Multi-angle in situ dynamic light scattering at a neutron spin echo spectrometer.

A new sample environment, called Bio-Oven, has been built for the Neutron Spin Echo (NSE) Spectrometer J-NSE Phoenix. It provides active temperature control and the possibility to perform Dynamic Light Scattering (DLS) measurements during the neutron measurement. DLS provides diffusion coefficients of the dissolved nanoparticles, and thus one can monitor the aggregation state of the sample on a time scale of minutes during the spin echo measurement times on the order of days. This approach helps to validate the NSE data or to replace the sample when its aggregation state influences the spin echo measurement results. The new Bio-Oven is an in situ DLS setup based on optical fibers decoupling the free space optics around the sample cuvette in a lightproof casing from the laser sources and the detectors. It collects light from three scattering angles simultaneously. Six different values of momentum transfer can be accessed by switching between two different laser colors. Test experiments were performed with silica nanoparticles with diameters ranging from 20 nm up to 300 nm. Their hydrodynamic radii were determined from DLS measurements and compared with the ones obtained by a commercial particle sizer. It was demonstrated that also the static light scattering signal can be processed and gives meaningful results. The protein sample apomyoglobin was used for a long-term test and in a first neutron measurement using the new Bio-Oven. The results prove that the aggregation state of the sample can be followed using in situ DLS along with the neutron measurement.

Increased progesterone receptor A expression in labouring human myometrium is associated with decreased promoter occupancy by the histone demethylase JARID1A.

Progesterone regulates female reproductive function predominantly through two nuclear progesterone receptors (PRs), PR-A and PR-B. During human parturition myometrial PR expression is altered to favour PR-A, which activates pro-labour genes. We have previously identified histone H3 lysine 4 trimethylation (H3K4me3) as an activator of myometrial PR-A expression at labour. To further elucidate the mechanisms regulating PR isoform expression in the human uterus at labour, we have (i) determined the methylation profile of the cytosine-guanine dinucleotides (CpG) island in the promoter region of the PR gene and (ii) identified the histone-modifying enzymes that target the H3K4me3 mark at the PR promoters in term and preterm human myometrial tissues obtained before and after labour onset. Bisulphite sequencing showed that despite overall low levels of PR CpG island methylation, there was a significant decrease in methylated CpGs with labour in both preterm (P < 0.05) and term (P < 0.01) groups downstream of the PR-B transcription start site. This methylation change was not associated with altered PR-B expression, but may contribute to the increase in PR-A expression with labour. Chromatin immunoprecipitation revealed that the histone methyltransferase, SET and MYND domain-containing protein 3 (SMYD3), bound to the PR gene at significantly higher levels at the PR-A promoter compared with the PR-B promoter (P < 0.010), with no labour-associated changes observed. The H3K4 demethylase, Jumonji AT-rich interactive domain 1A (JARID1A), also bound to the PR-A, but not to the PR-B promoter prior to term labour, and decreased significantly at the onset of labour (P = 0.014), providing a mechanism for the previously reported increase in H3K4me3 level and PR-A expression with labour. Our studies suggest that epigenetic changes mediated by JARID1A, SMYD3 and DNA methylation may be responsible, at least in part, for the functional progesterone withdrawal that precipitates human labour.

Large domain fluctuations on 50-ns timescale enable catalytic activity in phosphoglycerate kinase.

Large-scale domain motions of enzymes are often essential for their biological function. Phosphoglycerate kinase has a wide open domain structure with a hinge near the active center between the two domains. Applying neutron spin echo spectroscopy and small-angle neutron scattering we have investigated the internal domain dynamics. Structural analysis reveals that the holoprotein in solution seems to be more compact compared to the crystal structure but would not allow the functionally important phosphoryl transfer between the substrates if the protein were static. Brownian large-scale domain fluctuation dynamics on a timescale of 50 ns was revealed by neutron spin echo spectroscopy. The dynamics observed was compared to the displacement patterns of low-frequency normal modes. The displacements along the normal-mode coordinates describe our experimental results reasonably well. In particular, the domain movements facilitate a close encounter of the key residues in the active center to build the active configuration. The observed dynamics shows that the protein has the flexibility to allow fluctuations and displacements that seem to enable the function of the protein. Moreover, the presence of the substrates increases the rigidity, which is deduced from a faster dynamics with smaller amplitude.

