Transient Structural Properties of the Rho GDP-Dissociation Inhibitor.

Rho GTPases, master spatial regulators of a wide range of cellular processes, are orchestrated by complex formation with guanine nucleotide dissociation inhibitors (RhoGDIs). These have been thought to possess an unstructured N-terminus that inhibits nucleotide exchange of their client upon binding/folding. Via NMR analyses, molecular dynamics simulations, and biochemical assays, we reveal instead pertinent structural properties transiently maintained both, in the presence and absence of the client, imposed onto the terminus context-specifically by modulating interactions with the surface of the folded C-terminal domain. These observations revise the long-standing textbook picture of the GTPases' mechanism of membrane extraction. Rather than by a disorder-to-order transition upon binding of an inhibitory peptide, the intricate and highly selective extraction process of RhoGTPases is orchestrated via a dynamic ensemble bearing preformed transient structural properties, suitably modulated by the specific surrounding along the multi-step process.

Light-induced dilation in nanosheets of charge-transfer complexes.

We report the observation of a sizable photostrictive effect of 5.7% with fast, submillisecond response times, arising from a light-induced lattice dilation of a molecular nanosheet, composed of the molecular charge-transfer compound dibenzotetrathiafulvalene (DBTTF) and C60 An interfacial self-assembly approach is introduced for the thickness-controlled growth of the thin films. From photoabsorption measurements, molecular simulations, and electronic structure calculations, we suggest that photostriction within these films arises from a transformation in the molecular structure of constituent molecules upon photoinduced charge transfer, as well as the accommodation of free charge carriers within the material. Additionally, we find that the photostrictive properties of the nanosheets are thickness-dependent, a phenomenon that we suggest arises from surface-induced conformational disorder in the molecular components of the film. Moreover, because of the molecular structure in the films, which results largely from interactions between the constituent π-systems and the sulfur atoms of DBTTF, the optoelectronic properties are found to be anisotropic. This work enables the fabrication of 2D molecular charge-transfer nanosheets with tunable thicknesses and properties, suitable for a wide range of applications in flexible electronic technologies.

Globular protein backbone conformational disorder in crystal structures.

Proteins are not static molecules but dynamic entities able to modify their structure for several reasons, from the necessity to recognize partners to the regulation of their thermodynamic stability. Conformational disorder is frequent in protein structures and atoms can have, in protein crystal structures, two or more alternative, equilibrium positions close to each other. Here, a set of protein crystal structures refined at very high resolution (1 Å or better) is examined to characterize the conformational disorder of the backbone atoms, which is not infrequent: about 15% of the protein backbone atoms are conformationally disordered and three quarters of them have been deposited with two or more equilibrium positions (most of the others were not detected in the electron density maps). Several structural features have been examined and it was observed that Cα atoms tend to be disordered more frequently than the other backbone atoms, likely because their disorder is induced by disordered side chains: side-chain disorder is two times more frequent than backbone disorder. Surprisingly, backbone disorder is only slightly more frequent in loops than in helices and strands and this is in agreement with the observation that backbone disorder is a localized phenomenon: in about 80% of the cases, it is observed in one amino acid and not in its neighbors. However, although backbone disorder does not cluster along the polypeptide sequence, it tends to cluster in 3D, since backbone-disordered amino acids distant in sequence are close in the 3D space.

Unraveling the chromophoric disorder of poly(3-hexylthiophene).

The spectral breadth of conjugated polymers gives these materials a clear advantage over other molecular compounds for organic photovoltaic applications and is a key factor in recent efficiencies topping 10%. However, why do excitonic transitions, which are inherently narrow, lead to absorption over such a broad range of wavelengths in the first place? Using single-molecule spectroscopy, we address this fundamental question in a model material, poly(3-hexylthiophene). Narrow zero-phonon lines from single chromophores are found to scatter over 200 nm, an unprecedented inhomogeneous broadening that maps the ensemble. The giant red shift between solution and bulk films arises from energy transfer to the lowest-energy chromophores in collapsed polymer chains that adopt a highly ordered morphology. We propose that the extreme energetic disorder of chromophores is structural in origin. This structural disorder on the single-chromophore level may actually enable the high degree of polymer chain ordering found in bulk films: both structural order and disorder are crucial to materials physics in devices.

