Ethical Stakes for Past, Present, and Prospective Tuberculosis Isolate Research Towards a Multicultural Data Sovereignty Model for Isolate Samples in Research.

Tuberculosis (TB) is a potentially fatal infectious disease that, in Aotearoa New Zealand (NZ), inequitably affects Asian, Pacific, Middle Eastern, Latin American, and African (MELAA), and Maori people. Medical research involving genome sequencing of TB samples enables more nuanced understanding of disease strains and their transmission. This could inform highly specific health interventions. However, the collection and management of TB isolate samples for research are currently informed by monocultural biomedical models often lacking key ethical considerations. Drawing on a qualitative kaupapa Maori-consistent study, this paper reports on preliminary discussions with groups of Maori, Pacific, and Afghan people in NZ, whose communities have been harmed by TB and TB stigma. Participants' discussions highlight key concerns and meanings that ought to inform the development of guidelines and a more robust consultative process for the governance of how TB isolate samples are collected and used both retrospectively and in future research. We argue for ethical processes to be culturally nuanced and community-generated, flexible and meaningful, and situated in relation to the physical and symbolic effects of TB. We discuss the significance of Indigenous data sovereignty, rights, and kawanatanga (governorship) in shaping a multicultural data sovereignty model.

Evidence for a short-lived resonance state in enzyme catalysis via rate-equation convolution.

At the cellular level, all biological function relies on enzymes to provide catalytic acceleration of essential biochemical processes driving cellular metabolism. The enzyme is presumed to lower the activation energy barrier separating reactants from products, but the precise mechanism remains unresolved. Here we examine the temperature dependence of the enzyme-catalyzed dissociation of p-nitrophenyl-α-D-glucopyranoside (pNPG), a chromogenic analog for maltose, isomaltose, and sucrose disaccharide sugars, into p-nitrophenol (pNP) and glucose (monosaccharide). The enzymes of interest are the wild type and mutant forms of glucosidase MalL produced by the probiotic bacterium Bacillus subtilis. The per-enzyme production rates k(T) for the pNPG→ glucose reaction all show a characteristic temperature profile with an Arrhenius-like (approximately exponential) slow acceleration at low temperatures, rising through a point of inflexion to reach a maximum, then turning over to decline steeply towards zero production at high temperatures. This asymmetric profile is found to be well fitted by convolving an exponential growth function f(T) with a Gaussian temperature distribution g(T) to produce an exponentially modified Gaussian function h(T). To give a physical interpretation of the convolution components, we make the temperature mapping Θ≡T_{ref}-T where T_{ref} marks the temperature at which a given mutant becomes fully denatured (unfolded) and therefore inactive, then convert the convolution components to probability density functions which obey the convolution theorem of statistics. Working in Θ space, we identify f(Θ) as the density function for an Arrhenius-like transition from ground-state A to metastable-state B, and g(Θ) as the Gaussian distribution of offset-temperature fluctuations for the metastable state. By mapping the standard thermodynamic relations for temperature and energy fluctuations to the enzyme frame of reference, we are able to derive an expression for the lifetime for the metastable B state. For the 15 enzyme experiments, we obtain a mean value 〈Δt〉≳(29.0±1.3)×10^{-15}s, in remarkably good agreement with the ∼30-fs estimate for the period of glycosidic bond oscillations extracted from published infrared spectroscopy. We suggest that the metastable B state provides a low-energy target that has the effect of lowering the activation energy barrier by presenting an alternative axis for the reaction coordinate.

A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability.

It is now over 30 years since Demchenko and Ladokhin first posited the potential of the tryptophan red edge excitation shift (REES) effect to capture information on protein molecular dynamics. While there have been many key efforts in the intervening years, a biophysical thermodynamic model to quantify the relationship between the REES effect and protein flexibility has been lacking. Without such a model the full potential of the REES effect cannot be realized. Here, we present a thermodynamic model of the tryptophan REES effect that captures information on protein conformational flexibility, even with proteins containing multiple tryptophan residues. Our study incorporates exemplars at every scale, from tryptophan in solution, single tryptophan peptides, to multitryptophan proteins, with examples including a structurally disordered peptide, de novo designed enzyme, human regulatory protein, therapeutic monoclonal antibodies in active commercial development, and a mesophilic and hyperthermophilic enzyme. Combined, our model and data suggest a route forward for the experimental measurement of the protein REES effect and point to the potential for integrating biomolecular simulation with experimental data to yield novel insights.

