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Motivation Accurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ∼300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases. Results Here we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes. Availability and implementation The source code is freely available at https://github.com/biocryst/IF; a web server to run the program is at http://pharm.kuleuven.be/Biocrystallography/cc. Supplementary information Supplementary data are available at Bioinformatics online.

Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical 'rod' domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the 'signature feature' of the IF family. Bioinformatics analysis reveals that the rod domain of all IF proteins contains three α-helical segments of largely conserved length, interconnected by linkers. Moreover, there is a conserved pattern of hydrophobic repeats within each segment, which includes heptads and hendecads. This defines the presence of both left-handed and almost parallel coiled-coil regions along the rod length. Using X-ray crystallography on multiple overlapping fragments of IF proteins, the atomic structure of the nearly complete rod domain has been determined. Here, we discuss some specific challenges of this procedure, such as crystallization and diffraction data phasing by molecular replacement. Further insights into the structure of the coiled coil and the terminal domains have been obtained using electron paramagnetic resonance measurements on the full-length protein, with spin labels attached at specific positions. This atomic resolution information, as well as further interesting findings, such as the variation of the coiled-coil stability along the rod length, provide clues towards interpreting the data on IF assembly, collected by a range of methods. However, a full description of this process at the molecular level is not yet at hand.

Small heat shock proteins (sHSPs) are present in all kingdoms of life and play fundamental roles in cell biology. sHSPs are key components of the cellular protein quality control system, acting as the first line of defense against conditions that affect protein homeostasis and proteome stability, from bacteria to plants to humans. sHSPs have the ability to bind to a large subset of substrates and to maintain them in a state competent for refolding or clearance with the assistance of the HSP70 machinery. sHSPs participate in a number of biological processes, from the cell cycle, to cell differentiation, from adaptation to stressful conditions, to apoptosis, and, even, to the transformation of a cell into a malignant state. As a consequence, sHSP malfunction has been implicated in abnormal placental development and preterm deliveries, in the prognosis of several types of cancer, and in the development of neurological diseases. Moreover, mutations in the genes encoding several mammalian sHSPs result in neurological, muscular, or cardiac age-related diseases in humans. Loss of protein homeostasis due to protein aggregation is typical of many age-related neurodegenerative and neuromuscular diseases. In light of the role of sHSPs in the clearance of un/misfolded aggregation-prone substrates, pharmacological modulation of sHSP expression or function and rescue of defective sHSPs represent possible routes to alleviate or cure protein conformation diseases. Here, we report the latest news and views on sHSPs discussed by many of the world’s experts in the sHSP field during a dedicated workshop organized in Italy (Bertinoro, CEUB, October 12–15, 2016).

Small heat-shock proteins (sHSPs) are a conserved group of molecular chaperones with important roles in cellular proteostasis. Although sHSPs are characterized by their small monomeric weight, they typically assemble into large polydisperse oligomers that vary in both size and shape but are principally composed of dimeric building blocks. These assemblies can include different sHSP orthologues, creating additional complexity that may affect chaperone activity. However, the structural and functional properties of such hetero-oligomers are poorly understood. We became interested in hetero-oligomer formation between human heat-shock protein family B (small) member 1 (HSPB1) and HSPB6, which are both highly expressed in skeletal muscle. When mixed in vitro, these two sHSPs form a polydisperse oligomer array composed solely of heterodimers, suggesting preferential association that is determined at the monomer level. Previously, we have shown that the sHSP N-terminal domains (NTDs), which have a high degree of intrinsic disorder, are essential for the biased formation. Here we employed iterative deletion mapping to elucidate how the NTD of HSPB6 influences its preferential association with HSPB1 and show that this region has multiple roles in this process. First, the highly conserved motif RLFDQXFG is necessary for subunit exchange among oligomers. Second, a site ∼20 residues downstream of this motif determines the size of the resultant hetero-oligomers. Third, a region unique to HSPB6 dictates the preferential formation of heterodimers. In conclusion, the disordered NTD of HSPB6 helps regulate the size and stability of hetero-oligomeric complexes, indicating that terminal sHSP regions define the assembly properties of these proteins.

Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical ‘rod’ domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the ‘signature feature’ of the IF family. Bioinformatics analysis reveals that the rod domain of all IF proteins contains three α-helical segments of largely conserved length, interconnected by linkers. Moreover, there is a conserved pattern of hydrophobic repeats within each segment, which includes heptads and hendecads. This defines the presence of both left-handed and almost parallel coiled-coil regions along the rod length. Using X-ray crystallography on multiple overlapping fragments of IF proteins, the atomic structure of the nearly complete rod domain has been determined. Here, we discuss some specific challenges of this procedure, such as crystallization and diffraction data phasing by molecular replacement. Further insights into the structure of the coiled coil and the terminal domains have been obtained using electron paramagnetic resonance measurements on the full-length protein, with spin labels attached at specific positions. This atomic resolution information, as well as further interesting findings, such as the variation of the coiled-coil stability along the rod length, provide clues towards interpreting the data on IF assembly, collected by a range of methods. However, a full description of this process at the molecular level is not yet at hand.

Transportin SR2 (TRN-SR2) is a -type karyopherin responsible for the nuclear import of specific cargoes, including serine/arginine-rich splicing factors. The protein has been implicated in a variety of human diseases, including HIV infection, primary biliary cirrhosis and limb-girdle muscular dystrophy 1F. Towards understanding its molecular mechanism, a 2.9 A ˚ resolution crystal structure of human TRN-SR2 complexed with the small GTPase Ran has been determined. TRN-SR2 is composed of 20 -helical HEAT repeats forming a solenoid-like fold. The first nine repeats form a ‘cradle’ for the binding of RanGTP, revealing similarities but also differences with respect to the related importin 13 complex. journal: Acta Crystallographica Section F: Structural Biology Communications content_type: structural communications peer_reviewed: Yes review_process: Single blind received: 21 March 2014 accepted: 28 April 2014 published_online: 24 May 2014 supplementary_materials: This article has supporting information copyright: © 2014 International Union of Crystallography ispartof: Acta Crystallographica F, Structural Biology and Crystallization Communications Online vol:70 issue:6 pages:723-729 ispartof: location:United States status: published

ATP-independent small heat-shock proteins (sHSPs) are an essential component of the cellular chaperoning machinery. Under both normal and stress conditions, sHSPs bind partially unfolded proteins and prevent their irreversible aggregation. Canonical vertebrate sHSPs, such as the α-crystallins, form large polydisperse oligomers from which smaller, functionally active subspecies dissociate. Here we focus on human HSPB6 which, despite having considerable homology to the α-crystallins in both the N-terminal region and the signature α-crystallin domain (ACD), only forms dimers in solution that represent the basic chaperoning subspecies. We addressed the three-dimensional structure and functional properties of HSPB6 in a hybrid study employing X-ray crystallography, solution small-angle X-ray scattering (SAXS), mutagenesis, size-exclusion chromatography and chaperoning assays. The crystal structure of a proteolytically stable fragment reveals typical ACD dimers which further form tetrameric assemblies as a result of extensive inter-dimer patching of the β4/β8 grooves. The patching is surprisingly mediated by tripeptide motifs, found in the N-terminal domain directly adjacent to the ACD, that are resembling but distinct from the canonical IxI sequence commonly binding this groove. By combining the crystal structure with SAXS data for the full-length protein, we derive a molecular model of the latter. In solution, HSPB6 shows a strong attractive self-interaction, a property that correlates with its chaperoning activity. Both properties are dictated by the unstructured yet compact N-terminal domain, specifically a region highly conserved across vertebrate sHSPs.

The authors analyzed laser-induced fluorescence spectra of healthy vegetation and greenery under stress at fluorescence excitation in blue spectral range. It is shown that use of fluorescence excitation in blue spectral range and registration of fluorescent radiation in three narrow spectral ranges with central wavelengths of 680, 690 and 740 nm allows reliable detection of vegetation stress. Identifiable characteristics of plant stress situation are radiation fluorescence intensity ratio at wavelengths 680, 740 nm and ratio at wavelengths 690, 740 nm.

