-2 function; an approach also ideal as a fragment-based drug discovery platform for further identification and development of promising molecular Bcl-2 inhibitors. By using solution NMR spectroscopy on fully functional intact human Bcl-2 protein in a membrane-mimicking micellar environment, and constructs with specific functions remaining, we present a strategy for structure determination and specific drug screening of functional subunits of the Bcl-2 protein as targets. Using 19F NMR and a specific fragment library (Bionet) with fluorinated compounds we can successfully identify various binders and validate our strategy in the hunt for novel Bcl-2 selective cancer drug strategies to treat currently incurable Bcl-2 sensitive tumors.

Thermodynamics of Hg(II) Bonding to Thiol Groups in Suwannee River Natural Organic Matter Resolved by Competitive Ligand Exchange, Hg LIII-Edge EXAFS and 1H NMR Spectroscopy.

A molecular level understanding of the thermodynamics and kinetics of the chemical bonding between mercury, Hg(II), and natural organic matter (NOM) associated thiol functional groups (NOM-RSH) is required if bioavailability and transformation processes of Hg in the environment are to be fully understood. This study provides the thermodynamic stability of the Hg(NOM-RS)2 structure using a robust method in which cysteine (Cys) served as a competing ligand to NOM (Suwannee River 2R101N sample) associated RSH groups. The concentration of the latter was quantified to be 7.5 ± 0.4 µmol g-1 NOM by Hg LIII-edge EXAFS spectroscopy. The Hg(Cys)2 molecule concentration in chemical equilibrium with the Hg(II)-NOM complexes was directly determined by HPLC-ICPMS and losses of free Cys due to secondary reactions with NOM was accounted for in experiments using 1H NMR spectroscopy and 13C isotope labeled Cys. The log K ± SD for the formation of the Hg(NOM-RS)2 molecular structure, Hg2+ + 2NOM-RS- = Hg(NOM-RS)2, and for the Hg(Cys)(NOM-RS) mixed complex, Hg2+ + Cys- + NOM-RS- = Hg(Cys)(NOM-RS), were determined to be 40.0 ± 0.2 and 38.5 ± 0.2, respectively, at pH 3.0. The magnitude of these constants was further confirmed by 1H NMR spectroscopy and the Hg(NOM-RS)2 structure was verified by Hg LIII-edge EXAFS spectroscopy. An important finding is that the thermodynamic stabilities of the complexes Hg(NOM-RS)2, Hg(Cys)(NOM-RS) and Hg(Cys)2 are very similar in magnitude at pH values <7, when all thiol groups are protonated. Together with data on 15 low molecular mass (LMM) thiols, as determined by the same method ( Liem-Ngyuen et al. Thermodynamic stability of mercury(II) complexes formed with environmentally relevant low-molecular-mass thiols studied by competing ligand exchange and density functional theory . Environ. Chem. 2017 , 14 , ( 4 ), 243 - 253 .), the constants for Hg(NOM-RS)2 and Hg(Cys)(NOM-RS) represent an internally consistent thermodynamic data set that we recommend is used in studies where the chemical speciation of Hg(II) is determined in the presence of NOM and LMM thiols.

Apoptotic Bax at Oxidatively Stressed Mitochondrial Membranes: Lipid Dynamics and Permeabilization.