Structural analysis of the GH43 enzyme Xsa43E from Butyrivibrio proteoclasticus.

The rumen of dairy cattle can be thought of as a large, stable fermentation vat and as such it houses a large and diverse community of microorganisms. The bacterium Butyrivibrio proteoclasticus is a representative of a significant component of this microbial community. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fibre-degrading enzymes. This suite of enzymes is essential for the organism to utilize the plant material within the rumen as a fuel source, facilitating its survival in this competitive environment. Xsa43E, a GH43 enzyme from B. proteoclasticus, has been structurally and functionally characterized. Here, the structure of selenomethionine-derived Xsa43E determined to 1.3 Šresolution using single-wavelength anomalous diffraction is reported. Xsa43E possesses the characteristic five-bladed ß-propeller domain seen in all GH43 enzymes. GH43 enzymes can have a range of functions, and the functional characterization of Xsa43E shows it to be an arabinofuranosidase capable of cleaving arabinose side chains from short segments of xylan. Full functional and structural characterization of xylan-degrading enzymes will aid in creating an enzyme cocktail that can be used to completely degrade plant material into simple sugars. These molecules have a range of applications as starting materials for many industrial processes, including renewable alternatives to fossil fuels.

The multifunctional histone-like protein Lsr2 protects mycobacteria against reactive oxygen intermediates.

Mycobacterium tuberculosis has evolved a number of strategies to survive within the hostile environment of host phagocytes. Reactive nitrogen and oxygen intermediates (RNI and ROI) are among the most effective antimycobacterial molecules generated by the host during infection. Lsr2 is a M. tuberculosis protein with histone-like features, including the ability to regulate a variety of transcriptional responses in mycobacteria. Here we demonstrate that Lsr2 protects mycobacteria against ROI in vitro and during macrophage infection. Furthermore, using macrophages derived from NOS(-/-) and Phox(-/-) mice, we demonstrate that Lsr2 is important in protecting against ROI but not RNI. The protection provided by Lsr2 protein is not the result of its ability to either bind iron or scavenge hydroxyl radicals. Instead, electron microscopy and DNA-binding studies suggest that Lsr2 shields DNA from reactive intermediates by binding bacterial DNA and physically protecting it. Thus, Lsr2 appears to be a unique protein with both histone-like properties and protective features that may be central to M. tuberculosis pathogenesis. In addition, evidence indicates that lsr2 is an essential gene in M. tuberculosis. Because of its essentiality, Lsr2 may represent an excellent candidate as a drug target.

The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology.

The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.

Structure of HisF, a histidine biosynthetic protein from Pyrobaculum aerophilum.

HisF (imidazole glycerol phosphate synthase) is an important branch-point enzyme in the histidine biosynthetic pathway of microorganisms. Because of its potential relevance for structure-based drug design, the crystal structure of HisF from the hyperthermophilic archaeon Pyrobaculum aerophilum has been determined. The structure was determined by molecular replacement and refined at 2.0 A resolution to a crystallographic R factor of 20.6% and a free R of 22.7%. The structure adopts a classic (beta/alpha)(8) barrel fold and has networks of surface salt bridges that may contribute to thermostability. The active site is marked out by the presence of two bound phosphate ions and two glycerol molecules that delineate a long groove at one end of the (beta/alpha)(8) barrel. The two phosphate ions, 17 A apart, are bound to sequence-conserved structural motifs that seem likely to provide much of the specificity for the two phosphate groups of the HisF substrate. The two glycerol molecules bind in the vicinity of other sequence-conserved residues that are likely to be involved in binding and/or catalysis. Comparisons with the homologous HisF from Thermatoga maritima reveal a displaced loop that may serve as a lid over the active site.