The perspectives of studying multi-domain protein folding.

Most of fundamental studies on protein folding have been performed with small globular proteins consisting of a single domain. In vitro many of these proteins are well characterized by a reversible two-state folding scheme. However, the majority of proteins in the cell belong to the class of larger multi-domain proteins that often unfold irreversibly under in vitro conditions. This makes folding studies difficult or even impossible. In spite of these problems for many multi-domain proteins, folding has been investigated by classical refolding. Co-translational folding of nascent polypeptide chains when synthesized by ribosomes has also been studied. Single molecule techniques represent a promising approach for future studies on the folding of multi-domain proteins, and tremendous advances have been made in these techniques in recent years. In particular, fluorescence-based methods can contribute significantly to an understanding of the fundamental principles of multi-domain protein folding.

Sensory rhodopsin II/transducer complex formation in detergent and in lipid bilayers studied with FRET.

The photophobic receptor from Natronomonas pharaonis (NpSRII) forms a photo-signalling complex with its cognate transducer (NpHtrII). In order to elucidate the complex formation in more detail, we have studied the intermolecular binding of both constituents (NpSRII and NpHtrII157; truncated at residue 157) in detergent buffers, and in lipid bilayers using FRET. The data for hetero-dimer formation of NpSRII/NpHtrII in detergent agrees well with KD values (approximately 200 nM) described in the literature. In lipid bilayers, the binding affinity between proteins in the NpSRII/NpHtrII complex is at least one order of magnitude stronger. In detergent the strength of binding is similar for both homo-dimers (NpSRII/NpSRII and NpHtrII/NpHtrII) but significantly weaker (KD approximately 16 microM) when compared to the hetero-dimer. The intermolecular binding is again considerably stronger in lipid bilayers; however, it is not as strong as that observed for the hetero-dimer. At a molar transducer/lipid ratio of 1:2000, which is still well above physiological concentrations, only 40% homo-dimers are formed. Apparently, in cell membranes the formation of the assumed functionally active oligomeric 2:2 complex depends on the full-length transducer including the helical cytoplasmic part, which is thought to tighten the transducer-dimer association.

Reversible and irreversible unfolding of multi-domain proteins.

In contrast to single-domain proteins unfolding of larger multi-domain proteins is often irreversible. In a comparative case study on three different multi-domain proteins (phosphoglycerate kinase: PGK and two homologous alpha-amylases: TAKA and BLA) we investigated properties of unfolded states and their ability to fold back into the native state. For this purpose guanidine hydrochloride, alkaline pH, and thermal unfolded states were characterized. Structural alterations upon unfolding and refolding transitions were monitored using fluorescence and CD spectroscopy. Static and dynamic light scattering was employed to follow aggregation processes. Furthermore, proper refolding was also investigated by enzyme activity measurements. While for PGK at least partial reversible unfolding transitions were observed in most cases, we found reversible unfolding for TAKA in the case of alkaline pH and GndHCl induced unfolding. BLA exhibits reversible unfolding only under conditions with high concentrations of protecting osmolytes (glycerol), indicating that aggregation of the unfolded state is the main obstacle to achieve proper refolding for this protein. Structural properties, such as number and size of domains, secondary structure contents and compositions within domains, and domain topology were analyzed and considered in the interpretation of differences in refolding behavior of the investigated proteins.

How aggregation and conformational scrambling of unfolded states govern fluorescence emission spectra.

In a case study on five homologous alpha-amylases we analyzed the properties of unfolded states as obtained from treatments with GndHCl and with elevated temperatures. In particular the wavelength of the tryptophan fluorescence emission peak (lambda(max)) is a valuable parameter to characterize properties of the unfolded state. In all cases with a typical red shift of the emission spectrum occurring during structural unfolding we observed a larger magnitude of this shift for GndHCl-induced unfolding as compared to thermal unfolding. Although a quantitative relation between aggregation and reduction of the unfolding induced red shifts cannot be given, our data indicate that protein aggregation contributes significantly to smaller magnitudes of red shifts as observed during thermal unfolding. In addition, other properties of the unfolded states, most probable structural compactness or simply differences in the conformational scrambling, also affect the magnitude of red shifts. For the irreversible unfolding alpha-amylases studied here, transition temperatures and magnitudes of red shifts are strongly depending on heating rates. Lower protein concentrations and smaller heating rates lead to larger red shifts upon thermal unfolding, indicating that under these conditions the protein aggregation is less pronounced.