We study theoretically the effect of the giant resonance in Xe on the phase difference between the consecutive high order resonantly-enhanced harmonics and calculate the duration of the attosecond pulses produced by these harmonics. For certain conditions resonantly-induced dephasing compensates the phase difference which is intrinsic for the off-resonance harmonics. We find these conditions analytically and compare them with the numerical results. This harmonic synchronization allows attosecond pulse shortening in conjunction with the resonance-induced intensity increase by more than an order of magnitude; the latter enhancement relaxes the requirements for the UV filtering needed for the attosecond pulse production. Using a two-color driving field allows further increase of the intensity. In particular, a caustic-like feature in the harmonic spectrum leads to the generation efficiency growth up to two orders of magnitude, however accompanied by an elongation of the XUV pulse.

Some properties of G84R and L99M mutants of HspB1 associated with peripheral distal neuropathies were investigated. Homooligomers formed by these mutants are larger than those of the wild type HspB1. Large oligomers of G84R and L99M mutants have compromised stability and tend to dissociate at low protein concentration. G84R and L99M mutations promote phosphorylation-dependent dissociation of HspB1 oligomers without affecting kinetics of HspB1 phosphorylation by MAPKAP2 kinase. Both mutants weakly interact with HspB6 forming small heterooligomers and being unable to form large heterooligomers characteristic for the wild type HspB1. G84R and L99M mutants possess lower chaperone-like activity than the wild type HspB1 with several model substrates. We suggest that G84R mutation affects mobility and accessibility of the N-terminal domain thus modifying interdimer contacts in HspB1 oligomers. The L99M mutation is located within the hydrophobic core of the α-crystallin domain close to the key R140 residue, and could affect the dimer stability.

The RAS-like GTPase RALB mediates cellular responses to nutrient availability or viral infection by respectively engaging two components of the exocyst complex, EXO84 and SEC5. RALB employs SEC5 to trigger innate immunity signalling, whereas RALB-EXO84 interaction induces autophagocytosis. How this differential interaction is achieved molecularly by the RAL GTPase remains unknown. We found that whereas GTP binding turns on RALB activity, ubiquitylation of RALB at Lys 47 tunes its activity towards a particular effector. Specifically, ubiquitylation at Lys 47 sterically inhibits RALB binding to EXO84, while facilitating its interaction with SEC5. Double-stranded RNA promotes RALB ubiquitylation and SEC5-TBK1 complex formation. In contrast, nutrient starvation induces RALB deubiquitylation by accumulation and relocalization of the deubiquitylase USP33 to RALB-positive vesicles. Deubiquitylated RALB promotes the assembly of the RALB-EXO84-beclin-1 complexes driving autophagosome formation. Thus, ubiquitylation within the effector-binding domain provides the switch for the dual functions of RALB in autophagy and innate immune responses.

Analyzing new experiments with ultracold neutrons (UCNs) we show that physical adsorption of nanoparticles/nano-droplets, levitating in high-excited states in a deep and broad potential well formed by van der Waals/Casimir-Polder (vdW/CP) forces results in new effects on a cross-road of fundamental interactions, neutron, surface and nanoparticle physics. Accounting for the interaction of UCNs with nanoparticles explains a recently discovered intriguing small heating of UCNs in traps. It might be relevant to the striking conflict of the neutron lifetime experiments with smallest reported uncertainties by adding false effects there., 5 pages, 4 figures

The human immunodeficiency virus type 1 (HIV-1) and other lentiviruses are capable of infecting non-dividing cells and therefore need to be imported into the nucleus prior to integration into the host cell chromatin. Transportin-SR2 (TRN-SR2, Transportin-3, TNPO3) is a cellular karyopherin implicated in nuclear import of HIV-1. A model in which TRN-SR2 imports the viral preintegration complex (PIC) into the nucleus is supported by direct interaction between TRN-SR2 and HIV-1 integrase (IN). Residues in the C-terminal domain of HIV-1 IN that mediate binding to TRN-SR2 were recently delineated. As for most nuclear import cargoes, the driving force behind HIV-1 PIC import is likely a gradient of the GDP- and GTP-bound forms of Ran, a small GTPase. In this study we offer biochemical and structural characterization of the interaction between TRN-SR2 and Ran. By size exclusion chromatography we demonstrate stable complex formation of TRN-SR2 and RanGTP in solution. Consistent with the behavior of normal nuclear import cargoes, HIV-1 IN is released from the complex with TRN-SR2 by RanGTP. While in concentrated solutions TRN-SR2 by itself was predominantly present as a dimer, the TRN-SR2-RanGTP complex was significantly more compact. Further analysis supported a model wherein one monomer of TRN-SR2 is bound to one monomer of RanGTP. Finally, we present a homology model of the TRN-SR2-RanGTP complex, which is in excellent agreement with the experimental SAXS data. ispartof: Journal of Biological Chemistry vol:288 issue:35 pages:25603-25613 ispartof: location:United States status: published