LISA: an intranet-based flexible database for protein crystallography project management.

The increase in the number of projects carried out in protein crystallography laboratories has emphasized the need for effective management of project information and data. To meet this need, a flexible web-accessible database for protein crystallography project management (LISA) has been developed using the open-source software MySQL and PHP4. The database contains information about all aspects of structure-determination projects, including primer and plasmid sequences, protein expression, purification and crystallization results, structure coordinate files and resultant publications. The database web pages include links to relevant servers and contain, in addition, tools for processing stored information. The software package is freely available.

Immunological and biochemical characterization of streptococcal pyrogenic exotoxins I and J (SPE-I and SPE-J) from Streptococcus pyogenes.

Recently, we described the identification of novel streptococcal superantigens (SAgs) by mining the Streptococcus pyogenes M1 genome database at Oklahoma University. Here, we report the cloning, expression, and functional analysis of streptococcal pyrogenic exotoxin (SPE)-J and another novel SAg (SPE-I). SPE-I is most closely related to SPE-H and staphylococcal enterotoxin I, whereas SPE-J is most closely related to SPE-C. Recombinant forms of SPE-I and SPE-J were mitogenic for PBL, both reaching half maximum responses at 0.1 pg/ml. Evidence from binding studies and cell aggregation assays using a human B-lymphoblastoid cell line (LG-2) suggests that both toxins exclusively bind to the polymorphic MHC class II beta-chain in a zinc-dependent mode but not to the generic MHC class II alpha-chain. The results from analysis by light scattering indicate that SPE-J exists as a dimer in solution above concentrations of 4.0 mg/ml. Moreover, SPE-J induced a rapid homotypic aggregation of LG-2 cells, suggesting that this toxin might cross-link MHC class II molecules on the cell surface by building tetramers of the type HLA-DRbeta-SPE-J-SPE-J-HLA-DRbeta. SPE-I preferably stimulates T cells bearing the Vbeta18.1 TCR, which is not targeted by any other known SAG: SPE-J almost exclusively stimulates Vbeta2.1 T cells, a Vbeta that is targeted by several other streptococcal SAgs, suggesting a specific role for this T cell subpopulation in immune defense. Despite a primary sequence diversity of 51%, SPE-J is functionally indistinguishable from SPE-C and might play a role in streptococcal disease, which has previously been addressed to SPE-C.

Conservation and variation in superantigen structure and activity highlighted by the three-dimensional structures of two new superantigens from Streptococcus pyogenes.

Bacterial superantigens (SAgs) are a structurally related group of protein toxins secreted by Staphylococcus aureus and Streptococcus pyogenes. They are implicated in a range of human pathologies associated with bacterial infection whose symptoms result from SAg-mediated stimulation of a large number (2-20%) of T-cells. At the molecular level, bacterial SAgs bind to major histocompatability class II (MHC-II) molecules and disrupt the normal interaction between MHC-II and T-cell receptors (TCRs). We have determined high-resolution crystal structures of two newly identified streptococcal superantigens, SPE-H and SMEZ-2. Both structures conform to the generic bacterial superantigen folding pattern, comprising an OB-fold N-terminal domain and a beta-grasp C-terminal domain. SPE-H and SMEZ-2 also display very similar zinc-binding sites on the outer concave surfaces of their C-terminal domains. Structural comparisons with other SAgs identify two structural sub-families. Sub-families are related by conserved core residues and demarcated by variable binding surfaces for MHC-II and TCR. SMEZ-2 is most closely related to the streptococcal SAg SPE-C, and together they constitute one structural sub-family. In contrast, SPE-H appears to be a hybrid whose N-terminal domain is most closely related to the SEB sub-family and whose C-terminal domain is most closely related to the SPE-C/SMEZ-2 sub-family. MHC-II binding for both SPE-H and SMEZ-2 is mediated by the zinc ion at their C-terminal face, whereas the generic N-terminal domain MHC-II binding site found on many SAgs appears not to be present. Structural comparisons provide evidence for variations in TCR binding between SPE-H, SMEZ-2 and other members of the SAg family; the extreme potency of SMEZ-2 (active at 10(-15) g ml-1 levels) is likely to be related to its TCR binding properties. The smez gene shows allelic variation that maps onto a considerable proportion of the protein surface. This allelic variation, coupled with the varied binding modes of SAgs to MHC-II and TCR, highlights the pressure on SAgs to avoid host immune defences.