Structural and dynamical features contributing to thermostability in alpha-amylases.

In recent years an increasing number of studies on thermophilic and hyperthermophilic proteins aiming to elucidate determinants of protein thermostability have yielded valuable insights about the relevant mechanisms. In particular, comparison of homologous enzymes with different thermostabilities (isolated from psychrophilic, mesophilic, thermophilic and hyperthermophilic organisms) offers a unique opportunity to determine the strategies of thermal adaptation. In this respect, the medium-sized amylolytic enzyme alpha-amylase is a well-established representative. Various studies on alpha-amylases with very different thermostabilities (melting temperature T(m) = 40-110 degrees C) report structural and dynamical features as well as thermodynamical properties which are supposed to play key roles in thermal adaptation. Here, results from selected homologous alpha-amylases are presented and discussed with respect to some new and recently proposed strategies to achieve thermostability.

Structural stability and unfolding properties of thermostable bacterial alpha-amylases: a comparative study of homologous enzymes.

In a comparative investigation on two thermostable alpha-amylases [Bacillus amyloliquefaciens (BAA), T(m) = 86 degrees C and Bacillus licheniformis (BLA), T(m) = 101 degrees C], we studied thermal and guanidine hydrochloride (GndHCl)-induced unfolding using fluorescence and CD spectroscopy, as well as dynamic light scattering. Depletion of calcium from specific ion-binding sites in the protein structures reduces the melting temperature tremendously for both alpha-amylases. The reduction is nearly the same for both enzymes, namely, in the order of 50 degrees C. Thus, the difference in thermostability between BLA and BAA (DeltaT(m) approximately 15 degrees C) is related to intrinsic properties of the respective protein structures themselves and is not related to the strength of ion binding. The thermal unfolding of both proteins is characterized by a full disappearance of secondary structure elements and by a concurrent expansion of the 3D structure. GndHCl-induced unfolding also yields a fully vanishing secondary structure but with more expanded 3D structures. Both alpha-amylases remain much more compact upon thermal unfolding as compared to the fully unfolded state induced by chemical denaturants. Such rather compact thermal unfolded structures lower the conformational entropy change during the unfolding transition, which principally can contribute to an increased thermal stability. Structural flexibilities of both enzymes, as measured with tryptophan fluorescence quenching, are almost identical for both enzymes in the native states, as well as in the unfolded states. Furthermore, we do not observe any difference in the temperature dependence of the structural flexibilities between BLA and BAA. These results indicate that conformational dynamics on the time scale of our studies seem not to be related to thermal stability or to thermal adaptation.

Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation.

To elucidate how enzymes adapt to extreme environmental conditions, a comparative study with a thermostable alpha-amylase from Bacillus licheniformis (BLA) and its mesophilic homologue from Bacillus amyloliquefaciens (BAA) was performed. We measured conformational stability, catalytic activity, and conformational fluctuations on the picosecond time scale for both enzymes as a function of temperature. The objective of this study is to analyze how these properties are related to each other. BLA shows its maximal catalytic activity at about 90-95 degrees C and a strongly reduced activity (only 20% of the maximum) at room temperature. Although B. licheniformis itself is a mesophilic organism, BLA shows an activity profile typical for a thermophilic enzyme. In contrast to this, BAA exhibits its maximal activity at about 80 degrees C but with a level of about 60% activity at room temperature. In both cases the unfolding temperatures T(m) are only 6 degrees C (BAA, T(m) = 86 degrees C) and 10 degrees C (BLA, T(m) = 103 degrees C), respectively, higher than the temperatures for maximal activity. In contrast to many previous studies on other thermophilic-mesophilic pairs, in this study a higher structural flexibility of the thermostable BLA was measured as compared to the mesophilic BAA. The findings of this study neither indicate a proportionality between the observed dynamics and the catalytic activity nor support the idea of more "rigid" thermostable proteins, as often proposed in the concept of "corresponding states".