Mitochondria are crucial compartments of eukaryotic cells because they function as the cellular power plant and play a central role in the early stages of programmed cell death (apoptosis). To avoid undesired cell death, this apoptotic pathway is tightly regulated by members of the Bcl-2 protein family, which interact on the external surface of the mitochondria, i.e., the mitochondrial outer membrane (MOM), and modulate its permeability to apoptotic factors, controlling their release into the cytosol. A growing body of evidence suggests that the MOM lipids play active roles in this permeabilization process. In particular, oxidized phospholipids (OxPls) formed under intracellular stress seem to directly induce apoptotic activity at the MOM. Here we show that the process of MOM pore formation is sensitive to the type of OxPls species that are generated. We created MOM-mimicking liposome systems, which resemble the cellular situation before apoptosis and upon triggering of oxidative stress conditions. These vesicles were studied using 31P solid-state magic-angle-spinning nuclear magnetic resonance spectroscopy and differential scanning calorimetry, together with dye leakage assays. Direct polarization and cross-polarization nuclear magnetic resonance experiments enabled us to probe the heterogeneity of these membranes and their associated molecular dynamics. The addition of apoptotic Bax protein to OxPls-containing vesicles drastically changed the membranes' dynamic behavior, almost completely negating the previously observed effect of temperature on the lipids' molecular dynamics and inducing an ordering effect that led to more cooperative membrane melting. Our results support the hypothesis that the mitochondrion-specific lipid cardiolipin functions as a first contact site for Bax during its translocation to the MOM in the onset of apoptosis. In addition, dye leakage assays revealed that different OxPls species in the MOM-mimicking vesicles can have opposing effects on Bax pore formation.

The oxidized phospholipid PazePC promotes permeabilization of mitochondrial membranes by Bax.

Mitochondria play a crucial role in programmed cell death via the intrinsic apoptotic pathway, which is tightly regulated by the B-cell CLL/lymphoma-2 (Bcl-2) protein family. Intracellular oxidative stress causes the translocation of Bax, a pro-apoptotic family member, to the mitochondrial outer membrane (MOM) where it induces membrane permeabilization. Oxidized phospholipids (OxPls) generated in the MOM during oxidative stress directly affect the onset and progression of mitochondria-mediated apoptosis. Here we use MOM-mimicking lipid vesicles doped with varying concentrations of 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), an OxPl species known to significantly enhance Bax-membrane association, to investigate three key aspects of Bax's action at the MOM: 1) induction of Bax pores in membranes without additional mediator proteins, 2) existence of a threshold OxPl concentration required for Bax-membrane action and 3) mechanism by which PazePC disturbs membrane organization to facilitate Bax penetration. Fluorescence leakage studies revealed that Bax-induced leakage, especially its rate, increased with the vesicles' PazePC content without any detectable threshold neither for OxPl nor Bax. Moreover, the leakage rate correlated with the Bax to lipid ratio and the PazePC content. Solid state NMR studies and calorimetric experiments on the lipid vesicles confirmed that OxPl incorporation disrupted the membrane's organization, enabling Bax to penetrate into the membrane. In addition, 15N cross polarization (CP) and insensitive nuclei enhanced by polarization transfer (INEPT) MAS NMR experiments using uniformly (15)N-labeled Bax revealed dynamically restricted helical segments of Bax embedded in the membrane, while highly flexible protein segments were located outside or at the membrane surface.

Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification.

High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula × tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.

Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers.

The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to ß-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into ß-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.

Temperature response of litter and soil organic matter decomposition is determined by chemical composition of organic material.

The global soil carbon pool is approximately three times larger than the contemporary atmospheric pool, therefore even minor changes to its integrity may have major implications for atmospheric CO2 concentrations. While theory predicts that the chemical composition of organic matter should constitute a master control on the temperature response of its decomposition, this relationship has not yet been fully demonstrated. We used laboratory incubations of forest soil organic matter (SOM) and fresh litter material together with NMR spectroscopy to make this connection between organic chemical composition and temperature sensitivity of decomposition. Temperature response of decomposition in both fresh litter and SOM was directly related to the chemical composition of the constituent organic matter, explaining 90% and 70% of the variance in Q10 in litter and SOM, respectively. The Q10 of litter decreased with increasing proportions of aromatic and O-aromatic compounds, and increased with increased contents of alkyl- and O-alkyl carbons. In contrast, in SOM, decomposition was affected only by carbonyl compounds. To reveal why a certain group of organic chemical compounds affected the temperature sensitivity of organic matter decomposition in litter and SOM, a more detailed characterization of the (13) C aromatic region using Heteronuclear Single Quantum Coherence (HSQC) was conducted. The results revealed considerable differences in the aromatic region between litter and SOM. This suggests that the correlation between chemical composition of organic matter and the temperature response of decomposition differed between litter and SOM. The temperature response of soil decomposition processes can thus be described by the chemical composition of its constituent organic matter, this paves the way for improved ecosystem modeling of biosphere feedbacks under a changing climate.