Superantigens - powerful modifiers of the immune system.

Superantigens are powerful microbial toxins that activate the immune system by binding to class II major histocompatibility complex and T-cell receptor molecules. They cause a number of diseases characterized by fever and shock and are important virulence factors for two human commensal organisms, Staphylococcus aureus and Streptococcus pyogenes, as well as for some viruses. Their mode of action and variation around the common theme of over-stimulating T cells, provides a rich insight into the constant battle between microbes and the immune system.

The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin.

The third fibronectin type III domain from human tenascin adopts a compact beta-sandwich fold. Its boundaries were originally selected to encode a 90-residue domain (TNfn31-90). We conclude that the dynamic properties of TNfn3 are more accurately represented when the C terminus is extended by the two naturally succeeding residues. Longitudinal (R1) and transverse (R2) 15N relaxation rates, and ¿1H-15N¿ NOE enhancements at pH 4.9 and 300 K are presented for TNfn31-90 and TNfn31-92, the extended form, at two field strengths (11.74 and 14.10 T). Nearly identical results confirm their similar motional properties over a broad range of timescales. However, a number of residues near the C terminus in TNfn31-90 exhibit elevated transverse relaxation rates and broadened signals in 1H-15N HSQC spectra. Explicit rates of chemical exchange for five residues in TNfn31-90 were determined by measuring transverse relaxation rates in a series of CPMG experiments with spin-echo refocusing delays increasing from 311 to 1436 micros. Calculated exchange rates average 1000(+/-311) s-1, with individual uncertainties near 20%. Homonuclear TOCSY experiments collected between pH 4 and 7 reveal the coincident titration of two acidic clusters in TNfn31-90 at pH 5. 64(+/-0.47). The repulsive electrostatic interaction of the C-terminal carboxylate with one of these clusters may promote chemical exchange in the shorter domain. Additionally, NOE and chemical shift data suggest hydrogen bond formation between the added residues and adjacent loops. The data affirm the importance of judiciously selecting domain boundaries prior to the characterization of molecular properties.

A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding.

The denatured states of barnase that are induced by urea, acid, and high temperature and acid have been assigned and characterised by high resolution heteronuclear NMR. The assignment was completed using a combination of triple-resonance and magnetisation-transfer methods. The latter was facilitated by selecting a suitable mutant of barnase (Ile-->Val51) which has an appropriate rate of interconversion between native and denatured states in urea. 3J NH-C alpha H coupling constants were determined for pH and urea-denatured barnase and intrinsic "random coil" coupling constants are shown to be different for different residue types. All the denatured states are highly unfolded. But, a consistent series of weak correlations in chemical shift, NOESY and coupling constant data provides evidence that the acid-denatured state has some residual structure in regions that form the first and second helices and the central strands of beta-sheet in the native protein. The acid/temperature-denatured states has less structure in these regions, and the urea-denatured state, less still. These observations may be combined with detailed analyses of the folding pathway of barnase from kinetic studies to illuminate the relevance of residual structure in the denatured states of proteins to the mechanism of protein folding. First, the folding of barnase is known to proceed in its later stages through structures in which the first helix and centre of the beta-sheet are extensively formed. Thus, embryonic initiation sites for these do exist in the denatured states and so could well develop into true nuclei. Second, it has been clearly established that the second helix is unfolded in these later states, and so residual structure in this region of the protein is non-productive. These data fit a model of protein folding in which local nucleation sites are latent in the denatured state and develop only when they make interactions elsewhere in the protein that stabilise them during the folding process. Thus, studies of the structure of denatured states pinpoint where nucleation sites may be, and the kinetic and protein engineering studies show which ones are productive.

pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds.