Clinical HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) potently inhibit viral replication with a dramatic drop in viral load. However, the emergence of resistance to these drugs underscores the need to develop next-generation IN catalytic site inhibitors with improved resistance profiles. Here, we present a novel candidate IN inhibitor, MB-76, a 2-hydroxyisoquinoline-1,3(2H,4H)-dione (HID) derivative. MB-76 potently blocks HIV integration and is active against a panel of wild-type as well as raltegravir-resistant HIV-1 variants. The lack of cross-resistance with other INSTIs and the absence of resistance selection in cell culture indicate the potential of HID derivatives compared to previous INSTIs. A crystal structure of MB-76 bound to the wild-type prototype foamy virus intasome reveals an overall binding mode similar to that of INSTIs. Its compact scaffold displays all three Mg(2+) chelating oxygen atoms from a single ring, ensuring that the only direct contacts with IN are the invariant P214 and Q215 residues of PFV IN (P145 and Q146 for HIV-1 IN, respectively), which may partially explain the difficulty of selecting replicating resistant variants. Moreover, the extended, dolutegravir-like linker connecting the MB-76 metal chelating core and p-fluorobenzyl group can provide additional flexibility in the perturbed active sites of raltegravir-resistant INs. The compound identified represents a potential candidate for further (pre)clinical development as next-generation HIV IN catalytic site inhibitor.

The cysteine-rich secretory/antigen 5/pathogenesis-related 1 (CAP) protein superfamily is composed of a functionally diverse group of members that are found in both eukaryotes and prokaryotes. The excretome/secretome of numerous helminths (parasitic nematodes) contains abundant amounts of CAP members termed activation-associated secreted proteins (ASPs). Although ASPs are necessary for the parasitic life cycle in the host, the current lack of structural and functional information limits both understanding of their actual role in host-parasite interactions and the development of new routes in controlling parasitic infections and diseases. Alleviating this knowledge gap, a 1.85 Å resolution structure of recombinantly produced Oo-ASP-1 from Ostertagia ostertagi, which is one of the most prevalent gastrointestinal parasites in cattle worldwide, was solved. Overall, Oo-ASP-1 displays the common hallmark architecture shared by all CAP-superfamily members, including the N-terminal CAP and C-terminal cysteine-rich domains, but it also reveals a number of highly peculiar features. In agreement with studies of the natively produced protein, the crystal structure shows that Oo-ASP-1 forms a stable dimer that has been found to be primarily maintained via an intermolecular disulfide bridge, hence the small interaction surface of only 306.8 Å(2). Moreover, unlike any other ASP described to date, an additional intramolecular disulfide bridge links the N- and C-termini of each monomer, thereby yielding a quasi-cyclic molecule. Taken together, the insights presented here form an initial step towards a better understanding of the actual biological role(s) that this ASP plays in host-parasite interactions. The structure is also essential to help to define the key regions of the protein suitable for development of ASP-based vaccines, which would enable the current issues surrounding anthelmintic resistance in the treatment of parasitic infections and diseases to be circumvented. journal: Acta Crystallographica Section D: Biological Crystallography content_type: research papers peer_reviewed: Yes review_process: Single blind received: 29 August 2012 accepted: 6 December 2012 published_online: 9 March 2013 supplementary_materials: This article has supplementary materials copyright: © 2013 International Union of Crystallography ispartof: Acta Crystallographica D, Biological Crystallography vol:69 issue:Pt 4 pages:493-503 ispartof: location:United States status: published