Both catabolic and anabolic heterotrophic microbial activity proceed in frozen soils.

A large proportion of the global soil carbon pool is stored in soils of high-latitude ecosystems in which microbial processes and production of greenhouse gases proceed during the winter months. It has been suggested that microorganisms have limited ability to sequester substrates at temperatures around and below 0 °C and that a metabolic shift to dominance of catabolic processes occurs around these temperatures. However, there are contrary indications that anabolic processes can proceed, because microbial growth has been observed at far lower temperatures. Therefore, we investigated the utilization of the microbial substrate under unfrozen and frozen conditions in a boreal forest soil across a temperature range from -9 °C to +9 °C, by using gas chromatography-isotopic ratio mass spectrometry and (13)C magic-angle spinning NMR spectroscopy to determine microbial turnover and incorporation of (13)C-labeled glucose. Our results conclusively demonstrate that the soil microorganisms maintain both catabolic (CO(2) production) and anabolic (biomass synthesis) processes under frozen conditions and that no significant differences in carbon allocation from [(13)C]glucose into [(13)C]CO(2) and cell organic (13)C-compounds occurred between +9 °C and -4 °C. The only significant metabolic changes detected were increased fluidity of the cell membranes synthesized at frozen conditions and increased production of glycerol in the frozen samples. The finding that the processes in frozen soil are similar to those in unfrozen soil has important implications for our general understanding and conceptualization of soil carbon dynamics in high-latitude ecosystems.

Elucidation of the Binding Orientation in α2,3- and α2,6-Linked Neu5Ac-Gal Epitopes toward a Hydrophilic Molecularly Imprinted Monolith.

N-Acetylneuraminic acid and its α2,3/α2,6-glycosidic linkages with galactose (Neu5Ac-Gal) are major carbohydrate antigen epitopes expressed in various pathological processes, such as cancer, influenza, and SARS-CoV-2. We here report a strategy for the synthesis and binding investigation of molecularly imprinted polymers (MIPs) toward α2,3 and α2,6 conformations of Neu5Ac-Gal antigens. Hydrophilic imprinted monoliths were synthesized from melamine monomer in the presence of four different templates, namely, N-acetylneuraminic acid (Neu5Ac), N-acetylneuraminic acid methyl ester (Neu5Ac-M), 3'-sialyllactose (3SL), and 6'-sialyllactose (6SL), in a tertiary solvent mixture at temperatures varying from -20 to +80 °C. The MIPs prepared at cryotemperatures showed a preferential affinity for the α2,6 linkage sequence of 6SL, with an imprinting factor of 2.21, whereas the α2,3 linkage sequence of 3SL resulted in nonspecific binding to the polymer scaffold. The preferable affinity for the α2,6 conformation of Neu5Ac-Gal was evident also when challenged by a mixture of other mono- and disaccharides in an aqueous test mixture. The use of saturation transfer difference nuclear magnetic resonance (STD-NMR) on suspensions of crushed monoliths allowed for directional interactions between the α2,3/α2,6 linkage sequences on their corresponding MIPs to be revealed. The Neu5Ac epitope, containing acetyl and polyalcohol moieties, was the major contributor to the sequence recognition for Neu5Ac(α2,6)Gal(ß1,4)Glc, whereas contributions from the Gal and Glc segments were substantially lower.

Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis.

Apotosis is an essential process tightly regulated by the Bcl-2 protein family where proapoptotic Bax triggers cell death by perforating the mitochondrial outer membrane. Although intensively studied, the molecular mechanism by which these proteins create apoptotic pores remains elusive. Here, we show that Bax creates pores by extracting lipids from outer mitochondrial membrane mimics by formation of Bax/lipid clusters that are deposited on the membrane surface. Time-resolved neutron reflectometry and Fourier transform infrared spectroscopy revealed two kinetically distinct phases in the pore formation process, both of which were critically dependent on cardiolipin levels. The initially fast adsorption of Bax on the mitochondrial membrane surface is followed by a slower formation of pores and Bax-lipid clusters on the membrane surface. Our findings provide a robust molecular understanding of mitochondrial membrane perforation by cell-killing Bax protein and illuminate the initial phases of programmed cellular death.