We have determined the pKA values of the 12 carboxyl residues in the native and denatured state of barnase by a combination of thermodynamic measurements on mutants of charged residues and NMR titration data. The pKA values of the 11 residues titrating under folding conditions (above pH 2.2) were determined by two-dimensional 1H NMR. The pKA value of the remaining residue, Asp 93 which forms a salt link with Arg 69 and titrates at much lower pH values, was determined by changes in the pH dependence of the stability of the protein upon mutation to Asn: pKAsp93A at low ionic strength (50 mM) and pKAsp93A at high ionic strength (600 mM). The overall titration of the native state is nonideal, and the protein retains fractionally ionized residues other than Asp 93 throughout the experimental pH range of 0.2-6.3. Protonation events taking place at pH values below 2 were further characterized by the pH dependence of the unfolding kinetics of wild-type and charge-mutant proteins. By comparing the observed pH dependence of the protein stability with that calculated from the pKA values for the native protein, we demonstrate that the pKA values of the denatured state are significantly lower than those reported for model compounds: the pKA values of the denatured state appear on average 0.4 units lower than previous estimates in the presence of chemical denaturant. The results have direct implications for calculations of the energetics of proton equilibria and suggest that the acid/thermally denatured state is not an extended coil where the residues are isolated from one another by the intervening solvent but is compact and involves intramolecular charge repulsion.

Toward solving the folding pathway of barnase: the complete backbone 13C, 15N, and 1H NMR assignments of its pH-denatured state.

The structures of the major folding intermediate, the transition state for folding, and the folded state of barnase have been previously characterized. We now add a further step toward a complete picture of the folding of barnase by reporting the backbone 15N, 13C, and 1H NMR assignments for barnase unfolded at pH 1.8 and 30 degrees C. These assignments, which were obtained from a combination of heteronuclear magnetization transfer and backbone triple-resonance NMR experiments, constitute the first stage in the structural characterization of this denatured state by NMR. Interresidue nuclear Overhauser effect contacts and deviations from 1H random-coil chemical shifts provide evidence for stable residual structure. The structured regions span residues in the native protein that contain its major alpha-helix and central strands of the beta-sheet. Earlier experiments have shown that these regions are predominantly intact in the major folding intermediate and that their docking is partly rate determining in folding.

Structural studies on peptides corresponding to mutants of the major alpha-helix of barnase.

The structures of a family of peptides that contain variants of the major alpha-helix of barnase (residues 6-18) have been analyzed in solution by circular dichroism (CD) and 1H NMR at various concentrations of the helix-inducing cosolvent trifluoroethanol (TFE). The very low equilibrium constant (approximately 10(-2) for the formation of helix in water KH2O was estimated from titration of the helical ellipticity signal at 222 nm with [TFE] using the equation, KTFE = KH2O exp((m/RT) [TFE]/[H2O]), where KTFE is the equilibrium constant for the formation of helix in TFE/H2O and m is characteristic for each peptide but appears to be proportional to the lengths of related helices. NMR studies show that the peptide is mainly random coil in water, but that the helix is induced cooperatively by TFE and extends from residues 6 to 18 for wild-type peptide in 35% TFE. The mutant peptide Tyr-17-->Ala, however, has a helical region extending only for residues 9-15. Truncation of the helix upon mutation is also detected in the TFE titration procedure, which finds correspondingly lowered m-values upon mutation. This is is also supported by measurements of the pH dependence of KH2O, which is caused by the ionization of the C-cap residue, His-18, whose pKa is raised by the interaction of the protonated form with the helix dipole. Whereas there is an apparent charge/dipole interaction energy of 1.1 kcal mol-1 in the wild-type peptide, similar to that measured in the native protein, this drops dramatically upon mutations that disrupt the C-terminus of the helix. Mutation of Tyr-17-->Ala lowers KH2O only slightly, as do the other helix-destabilizing mutations. The combined results show that the helix-weakening effects of mutations act here primarily by shortening the length of the helix, with smaller effects on the equilibrium constants between helix and coil (KH2O).(ABSTRACT TRUNCATED AT 250 WORDS)