Background: Pentameric ligand-gated ion channels are modulated by general anesthetics. Results: The crystal structure of ELIC in complex with bromoform reveals anesthetic binding in the channel pore and in novel sites in the transmembrane and extracellular domain. Conclusion: General anesthetics allosterically modulate channel function via multisite binding. Significance: Our data reveal detailed insight into multisite recognition of general anesthetics at the structural level., Pentameric ligand-gated ion channels (pLGICs), such as nicotinic acetylcholine, glycine, γ-aminobutyric acid GABAA/C receptors, and the Gloeobacter violaceus ligand-gated ion channel (GLIC), are receptors that contain multiple allosteric binding sites for a variety of therapeutics, including general anesthetics. Here, we report the x-ray crystal structure of the Erwinia chrysanthemi ligand-gated ion channel (ELIC) in complex with a derivative of chloroform, which reveals important features of anesthetic recognition, involving multiple binding at three different sites. One site is located in the channel pore and equates with a noncompetitive inhibitor site found in many pLGICs. A second transmembrane site is novel and is located in the lower part of the transmembrane domain, at an interface formed between adjacent subunits. A third site is also novel and is located in the extracellular domain in a hydrophobic pocket between the β7–β10 strands. Together, these results extend our understanding of pLGIC modulation and reveal several specific binding interactions that may contribute to modulator recognition, further substantiating a multisite model of allosteric modulation in this family of ion channels.

In high-order harmonic generation, resonant harmonics (RH) are sources of intense, coherent extreme-ultraviolet radiation. However, intensity enhancement of RH only occurs for a single harmonic order, making it challenging to generate short attosecond pulses. Moreover, the mechanism involved behind such RH was circumstantial, because of the lack of direct experimental proofs. Here, we demonstrate the exact quantum paths that electron follows for RH generation using tin, showing that it involves not only the autoionizing state, but also a harmonic generation from dressed-AIS that appears as two coherent satellite harmonics at frequencies ±2Ω from the RH (Ω represents laser frequency). Our observations of harmonic emission from dressed states open the possibilities of generating intense and broadband attosecond pulses, thus contributing to future applications in attosecond science, as well as the perspective of studying the femtosecond and attosecond dynamics of autoionizing states., High-energy photons in XUV range and attosecond pulses are generated from infrared laser pulses through high harmonic generation in gases and solids. Here, the authors demonstrate the microscopic origin of resonant harmonic generation involving the autoionizing states of Sn in plasma plumes.

We develop an approach describing nonlinear-optical processes in the strong-field domain characterized by the nonperturbative field-with-matter interaction. The polarization of an isolated atom in the external field calculated via the numerical solution of the time-dependent Schr\"odinger equation agrees with our analytical findings. For the practically important case of one strong laser field and several weaker fields, we derive and analytically solve propagation equations describing high-order (HO) wave mixing, HO parametric amplification, and HO stimulated scattering. These processes provide a way of efficient coherent xuv generation. Some properties of HO processes are new in nonlinear optics: essentially complex values of the coefficients in the propagation equations, the superexponential (hyperbolic) growing solutions, etc. Finally, we suggest conditions for the practical realization of these processes and discuss published numerical and experimental results where such processes could have been observed.