Synthesis of poly(N-[tris(hydroxymethyl)methyl]acrylamide) functionalized porous silica for application in hydrophilic interaction chromatography.

Porous silica coated by a highly hydrophilic and nonionic tentacle-type polymeric layer was synthesized by free radical "grafting from" polymerization of N-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]-2-propenamide (TRIS-acrylamide) in partly aqueous solutions. The radical initiator sites were incorporated on the silica surfaces via a two-step reaction comprising thionyl chloride activation and subsequent reaction with tert-butyl hydroperoxide. The surface-bound tert-butylperoxy groups were then used as thermally triggered initiators for graft polymerization of TRIS-acrylamide. The synthesized materials were characterized by diffusive reflectance Fourier transform infrared specotroscopy, X-ray photoelectron spectroscopy, and CHN elemental analysis. Photon correlation spectroscopy was used to determine changes in ζ-potentials resulting from grafting, (29)Si magic angle spinning nuclear magnetic resonance spectroscopy (MAS-NMR) spectroscopy was used to assess the ratio of silanol to siloxane groups in the substrate and the grafted material, and the changes in surface area and mesopore distribution were determined by nitrogen cryosorption. Chromatographic evaluation in hydrophilic interaction chromatography (HILIC) mode showed that the materials were suitable for use as stationary phases, featuring good separation efficiency, a comparatively high retention, and a selectivity that differed from most commercially available HILIC phases. A comparison of this neutral phase with a previously reported N-(2-hydroxypropyl)-linked TRIS-type hydrophilic tentacle phase with weak anion exchange functionality revealed substantial differences in retention patterns.

Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.

Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.

Macromolecular crowding extended to a heptameric system: the Co-chaperonin protein 10.

Experiments on monomeric proteins have shown that macromolecular crowding can stabilize toward heat perturbation and also modulate native-state structure. To assess the effects of macromolecular crowding on unfolding of an oligomeric protein, we here tested the effects of the synthetic crowding agent Ficoll 70 on human cpn10 (GroES in E. coli), a heptameric protein consisting of seven identical ß-barrel subunits assembling into a ring. Using far-UV circular dichroism (CD), tyrosine fluorescence, nuclear magnetic resonance (NMR), and cross-linking experiments, we investigated thermal and chemical stability, as well as the heptamer-monomer dissociation constant, without and with crowding agent. We find that crowding shifts the heptamer-monomer equilibrium constant in the direction of the heptamer. The cpn10 heptamer is both thermally and thermodynamically stabilized in 300 mg/mL Ficoll 70 as compared to regular buffer conditions. Kinetic unfolding experiments show that the increased stability in crowded conditions, in part, is explained by slower unfolding rates. A thermodynamic cycle reveals that in presence of 300 mg/mL Ficoll the thermodynamic stability of each cpn10 monomer increases by over 30%, whereas the interfaces are stabilized by less than 10%. We also introduce a new approach to analyze the spectroscopic data that makes use of multiple wavelengths: this provides robust error estimates of thermodynamic parameters.

Interaction of a poly(acrylic acid) oligomer with dimyristoylphosphatidylcholine bilayers.