Proline-poor hydrophobic domains modulate the assembly and material properties of polymeric elastin.

Elastin is a self-assembling extracellular matrix protein that provides elasticity to tissues. For entropic elastomers such as elastin, conformational disorder of the monomer building block, even in the polymeric form, is essential for elastomeric recoil. The highly hydrophobic monomer employs a range of strategies for maintaining disorder and flexibility within hydrophobic domains, particularly involving a minimum compositional threshold of proline and glycine residues. However, the native sequence of hydrophobic elastin domain 30 is uncharacteristically proline-poor and, as an isolated polypeptide, is susceptible to formation of amyloid-like structures comprised of stacked ß-sheet. Here we investigated the biophysical and mechanical properties of multiple sets of elastin-like polypeptides designed with different numbers of proline-poor domain 30 from human or rat tropoelastins. We compared the contributions of these proline-poor hydrophobic sequences to self-assembly through characterization of phase separation, and to the tensile properties of cross-linked, polymeric materials. We demonstrate that length of hydrophobic domains and propensity to form ß-structure, both affecting polypeptide chain flexibility and cross-link density, play key roles in modulating elastin mechanical properties. This study advances the understanding of elastin sequence-structure-function relationships, and provides new insights that will directly support rational approaches to the design of biomaterials with defined suites of mechanical properties.

Cellular turnover and degradation of the most common missense cystathionine beta-synthase variants causing homocystinuria.

Homocystinuria (HCU) due to cystathionine beta-synthase (CBS) deficiency is the most common inborn error of sulfur amino acid metabolism. Recent work suggests that missense pathogenic mutations-regardless of their topology-cause instability of the C-terminal regulatory domain, which likely translates into CBS misfolding, impaired assembly, and loss of function. However, it is unknown how instability of the regulatory domain translates into cellular CBS turnover and which degradation pathways are involved in CBS proteostasis. Here, we developed a human HEK293-based cellular model lacking intrinsic CBS and stably overexpressing wild-type (WT) CBS or its 10 most common missense HCU mutants. We found that HCU mutants, except the I278T variant, expressed similarly or better than CBS WT, with some of them showing impaired oligomerization, activity and response to allosteric activator S-adenosylmethionine. Cellular stability of all HCU mutants, except P49L and A114V, was significantly lower than the stability of CBS WT, suggesting their increased degradation. Ubiquitination analysis of CBS WT and two representative CBS mutants (T191M and I278T) showed that proteasomal degradation is the major pathway for CBS disposal, with a minor involvement of lysosomal-autophagic and endoplasmic reticulum-associated degradation (ERAD) pathways for HCU mutants. Proteasomal inhibition significantly increased the half-life and activity of T191M and I278T CBS mutants. Lysosomal and ERAD inhibition had only a minor impact on CBS turnover, but ERAD inhibition rescued the activity of T191M and I278T CBS mutants similarly as proteasomal inhibition. In conclusion, the present study provides new insights into proteostasis of CBS in HCU.

B-Cell Epitope Prediction for Antipeptide Paratopes with the HAPTIC2/HEPTAD User Toolkit (HUT).

B-cell epitope prediction is key to developing peptide-based vaccines and immunodiagnostics along with antibodies for prophylactic, therapeutic and/or diagnostic use. This entails estimating paratope binding affinity for variable-length peptidic sequences subject to constraints on both paratope accessibility and antigen conformational flexibility, as described herein for the HAPTIC2/HEPTAD User Toolkit (HUT). HUT comprises the Heuristic Affinity Prediction Tool for Immune Complexes 2 (HAPTIC2), the HAPTIC2-like Epitope Prediction Tool for Antigen with Disulfide (HEPTAD) and the HAPTIC2/HEPTAD Input Preprocessor (HIP). HIP enables tagging of residues (e.g., in hydrophobic blobs, ordered regions and glycosylation motifs) for exclusion from downstream analyses by HAPTIC2 and HEPTAD. HAPTIC2 estimates paratope binding affinity for disulfide-free disordered peptidic antigens (by analogy between flexible-ligand docking and protein folding), from terms attributed to compaction (in view of sequence length, charge and temperature-dependent polyproline-II helical propensity), collapse (disfavored by residue bulkiness) and contact (with glycine and proline regarded as polar residues that hydrogen bond with paratopes). HEPTAD analyzes antigen sequences that each contain two cysteine residues for which the impact of disulfide pairing is estimated as a correction to the free-energy penalty of compaction. All of HUT is freely accessible online ( https://freeshell.de/~badong/hut.htm ).