Structural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.

By comparing a mesophilic alpha-amylase with its thermophilic homolog, we investigated the relationship between thermal stability and internal equilibrium fluctuations. Fourier transform infrared spectroscopy monitoring hydrogen/deuterium (H/D) exchange kinetics and incoherent neutron scattering measuring picosecond dynamics were used to study dynamic features of the folded state at room temperature. Fairly similar rates of slowly exchanging amide protons indicate about the same free energy of stabilization DeltaG(stab) for both enzymes at room temperature. With respect to motions on shorter time scales, the thermophilic enzyme is characterized by an unexpected higher structural flexibility as compared to the mesophilic counterpart. In particular, the picosecond dynamics revealed a higher degree of conformational freedom for the thermophilic alpha-amylase. The mechanism proposed for increasing thermal stability in the present case is characterized by entropic stabilization and by flattening of the curvature of DeltaG(stab) as a function of temperature.

Bacteriorhodopsin: the functional details of a molecular machine are being resolved

The photon-driven proton translocator bacteriorhodopsin is considered to be the best understood membrane protein so far. It is nowadays regarded as a model system for photosynthesis, ion pumps and seven transmembrane receptors. The profound knowledge came from the applicability of a variety of modern biophysical techniques which have often been further developed with research on bacteriorhodopsin and have delivered major contributions also to other areas. Most prominent examples are electron crystallography, solid-state NMR spectroscopy and time-resolved vibrational spectroscopy. The recently introduced method of crystallising a membrane protein in the lipidic cubic phase led to high-resolution structures of ground state bacteriorhodopsin and some of the photocycle intermediates. This achievement in combination with spectroscopic results will strongly advance our understanding of the functional mechanism of bacteriorhodopsin on the atomic level. We present here the current knowledge on specific aspects of the structural and functional dynamics of the photoreaction of bacteriorhodopsin with a focus on techniques established in our institute.

Role of phosphoglucomutase of Bordetella bronchiseptica in lipopolysaccharide biosynthesis and virulence.

The phosphoglucomutase (PGM)-encoding gene of Bordetella bronchiseptica is required for lipopolysaccharide (LPS) biosynthesis. An insertion mutant of the wild-type B. bronchiseptica strain BB7865 which disrupted LPS biosynthesis was created and characterized (BB7865pgm). Genetic analysis of the mutated gene showed it shares high identity with PGM genes of various bacterial species and forms part of an operon which also encompasses the gene encoding phosphoglucose isomerase. Functional assays for PGM revealed that enzyme activity is expressed in both bvg-positive and bvg-negative strains of B. bronchiseptica and is substantially reduced in BB7865pgm. Complementation of the mutated PGM gene with that from BB7865 restored the wild-type condition for all phenotypes tested. The ability of the mutant BB7865pgm to survive within J774. A1 cells was significantly reduced at 2 h (40% reduction) and 24 h (56% reduction) postinfection. BB7865pgm was also significantly attenuated in its ability to survive in vivo following intranasal infection of mice, being effectively cleared from the lungs within 4 days, whereas the wild-type strain persisted at least 35 days. The activities of superoxide dismutase, urease, and acid phosphatase were unaffected in the PGM-deficient strain. In contrast, the inability to produce wild-type LPS resulted in a reduced bacterial resistance to oxidative stress and a higher susceptibility to the antimicrobial peptide cecropin P.

Glucocorticoid stimulation of corticotropin-releasing hormone gene expression requires a cyclic adenosine 3',5'-monophosphate regulatory element in human primary placental cytotrophoblast cells.