We studied the influence of 5 kDa poly(acrylic acid) (PAA) on the phase state, thermal properties, and lateral diffusion in bilayered systems of dimyristoylphosphatidylcholine (DMPC) using (31)P NMR spectroscopy, differential scanning calorimetry (DSC), (1)H NMR with a pulsed field gradient, and (1)H nuclear Overhauser enhancement spectroscopy (NOESY). The presence of PAA does not change the lamellar structure of the system. (1)H MAS NOESY cross-peaks observed for the interaction between lipid headgroups and polyion protons demonstrated only surface PAA-biomembrane interaction. Small concentrations of PAA (up to ∼4 mol %) lead to the appearance of a new lateral phase with a higher main transition temperature, a lower cooperativity, and a lower enthalpy of transition. Higher concentrations lead to the disappearance of measurable thermal effects. The lateral diffusion coefficient of DMPC and the apparent activation energy of diffusion gradually decreased at PAA concentrations up to around 4 mol %. The observed effects were explained by the formation of at least two types of PAA-DMPC lateral complexes as has been described earlier (Fujiwara, M.; Grubbs, R. H.; Baldeschwieler, J. D. J. Colloid Interface Sci., 1997, 185, 210). The first one is characterized by a stoichiometry of around 28 lipids per polymer, which corresponds to the adsorption of the entire PAA molecule onto the membrane. Lipid molecules of the complex are exchanged with the "pure" lipid bilayer, with the lifetime of the complex being less than 0.1 s. The second type of DMPC-PAA complex is characterized by a stoichiometry of 6 to 7 lipids per polymer and contains PAA molecules that are only partially adsorbed onto the membrane. A decrease in the DMPC diffusion coefficient and activation energy for diffusion in the presence of PAA was explained by the formation of a new cooperative unit for diffusion, which contains the PAA molecule and several molecules of lipids.

Neutron reflectometry and NMR spectroscopy of full-length Bcl-2 protein reveal its membrane localization and conformation.

B-cell lymphoma 2 (Bcl-2) proteins are the main regulators of mitochondrial apoptosis. Anti-apoptotic Bcl-2 proteins possess a hydrophobic tail-anchor enabling them to translocate to their target membrane and to shift into an active conformation where they inhibit pro-apoptotic Bcl-2 proteins to ensure cell survival. To address the unknown molecular basis of their cell-protecting functionality, we used intact human Bcl-2 protein natively residing at the mitochondrial outer membrane and applied neutron reflectometry and NMR spectroscopy. Here we show that the active full-length protein is entirely buried into its target membrane except for the regulatory flexible loop domain (FLD), which stretches into the aqueous exterior. The membrane location of Bcl-2 and its conformational state seems to be important for its cell-protecting activity, often infamously upregulated in cancers. Most likely, this situation enables the Bcl-2 protein to sequester pro-apoptotic Bcl-2 proteins at the membrane level while sensing cytosolic regulative signals via its FLD region.

Probing the retention mechanism of small hydrophilic molecules in hydrophilic interaction chromatography using saturation transfer difference nuclear magnetic resonance spectroscopy.

The interactions and dynamic behavior of a select set of polar probe solutes have been investigated on three hydrophilic and polar commercial stationary phases using saturation transfer difference 1H nuclear magnetic resonance (STD-NMR) spectroscopy under magic angle spinning conditions. The stationary phases were equilibrated with a select set of polar solutes expected to show different interaction patterns in mixtures of deuterated acetonitrile and deuterium oxide, with ammonium acetate added to a total concentration that mimics typical eluent conditions for hydrophilic interaction chromatography (HILIC). The methylene groups of the stationary phases were selectively irradiated to saturate the ligand protons, at frequencies that minimized the overlaps with reporting protons in the test probes. During and after this radiation, the saturation rapidly spreads to all protons in the stationary phase by spin diffusion, and from those to probe protons in contact with the stationary phase. Probe protons that have been in close contact with the stationary phase and subsequently been released to the solution phase will have been more saturated due to a more efficient transfer of spin polarization by the nuclear Overhauser effect. They will therefore show a higher signal after processing of the data. Saturation transfers to protons in neutral and charged solutes could in some instances show clear orientation patterns of these solutes towards the stationary phases. The saturation profile of formamide and its N-methylated counterparts showed patterns that could be interpreted as oriented hydrogen bond interaction. From these studies, it is evident that the functional groups on the phase surface have a strong contribution to the selectivity in HILIC, and that the retention mechanism has a significant contribution from oriented interactions.

Noncooperative folding of subdomains in adenylate kinase.