What Patterns in Online Classified Puppy Advertisements Can Tell Us about the Current UK Puppy Trade.

The UK online puppy trade has rapidly outgrown the current legislation, aided by the anonymity provided by classified advertisement platforms. In an effort to meet increased demand, some unregulated and regulated breeders may have employed practices that negatively impact canine welfare. A paucity of up-to-date empirical data, necessary to characterise the scale and nature of this industry, makes intervention challenging. This study quantifies the online puppy trade via web-scraped online classified advertisements, providing empirical data that reveal market trends, along with spatial and temporal patterns. A total of 17,389 unique dog advertisements were collated and analysed over a 2-year period (1 June 2018 to 31 May 2020). The second year included the COVID-19 Lockdown (23 March 2020 to 31 May 2020). Statistical comparisons between dependent and independent variables were performed by linear regression. In the case of a single continuous variable, a one sample t-test was used. Of these advertisements, 57.2% were sourced from a pet-specific classified advertisement website (Pets4Homes, n = 9948), and the remaining 42.8% from two general classified advertisement websites (Gumtree, n = 7149, 41.1%; Preloved, n = 292, 1.7%, respectively). England exhibited the greatest number of advertisements (n = 10,493), followed by Wales (n = 1566), Scotland (n = 975), and Northern Ireland (NI; n = 344). Scaled for estimated human population density, Wales possessed as many advertisements per million inhabitants (489.4) as the other three combined (England = 186.4, Scotland = 177.3, and NI = 181.1). Across both years, 559 unique breeds were advertised, yet 66% of all advertisements focused on 20 breeds, and 48% advertisements focused on only 10 breeds. Regional breed popularity was suggested, with French Bulldog as the most advertised breed in England (7.3%), Scotland (6.8%), and Wales (6.8%), but Schnauzers were most popular within Northern Ireland (6.83%). Within the 559 unique breeds advertised, only 3.4% had links to conformational disorders CD); however, these breeds were among the most commonly advertised, totalling 46.9% of all ads. Across all regions, price density peaked between GBP 300 and GBP 1000, with Bulldogs presenting the greatest cost (mean = GBP 1461.38, SD = GBP 940.56), followed closely by French Bulldog (mean = GBP 1279.44, SD = GBP 664.76) and Cavapoo (mean = GBP 1064.56, SD = GBP 509.17). CD breeds were found to be GBP 208.07 more expensive, on average, than non-CD breeds. Our results represent a buoyant online market with regional and seasonal fluctuations in price, advertised breed frequency and total counts. This suggests a market influenced by consumer trends, with a particular focus on breed preference, despite links to illness/disease associated with conformation. Our findings highlight the value of utilising online classified advertisement data for long-term monitoring, in order to assist with evidence-based regulatory reform, impact measurement of targeted campaigns, and legislative enforcement.

Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms.

Intrinsically disordered proteins (IDPs) lack well-defined secondary or tertiary structures in solution but are found to be involved in a wide range of critical cellular processes that highlight their functional importance. IDPs usually undergo folding upon binding to their targets. Such binding coupled to folding behavior has widened our perspective on the protein structure-dynamics-function paradigm in molecular biology. However, characterizing the folding upon binding mechanism of IDPs experimentally remains quite challenging. Molecular simulations emerge as a potentially powerful tool that offers information complementary to experiments. Here we present a general computational framework for the molecular simulations of IDP folding upon binding processes that combines all-atom molecular dynamics (MD) and coarse-grained simulations. The classical all-atom molecular dynamics approach using GPU acceleration allows the researcher to explore the properties of the IDP conformational ensemble, whereas coarse-grained structure-based models implemented with parameters carefully calibrated to available experimental measurements can be used to simulate the entire folding upon binding process. We also discuss a set of tools for the analysis of MD trajectories and describe the details of the computational protocol to follow so that it can be adapted by the user to study any IDP in isolation and in complex with partners.