UNLABELLED Essentials Thrombin-activatable fibrinolysis inhibitor (TAFI) is a risk factor for cardiovascular disorders. TAFI inhibitory nanobodies represent a promising step in developing profibrinolytic therapeutics. We have solved three crystal structures of TAFI in complex with inhibitory nanobodies. Nanobodies inhibit TAFI through distinct mechanisms and represent novel profibrinolytic leads. SUMMARY Background Thrombin-activatable fibrinolysis inhibitor (TAFI) is converted to activated TAFI (TAFIa) by thrombin, plasmin, or the thrombin-thrombomodulin complex (T/TM). TAFIa is antifibrinolytic, and high levels of TAFIa are associated with an increased risk for cardiovascular disorders. TAFI-inhibitory nanobodies represent a promising approach for developing profibrinolytic therapeutics. Objective To elucidate the molecular mechanisms of inhibition of TAFI activation and TAFIa activity by nanobodies with the use of X-ray crystallography and biochemical characterization. Methods and results We selected two nanobodies for cocrystallization with TAFI. VHH-a204 interferes with all TAFI activation modes, whereas VHH-i83 interferes with T/TM-mediated activation and also inhibits TAFIa activity. The 3.05-A-resolution crystal structure of TAFI-VHH-a204 reveals that the VHH-a204 epitope is localized to the catalytic moiety (CM) in close proximity to the TAFI activation site at Arg92, indicating that VHH-a204 inhibits TAFI activation by steric hindrance. The 2.85-A-resolution crystal structure of TAFI-VHH-i83 reveals that the VHH-i83 epitope is located close to the presumptive thrombomodulin-binding site in the activation peptide (AP). The structure and supporting biochemical assays suggest that VHH-i83 inhibits TAFIa by bridging the AP to the CM following TAFI activation. In addition, the 3.00-A-resolution crystal structure of the triple TAFI-VHH-a204-VHH-i83 complex demonstrates that the two nanobodies can simultaneously bind to TAFI. Conclusions This study provides detailed insights into the molecular mechanisms of TAFI inhibition, and reveals a novel mode of TAFIa inhibition. VHH-a204 and VHH-i83 merit further evaluation as potential profibrinolytic therapeutics.

Small heat shock proteins are ATP-independent molecular chaperones. Their function is to bind partially unfolded proteins under stress conditions. In vivo, members of this chaperone family are known to preferentially assemble together forming large, polydisperse heterooligomers. The exact molecular mechanisms that drive specific heteroassociation are currently unknown. Here we study the oligomers formed between human HSPB1 and HSPB6. Using small-angle X-ray scattering we could characterize two distinct heterooligomeric species present in solution. By employing native mass spectrometry we show that such assemblies are formed purely from heterodimeric building blocks, in line with earlier cross-linking studies. Crucially, a detailed analysis of truncation variants reveals that the preferential association between these two sHSPs is solely mediated by their disordered N-terminal domains. publisher: Elsevier articletitle: The preferential heterodimerization of human small heat shock proteins HSPB1 and HSPB6 is dictated by the N-terminal domain journaltitle: Archives of Biochemistry and Biophysics articlelink: http://dx.doi.org/10.1016/j.abb.2016.10.002 content_type: article copyright: © 2016 Elsevier Inc. All rights reserved. ispartof: Archives of Biochemistry and Biophysics vol:610 pages:41-50 ispartof: location:United States status: published

Studies of the intermediate filament (IF) structure are a prerequisite of understanding their function. In addition, the structural information is indispensable if one wishes to gain a mechanistic view on the disease-related mutations in the IFs. Over the years, considerable progress has been made on the atomic structure of the elementary building block of all IFs, the coiled-coil dimer. Here, we discuss the approaches, methods and practices that have contributed to this advance. With abundant genetic information on hand, bioinformatics approaches give important insights into the dimer structure, including the head and tail regions poorly assessable experimentally. At the same time, the most important contribution has been provided by X-ray crystallography. Following the "divide-and-conquer" approach, many fragments from several IF proteins could be crystallized and resolved to atomic resolution. We will systematically cover the main procedures of these crystallographic studies, suggest ways to maximize their efficiency, and also discuss the possible pitfalls and limitations. In addition, electron paramagnetic resonance with site-directed spin labeling was another method providing a major impact toward the understanding of the IF structure. Upon placing the spin labels into specific positions within the full-length protein, one can evaluate the proximity of the labels and their mobility. This makes it possible to make conclusions about the dimer structure in the coiled-coil region and beyond, as well as to explore the dimer-dimer contacts.

The intermediate filament protein desmin is an essential component of the extra-sarcomeric cytoskeleton in muscle cells. This three-dimensional filamentous framework exerts central roles in the structural and functional alignment and anchorage of myofibrils, the positioning of cell organelles and signaling events. Mutations of the human desmin gene on chromosome 2q35 cause autosomal dominant, autosomal recessive, and sporadic myopathies and/or cardiomyopathies with marked phenotypic variability. The disease onset ranges from childhood to late adulthood. The clinical course is progressive and no specific treatment is currently available for this severely disabling disease. The muscle pathology is characterized by desmin-positive protein aggregates and degenerative changes of the myofibrillar apparatus. The molecular pathophysiology of desminopathies is a complex, multilevel issue. In addition to direct effects on the formation and maintenance of the extra-sarcomeric intermediate filament network, mutant desmin affects essential protein interactions, cell signaling cascades, mitochondrial functions, and protein quality control mechanisms. This review summarizes the currently available data on the epidemiology, clinical phenotypes, myopathology, and genetics of desminopathies. In addition, this work provides an overview on the expression, filament formation processes, biomechanical properties, post-translational modifications, interaction partners, subcellular localization, and functions of wild-type and mutant desmin as well as desmin-related cell and animal models.