Conformational change is regulating the biological activity of a large number of proteins and enzymes. Efforts in structural biology have provided molecular descriptions of the interactions that stabilize the stable ground states on the reaction trajectories during conformational change. Less is known about equilibrium thermodynamic stabilities of the polypeptide segments that participate in structural changes and whether the stabilities are relevant for the reaction pathway. Adenylate kinase (Adk) is composed of three subdomains: CORE, ATPlid, and AMPbd. ATPlid and AMPbd are flexible nucleotide binding subdomains where large-scale conformational changes are directly coupled to catalytic activity. In this report, the equilibrium thermodynamic stabilities of Adk from both mesophilic and hyperthermophilic bacteria were investigated using solution state NMR spectroscopy together with protein engineering experiments. Equilibrium hydrogen to deuterium exchange experiments indicate that the flexible subdomains are of significantly lower thermodynamic stability compared to the CORE subdomain. Using site-directed mutagenesis, parts of ATPlid and AMPbd could be selectively unfolded as a result of perturbation of hydrophobic clusters located in these respective subdomains. Analysis of the perturbed Adk variants using NMR spin relaxation and C(alpha) chemical shifts shows that the CORE subdomain can fold independently of ATPlid and AMPbd; consequently, folding of the two flexible subdomains occurs independently of each other. Based on the experimental results it is apparent that the flexible subdomains fold into their native structure in a noncooperative manner with respect to the CORE subdomain. These results are discussed in light of the catalytically relevant conformational change of ATPlid and AMPbd.

Preparation and characterization of sizable macroporous epoxy resin-based monolithic supports for flow-through systems.

This paper presents further results from our efforts to prepare sizable macroporous monolithic materials from epoxy resins and polyamines by emulsion polymerization. For their uses as supports in flow systems, the study aimed at developing materials possessing maximum fluid permeability, high mechanical stability, and a controlled porosity and surface area. Characterization of the materials has been carried out using different techniques, focusing on morphological and mechanical features, and on the surface chemistry. Morphology and porosity were studied with SEM, nitrogen adsorption/desorption, mercury intrusion porosimetry (MIP), and (2)H NMR cryoporosimetry. The chemical composition of the bulk structures and their surfaces was studied by means of bulk elemental analysis and X-ray photoelectron spectroscopy, and potentiometric titration was used to assess the relative amounts of amines and epoxy groups. Essentially, the morphological features were a high fluid permeability, but rather low specific surface area. Convective flow was facilitated by large, interconnected, and evenly spaced macropores which were formed by nonporous skeletons of the connected-rod type. Despite the interfacial nature of the polymerization, the bulk and the surface of the fully cured materials showed similar elemental compositions. All materials were found to have a high surface density of hydroxyl groups, which facilitates functionalization reactions.

Interaction of toluene with polar stationary phases under conditions typical of hydrophilic interaction chromatography probed by saturation transfer difference nuclear magnetic resonance spectroscopy.

Toluene has been used as void volume (zero retention) marker since the inception of hydrophilic interaction chromatography (HILIC), based on the assumption that its hydrophobicity should prevent it from interacting with stationary phases envisioned to be covered by relatively thick layers of water. Recent work has shown that the void volumes of partly water-swollen HILIC phases are not identical to the volumes probed by toluene, yet the compound is still ubiquitously used as void volume marker. As part of our investigations of the retention mechanisms in HILIC, we probed the extent to which toluene is capable of penetrating into the water-enriched layer and to interact with the functional groups of three commercially available hydrophilic and polar stationary phases with different charge properties and water-retaining abilities, using saturation transfer difference 1H nuclear magnetic resonance (STD-NMR) spectroscopy at high resolution magic angle spinning (HR-MAS) conditions. The test solutions were 1000 ppm of toluene in deuterated acetonitrile and water mixtures, with and without addition of ammonium acetate, in order to mimic a set of conditions typically encountered in HILIC separations. Interactions between toluene and the functional groups on the stationary phases were probed by equilibrating the phases with these eluent mimics and measuring the transfer of magnetization from stationary phase protons to the protons of toluene. Our results show that toluene is indeed capable of traversing the water-enriched layers of all the three tested phases and of interacting with protons that are tightly associated with the stationary phases.