Production of placental CRH, which is identical to the peptide synthesized and secreted in the hypothalamus, has been linked to human parturition. Glucocorticoids stimulate placental CRH secretion and messenger ribonucleic acid expression, in contrast to their inhibition of CRH synthesis in the hypothalamus. A positive feedforward loop involving glucocorticoid-CRH-ACTH-glucocorticoid is thought to drive the exponential increase in placental CRH leading to delivery. Tissue-specific effects of glucocorticoids on CRH expression are therefore of interest. Using human primary placental cells, we investigated the mechanism by which glucocorticoids stimulate placental CRH gene expression. Nuclear run-on transcription shows that in human placental cells glucocorticoids up-regulate transcription of human CRH (hCRH). Using transient transfection assays we demonstrate that dexamethasone up-regulates both basal and cAMP-stimulated hCRH promoter activity, correlating well with the increase in endogenous CRH peptide levels. Through mutagenesis and deletion analyses we show that dexamethasone stimulation of hCRH gene transcription requires a functional cAMP regulatory element (CRE); this CRE is adequate to confer dexamethasone stimulation upon a heterologous promoter, and electrophoretic mobility shift assay studies show that a placental nuclear protein specifically binds to the hCRH CRE.

Corticotropin-releasing hormone gene expression in primary placental cells is modulated by cyclic adenosine 3',5'-monophosphate.

CRH, the principal neuropeptide regulator of pituitary ACTH secretion, is also expressed in placenta. Placental CRH has been linked to the process of human parturition. However, the mechanisms regulating transcription of the CRH gene in placenta remain unclear. cAMP signaling pathways play important roles in regulating the expression of a diverse range of endocrine genes in the placenta. Therefore, we have explored the effect of cAMP on CRH promoter activity in primary cultures of human placental cells. Both forskolin and 8-bromo-cAMP, activators of protein kinase A, can increase CRH promoter activity 5-fold in transiently transfected human primary placental cells, in a manner that parallels the increase in endogenous CRH peptide. Maximal stimulation of CRH promoter activity occurs at 500 micromol/L 8-bromo-cAMP and 10 micromol/L forskolin. Electrophoretic mobility shift assay and mutation analysis combined with transient transfection demonstrate that in placental cells cAMP stimulates CRH gene expression through a cAMP regulatory element in the proximal CRH promoter region and involves a placental nuclear protein interacting specifically with the cAMP regulatory element.

The temperature dependence of internal molecular motions in hydrated and dry alpha-amylase: the role of hydration water in the dynamical transition of proteins.

Internal molecular motions of proteins are strongly affected by environmental conditions, like temperature and hydration. As known from numerous studies, the dynamical behavior of hydrated proteins on the picosecond time scale is characterized by vibrational motions in the low-temperature regime and by an onset of stochastic large-amplitude fluctuations at a transition temperature of 180-230 K. The present study reports on the temperature dependence of internal molecular motions as measured with incoherent neutron scattering from the globular water-soluble protein alpha-amylase and from a protein-lipid complex of rhodopsin in disk membranes. Samples of alpha-amylase have been measured in a hydrated and dehydrated state. In contrast to the hydrated sample, which exhibits a pronounced dynamical transition near 200 K, the dehydrated alpha-amylase does not show an appreciable proportion of stochastic large-amplitude fluctuations and no dynamical transition in the measured temperature range of 140-300 K. The obtained results, which are compared to the dynamical behavior of protein-lipid complexes, are discussed with respect to the influence of hydration on the dynamical transition and in the framework of the glass transition.

Molecular motions and hydration of purple membranes and disk membranes studied by neutron scattering.

Fast stochastic equilibrium fluctuations (time scale: 10(-10)-10(-13) seconds) in purple membranes (MP) and in disk membranes (DM) have been measured with quasielastic incoherent neutron scattering. The comparison of predominantly stochastic motions occurring in purple membranes and in disk membranes revealed qualitatively similar dynamical behaviour. Models of internal motions within restricted volumes have been shown to be useful to fit the spectra from both samples. From fits using these models we found "amplitudes" 15 to 20% larger for motions in DM samples compared to PM samples. This indicates a higher internal flexibility of the DM. Because the dynamical behaviour is very sensitive to the hydration of the protein-lipid complex, we also performed neutron diffraction experiments to determine lamellar spacings as a measure of level of hydration and as a function of temperature. From these studies the interaction of solvent molecules with the surface of the protein-lipid complex appears to be qualitatively similar for both types of membranes.

Function and picosecond dynamics of bacteriorhodopsin in purple membrane at different lipidation and hydration.