Prediction of Variable-Length B-Cell Epitopes for Antipeptide Paratopes Using the Program HAPTIC.

BACKGROUND: B-cell epitope prediction for antipeptide antibody responses enables peptide-based vaccine design and related translational applications. This entails estimating epitopeparatope binding free-energy changes from antigen sequence; but attempts to do so assuming uniform epitope length (e.g., of hexapeptide sequences, each spanning a typical paratope diameter when fully extended) have neglected empirically established variation in epitope length. OBJECTIVE: This work aimed to develop a sequence-based physicochemical approach to variablelength B-cell epitope prediction for antipeptide paratopes recognizing flexibly disordered targets. METHODS: Said approach was developed by analogy between epitope-paratope binding and protein folding modeled as polymer collapse, treating paratope structure implicitly. Epitope-paratope binding was thus conceptually resolved into processes of epitope compaction, collapse and contact, with epitope collapse presenting the main entropic barrier limiting epitope length among nonpolyproline sequences. The resulting algorithm was implemented as a computer program, namely the Heuristic Affinity Prediction Tool for Immune Complexes (HAPTIC), which is freely accessible via an online interface (http://badong.freeshell.org/haptic.htm). This was used in conjunction with published data on representative known peptide immunogens. RESULTS: HAPTIC predicted immunodominant epitope sequences with lengths limited by penalties for both compaction and collapse, consistent with known paratope-bound structures of flexibly disordered epitopes. In most cases, the predicted association constant was greater than its experimentally determined counterpart but below the predicted upper bound for affinity maturation in vivo. CONCLUSION: HAPTIC provides a physicochemically plausible means for estimating the affinity of antipeptide paratopes for sterically accessible and flexibly disordered peptidic antigen sequences by explicitly considering candidate B-cell epitopes of variable length.

Beyond B-Cell Epitopes: Curating Positive Data on Antipeptide Paratope Binding to Support Peptide-Based Vaccine Design.

BACKGROUND: B-cell epitope prediction is a computational approach originally developed to support the design of peptide-based vaccines for inducing protective antibody-mediated immunity, as exemplified by neutralization of biological activity (e.g., pathogen infectivity). Said approach is benchmarked against experimentally obtained data on paratope-epitope binding; but such data are curated primarily on the basis of immune-complex structure, obscuring the role of antigen conformational disorder in the underlying immune recognition process. OBJECTIVE: This work aimed to critically analyze the curation of epitope-paratope binding data that are relevant to B-cell epitope prediction for peptide-based vaccine design. METHODS: Database records on neutralizing monoclonal antipeptide antibody immune-complex structure were retrieved from the Immune Epitope Database (IEDB) and analyzed in relation to other data from both IEDB and external sources including the Protein Data Bank (PDB) and published literature, with special attention to data on conformational disorder among paratope-bound and unbound peptidic antigens. RESULTS: Data analysis revealed key examples of antipeptide antibodies that recognize conformationally disordered B-cell epitopes and thereby neutralize the biological activity of cognate targets (e.g., proteins and pathogens), with inconsistency noted in the mapping of some epitopes due to reliance on immune-complex structural details, which vary even among experiments utilizing the same paratope-epitope combination (e.g., with the epitope forming part of a peptide or a protein). CONCLUSION: The results suggest an alternative approach to curating paratope-epitope binding data based on neutralization of biological activity by polyclonal antipeptide antibodies, with reference to immunogenic peptide sequences and their conformational disorder in unbound antigen structures.

Achieving Submicrosecond Thermally Activated Delayed Fluorescence Lifetime and Highly Efficient Electroluminescence by Fine-Tuning of the Phenoxazine-Pyrimidine Structure.