Several Gram-negative bacteria protect themselves against the lytic action of host lysozymes by producing specific proteinaceous inhibitors. So far, four different families of lysozyme inhibitors have been identified including Ivy (Inhibitor of vertebrate lysozyme), MliC/PliC (Membrane associated/periplasmic inhibitor of C-type lysozyme), PliI and PliG (periplasmic inhibitors of I- and G-type lysozymes, respectively). Here we provide the first crystallographic description of the PliG family. Crystal structures were obtained for the PliG homologues from Escherichia coli, Salmonella enterica serotype Typhimurium and Aeromonas hydrophila. These structures show that the fold of the PliG family is very distinct from that of all other families of lysozyme inhibitors. Small-angle X-ray scattering studies reveal that PliG is monomeric in solution as opposed to the dimeric PliC and PliI. The PliG family shares a highly conserved SG(x)xY sequence motif with the MliC/PliC and PliI families where it was shown to reside on a loop that blocks the active site of lysozyme leading to inhibition. Surprisingly, we found that in PliG this motif is not well exposed and not involved in the inhibitory action. Instead, we could identify a distinct cluster of surface residues that are conserved across the PliG family and are essential for efficient G-type lysozyme inhibition, as evidenced by mutagenesis studies.

Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) “rod” domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

The laser plasma formed in gaseous media due to their optical breakdown under tightly focused femtosecond laser pulses has been experimentally investigated. Pump-probemicrointerferometry is chosen to perform spatial and temporal diagnostics of the plasma. Time dependences of the laser plasma electron density are obtained. It is shown that in breakdown of different gases (air, nitrogen, argon, and helium) at different pressures (in the range from 1 to 10 atm) the electron concentration continues to increase during ∼1 ps when the laser irradiation is over. This effect is related to the impact ionization of the plasma by the hot electrons formed in interaction of intense femtosecond laser pulses with matter. The results of theoretical simulation of the post-ionization processes are presented.

Fructans play important roles as reserve carbohydrates and stress protectants in plants, and additionally serve as prebiotics with emerging antioxidant properties. Various fructan types are synthesized by an array of plant fructosyltransferases belonging to family 32 of the glycoside hydrolases (GH32), clustering together with GH68 in Clan-J. Here, the 3D structure of a plant fructosyltransferase from a native source, the Pachysandra terminalis 6-SST/6-SFT (Pt6-SST/6-SFT), is reported. In addition to its 1-SST (1-kestose-forming) and hydrolytic side activities, the enzyme uses sucrose to create graminan- and levan-type fructans, which are probably associated with cold tolerance in this species. Furthermore, a Pt6-SST/6-SFT complex with 6-kestose was generated, representing a genuine acceptor binding modus at the +1, +2 and +3 subsites in the active site. The enzyme shows a unique configuration in the vicinity of its active site, including a unique D/Q couple located at the +1 subsite that plays a dual role in donor and acceptor substrate binding. Furthermore, it shows a unique orientation of some hydrophobic residues, probably contributing to its specific functionality. A model is presented showing formation of a β(2-6) fructosyl linkage on 6-kestose to create 6,6-nystose, a mechanism that differs from the creation of a β(2-1) fructosyl linkage on sucrose to produce 1-kestose. The structures shed light on the evolution of plant fructosyltransferases from their vacuolar invertase ancestors, and contribute to further understanding of the complex structure-function relationships within plant GH32 members.