By neutron scattering experiments and time-resolved absorption spectroscopy we have investigated picosecond equilibrium fluctuations and the kinetics of the photocycle of bacteriorhodopsin (BR) in the purple membrane (PM). Natural PM samples composed of 75% BR (w/w) and 25% lipid (w/w) as well as delipidated PM having only 5% lipid (w/w) were measured at different levels of hydration. We observed a reduced 'flexibility', due to a diminished weight of stochastic large-amplitude motions occurring in the delipidated PM as compared to the natural PM. This effect is more pronounced for wet samples, indicating the importance of lipid hydration for protein dynamics. The reduced flexibility is accompanied by significantly larger time constants describing the decay of the M-intermediate. Therefore, a correlation between the dynamical behavior of the protein-lipid complex and BR function emerges.

Dehydration of biological membranes by cooling: an investigation on the purple membrane.

The lamellar spacing dl of purple membrane (PM) multilayer systems was investigated with neutron diffraction as a function of temperature and of the level of hydration. The observed large T-dependent variations of dl indicate that PM is partially dehydrated when cooled below a "hydration water freezing point". This phenomenon is reversible, but a hysteresis is observed when PM is rehydrated upon reheating. The hydration water remaining bound to the membrane below about 240 K is non-freezing. Its amount was found to be hnf=0.24(+/-0.02) g 2H2O/g BR for all samples equilibrated at room temperature in the presence of 2H2O vapour at >/=84% r.h. It is evident, that the dehydration/rehydration behaviour of PM is strongly correlated with the temperature-dependent behaviour of the dynamical structure factor. Above the well-known "dynamical transition" announcing the onset of localized diffusive molecular motions between 190 K and 230 K, a second dynamical transition is caused by the temperature-induced rehydration of the PM starting near 255 K. This is also correlated with the deviation from a pure Arrhenius law of the rate-limiting process in the photocycle, known to occur upon cooling beyond the ice point into the same temperature region. Our results suggest that the phenomenon of dehydration and rehydration induced by cooling and reheating, respectively, is a general property of biological membranes.

Nitric oxide inhibits corticotropin-releasing hormone exocytosis but not synthesis by cultured human trophoblasts.

Nitric oxide (NO) plays an important role in many cell-cell signaling systems, but its mechanism of action is variable. We have previously reported that NO reduces secretion of the peptide hormone, CRH, from cultured placental cells and the perfused placenta. Because placental CRH production seems linked to human parturition, we wished to explore the mechanism of action of NO in this setting in more detail. We report here that in the placenta, NO specifically inhibited CRH exocytosis, not synthesis, and that endogenous NO affects this process. Cytotrophoblasts were prepared from term human placentas and cultured as monolayers. CRH immunoreactivity in the cell supernatants and cell extracts were measured by RIA. CRH messenger RNA was determined by Northern blot analysis. Sodium nitroprusside (SNP; 1-100 mumol/L) and S-nitroso-N-acetyl-penicillamine (SNAP; 1-100 mumol/L), NO donors, significantly reduced basal CRH concentration in the media, while increasing the concentration of CRH in the cells (P < 0.01), suggesting that exocytosis of CRH was inhibited. These effects could be attenuated by the NO scavenger hemoglobin (20 micrograms/mL). KCl (45 mmol/L), which causes exocytosis by depolarizing the cell membrane, increased CRH release by 2- to 3-fold, and this was inhibited by SNP. Basal release of CRH was augmented by the NO synthase competitive inhibitor N omega-L-arginine methyl ester (1 mmol/L; P < 0.01) and the guanylate cyclase inhibitor, LY83583 (1 mumol/L; P < 0.01). The inhibitory effect of SNP was also blocked by LY83583. CRH messenger RNA content did not change when the placental cells were incubated with SNP, N omega-L-arginine methyl ester, and LY83583 for 6 and 24 h, and this was consistent with studies showing that total CRH immunoreactivity (cells plus media) did not change in the presence of SNP. These studies indicate that exogenous NO inhibits CRH exocytosis, rather than biosynthesis, by human trophoblasts and that endogenous NO has tonic inhibitory effects on CRH release by these cells. The inhibitory effect of NO on basal and stimulated CRH release by placental trophoblasts seems to be a guanylate cyclase-mediated inhibition of exocytosis.