Thermally activated delayed fluorescence (TADF) materials, combining high fluorescence quantum efficiency and short delayed emission lifetime, are highly desirable for application in organic light-emitting diodes (OLEDs) with negligible external quantum efficiency (EQE) roll-off. Here, we present the pathway for shortening the TADF lifetime of highly emissive 4,6-bis[4-(10-phenoxazinyl)phenyl]pyrimidine derivatives. Tiny manipulation of the molecular structure with methyl groups was applied to tune the singlet-triplet energy-level scheme and the corresponding coupling strengths, enabling the boost of the reverse intersystem crossing (rISC) rate (from 0.7 to 6.5) × 106 s-1 and shorten the TADF lifetime down to only 800 ns in toluene solutions. An almost identical TADF lifetime of roughly 860 ns was attained also in solid films for the compound with the most rapid TADF decay in toluene despite the presence of inevitable conformational disorder. Concomitantly, the boost of fluorescence quantum efficiency to near unity was achieved in solid films due to the weakened nonradiative decay. Exceptional EQE peak values of 26.3-29.1% together with adjustable emission wavelength in the range of 502-536 nm were achieved in TADF OLEDs. Reduction of EQE roll-off was demonstrated by lowering the TADF lifetime.

Influence of Molecular Symmetry and Terminal Substituents on the Morphology and OFET Characteristics of S,N-Heteropentacenes.

Many heteroacenes have been extensively studied to improve device performances; however, the morphological effects stemmed from the chemical modification on a multiscale remain less explored. In this research, five axisymmetric S,N-heteropentacenes (DTPT, DTPT-Ph, DTPT-CN, DTPT-PYCN, and DTPT-BTCN) are studied to reveal the influences of molecular symmetry and end-capping substituents on the structure-property relationship, the thermal stability, crystallization behavior, film morphology, and OFET performance. Phase behavior was probed by differential scanning calorimetry (DSC), while the quality of the crystal array and structural details was investigated by optical microscopy (OM) and grazing-incidence wide-angle X-ray scattering (GIWAXS). The analytic results reveal that (1) the parent axisymmetric S,N-heteropentacene, DTPT, is hard to crystallize, which hinders the preparation of high-quality crystal arrays for the OFET application. (2) The incorporation of π-conjugated electron-withdrawing (π-EW) endcaps that provide extended conjugation length and enhanced molecular polarity is required to form oriented crystal arrays to deliver reasonable OFET characteristics. (3) The π-EW endcaps with conformational freedom, such as -BTCN, due to the asymmetric feature of benzothiadiazole (BT), can hinder bulk phase crystallization and cause conformational disorder in the crystal array. Hence, the tradeoff of introducing the end-substituents to reinforce the poor crystalline nature of S,N-heteroacenes should be carefully considered.

Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases.

Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.

Eight Schiff bases derived from various salicylaldehydes: phenol-imine and keto-amine forms, conformational disorder, and supramolecular assembly in one and two dimensions.

Structures are reported for eight Schiff bases derived from various salicylaldehydes: five are newly synthesized and re-investigations are reported for three previously reported structures, leading, in each case, to some revision of previous conclusions. In (E)-N-(3,4-dimethylisoxazol-5-yl)-4-[(2-hydroxybenzylidene)amino]benzenesulfonamide, C18H17N3O4S, (I), and (E)-4-[(5-bromo-2-hydroxy-3-methoxybenzylidene)amino]-N-(3,4-dimethylisoxazol-5-yl)benzenesulfonamide. C19H18BrN3O5S, (II), the isoxazole rings adopt different orientations relative to the rest of the molecules, despite the additional substituents in (II) being in the aryl ring remote from the isoxazole unit. The molecules of both (E)-4-bromo-2-[(2-hydroxyphenylimino)methyl]-6-methoxyphenol, C14H12BrNO3, (III), and (E)-4-bromo-2-methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H14BrNO3, (IV), are both effectively planar; while (III) adopts the phenol-imine constitution, (IV) adopts the keto-amine constitution. (E)-2-Methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H15NO3, (V), which was determined previously using powder X-ray data assuming the phenol-imine constitution, has now been refined from single-crystal X-ray data, confirming the phenol-imine constitution. In (E)-3-benzoyl-2-[(5-fluoro-2-hydroxybenzylidene)amino]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H18FNO2S, (VI), the fused carbocyclic ring exhibits conformational disorder; both disorder components, having populations of 0.705 (4) and 0.295 (4), adopt half-chair conformations. The isostructural (E)-3-benzoyl-2-[(2-hydroxybenzylidene)amino)]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H19NO2S, (VII), which was originally reported as having a fully ordered structure [Kaur et al. (2014). Acta Cryst. E70, o476-o477], has been rerefined using the original data set and found to exhibit the same type of disorder as found in (VI), with disordered populations having occupancies of 0.851 (3) and 0.149 (3). The triclinic polymorph of (E)-[(2-hydroxyphenylimino)methyl]phenol, C13H11NO2, (VIII), which crystallizes with Z' = 2 in the space group P-1, has been described variously as occurring as the keto-amine tautomer [Maciejewska et al. (1999). J. Phys. Org. Chem. 12, 875-880] and as the phenol-imine tautomer [Tunç et al. (2009). J. Chem. Crystallogr. 39, 672-676]. Rerefinement of this structure using one of the original data sets shows that both of the independent molecules exist in the keto-amine form. In the structures of compounds (I), (VI), (VII) and (VIII), hydrogen bonds generate simple chains, while a chain of rings is formed in (V). Sheets are formed by hydrogen bonds in both (II) and (III), while in (IV), the sheet structure is built from aromatic π-π stacking interactions.

Four closely related N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamides: order versus disorder, and similar molecular conformations but different modes of supramolecular aggregation, with a new disordered refinement of 2-amino-3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophene.

Four closely related N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamides, bearing different substituents on the benzamide ring, have been synthesized and structurally characterized. In each of N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-3-fluorobenzamide, C22H18FNO2S, (I), N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-4-chlorobenzamide, C22H18ClNO2S, (II), N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-2,6-difluorobenzamide, C22H17F2NO2S, (III), and N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-2-methoxybenzamide, C23H21NO3S, (IV), the last of which crystallizes with Z' = 2 in the space group P-1, the fused six-membered ring adopts a half-chair conformation. In each of (I)-(III), this ring is disordered over two sets of atomic sites having occupancies of 0.811 (6) and 0.189 (6) in (I), 0.645 (7) and 0.355 (7) in (II), and 0.784 (6) and 0.216 (6) in (III), such that the two disorder components of the ring are almost enantiomeric. Molecules of (I) are linked into chains by π-π stacking interactions, and those of (II) are linked into chains by a C-H...π hydrogen bond. A combination of two C-H...O hydrogen bonds and two C-H...π hydrogen bonds links the molecules of (III) into complex sheets, but the molecules of (IV) are linked by a combination of two hydrogen bonds, one each of the C-H...O and C-H...π types, to form centrosymmetric tetramers. The structures of (I)-(IV) are compared with that of the unsubstituted analogue N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamide and a new refinement of the parent amine 2-amino-3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophene, using the original data set, has found that here too the fused six-membered ring exhibits conformational disorder, with occupancies of 0.887 (9) and 0.113 (9). Comparisons are made with some related compounds.

A study of the oxidation-induced conformational and functional changes in neuroserpin.

BACKGROUND: Neuroserpin, a member of the Serine Proteinase Inhibitor (Serpin) superfamily, is known to be a neuroprotective factor in the focal ischemic stroke followed by reducing the microglial activation. Neuroserpin is a protein rich of methionine residues that can scavenge the free radical species which may increase its neuroprotective effect. On the other hand, the oxidative modifications of the amino acid residues in neuroserpin may lead to changes in its conformation and function. In this study, it was investigated the changes in the conformation and the function of the oxidized neuroserpin. METHODS: Neuroserpin expressed in E. coli, BL21 or M15 harboring plasmid pQE81L containing neuroserpin cDNA. Expressed neuroserpin was purified by resin sulfopropyl A50 precharged with 0.1 M NiSO4 under denaturing condition. Neuroserpin was oxidized under oxidative stress condition in the presence of different concentration of hydrogen peroxide. The oxidation of neuroserpin was conveniently detected by a carbonyl content assay using 2, 4 dinitrophenylhydrazine. Changes in tertiary structure of neuroserpin were monitored by spectrofluorimeter to study the alteration of intrinsic fluorescence and also fluorescence of 8-anilinonaphthalin-1 sulfonic acid (ANS) in native and oxidized form of neuroserpin. RESULTS: Total expressed neuroserpin was estimated 4-5 mg/lit in 2XYT culture media. SDS-PAGE analysis of purified neuroserpin showed a single band which reflects the efficiency of the resin SP A50 for purification of the proteins containing 6xHis tag. Carbonyl content of oxidized and native neuroserpin was estimated 12.3 +/- 0.3 and 0.45 +/- 0.05, respectively. The inhibitory activity of oxidized neuroserpin decreased up to 40-60% as compared with native form of neuroserpin. Intrinsic fluorescence and also the emission of ANS bind to the hydrophobic region of the protein altered from 380 to 85 and in the case of ANS from 105 to 150 in oxidized and native form of neuroserpin, respectively. CONCLUSION: The decreased intrinsic fluorescence intensity, an enhancement in the fluorescence of ANS, and loss of the inhibitory activity up to 40-60% in neuroserpin, all suggested a conformational modification in the protein under the oxidative stress condition. Remaining the inhibitory activity of neuroserpin reflects that the protein tolerates the oxidative stress condition effectively.

Imaging phospholipid conformational disorder and packing in giant multilamellar liposome by confocal Raman microspectroscopy.

Liposomes are closed phospholipid bilayer systems that have profound applications in fundamental cell biology, pharmaceutics and medicine. Depending on the composition (pure or mixture of phospholipids, presence of cholesterol) and preparation protocol, intra- and inter-chain molecular interactions vary leading to changes in the quality (order and packing) of liposomes. So far it is not possible to image conformational disorders and packing densities within a liposome in a straightforward manner. In this study, we utilized confocal Raman microspectroscopy to visualize structural disorders and packing efficiency within a giant multilamellar liposome model by focusing mainly on three regions in the vibrational spectrum (CC stretching, CH deformation and CH stretching). We estimated properties such as trans/gauche isomers and lateral packing probability. Interestingly, our Raman imaging studies revealed gel phase rich domains and heterogeneous lateral packing within the giant multilamellar liposome.

Crystal structures of 2-amino-4,4,7,7-tetra-methyl-4,5,6,7-tetra-hydro-1,3-benzo-thia-zol-3-ium benzoate and 2-amino-4,4,7,7-tetra-methyl-4,5,6,7-tetra-hydro-1,3-benzo-thia-zol-3-ium picrate.

In both 2-amino-4,4,7,7-tetra-methyl-4,5,6,7-tetra-hydro-1,3- benzo-thia-zol-3-ium benzoate, C11H19N2S+·C7H5O2-, (I), and 2-amino-4,4,7,7-tetra-methyl-4,5,6,7-tetra-hydro-1,3-benzo-thia-zol-3-ium picrate (2,4,6-tri-nitro-phenolate), C11H19N2S+·C6H2N3O7-, (II), the cations are conformationally chiral as the six-membered rings adopt half-chair conformations, which are disordered over two sets of atomic sites giving approximately enanti-omeric disorder. For both cations, the bond lengths indicate delocalization of the positive charge comparable to that in an amidinium cation. The bond lengths in the picrate anion in (II) are consistent with extensive delocalization of the negative charge into the ring and onto the nitro groups, in two of which the O atoms are disordered over two sets of sites. In (I), the ionic components are linked by N-H⋯O hydrogen bonds to form a chain of rings, and in (II), the N-H⋯O hydrogen bonds link the components into centrosymmetric four-ion aggregates containing seven hydrogen bonded rings of four different types.