Cytoskeletal intermediate filaments (IFs) assemble from the elementary dimers based on a segmented α-helical coiled-coil (CC) structure. Crystallographic studies of IF protein fragments remain the main route to access their atomic structure. To enable crystallization, such fragments must be sufficiently short. As a consequence, they often fail to assemble into the correct CC dimers. In particular, human vimentin fragment D3 corresponding to the first half of coil2 (residues 261–335) stays monomeric in solution. We have induced its dimerization via introducing a disulfide link between two cysteines engineered in the hydrophobic core of the CC close to its N-terminus. The 2.3 A crystal structure of the D3st (stabilized) fragment reveals a mostly parallel α-helical bundle structure in its N-terminal half which smoothly continues into a left-handed CC towards the C-terminus. This provides a direct evidence for a continuously α-helical structure of the coil2 segment and disproves the previously suggested existence of linker L2 separating it into two left-handed CCs. The general principles of CC dimer stabilization by disulfide introduction are also discussed.

In order to access feasibility of increasing albedo of very cold neutrons from powder of diamond nanoparticles, we studied hydrogen bound to surface of diamond nanoparticles, which causes unwanted losses of neutrons. We showed that one could decrease a fraction of hydrogen atoms from a ratio C7.4 ± 0.15H to a ratio C12.4 ± 0.2H by means of thermal treatment and outgasing of powder. Measurements of atomic excitation spectra of these samples, using a method of inelastic incoherent neutron scattering, indicate that residual hydrogen is chemically bound to carbon, while a removed fraction was composed of adsorbed water. The total cross section of scattering of neutrons with a wavelength of 4.4 A on residual hydrogen atoms equals 108 ± 2 b; it weakly changes with temperature. Thus preliminary cleaning of powder from hydrogen and its moderate cooling do not improve considerably neutron albedo from powder of nano-diamonds. An alternative approach is isotopic replacement of hydrogen by deuterium.

New methodical developments for the GRANIT spectrometer address further improvements of the critical parameters of this experimental installation, as well as its applications to new fields of research. Keeping in mind an extremely small fraction of ultra cold neutrons (UCN) that could be bound in gravitational quantum states, we look for methods to increase statistics due to: developing UCN sources with maximum phase-space density, counting simultaneously a large fraction of neutrons using position-sensitive detectors, and decreasing detector backgrounds. Also we explore an eventual application of the GRANIT spectrometer beyond the scope of its initial goals, for instance, for reflectometry with UCN.

Lysozymes play a key role in the innate immune system of vertebrates and invertebrates by hydrolyzing peptidoglycan, a vital component of the bacterial cell wall. Gram-negative bacteria produce various types of lysozyme inhibitors that allow them to survive the bactericidal action of lysozyme when their outer membrane is permeabilized. So far, three lysozyme inhibitor families have been described: the Ivy (inhibitor of vertebrate lysozyme) family, the MliC/PliC (membrane-associated/periplasmic lysozyme inhibitor of C-type lysozyme) family, and the PliI (periplasmic lysozyme inhibitor of I-type lysozyme) family. Here, we report high-resolution crystal structures of Salmonella typhimurium PliC (PliC-St) and Aeromonas hydrophila PliI (PliI-Ah). The structure of PliI-Ah is the first in the recently discovered PliI family of lysozyme inhibitors, while the structure of PliC-St is the first structure of a periplasmic lysozyme inhibitor from the PliC/MliC family. Using small-angle X-ray scattering, we demonstrate that both PliC-St and PliI-Ah form stable dimers in solution. The functional dimer architecture of PliC-St is very different from that of the recently described MliC from Pseudomonas aeruginosa (MliC-Pa), despite the close resemblance of their monomers. Furthermore, PliI-Ah has distinctly different monomer and dimer folds compared to PliC, MliC, and Ivy proteins. Site-directed mutagenesis suggests that the inhibitory action of PliI-Ah proceeds via an insertion of a loop containing the conserved SGxY motif into the active center of I-type lysozymes. This motif is related to the functional SGxxY motif found in the MliC/PliC family.

Covalent modification of alpha 7 W55C nicotinic acetylcholine receptors (nAChR) with the cysteine-modifying reagent [2-(trimethylammonium) ethyl] methanethiosulfonate (MTSET+) produces receptors that are unresponsive to acetylcholine, whereas methyl methanethiolsulfonate (MMTS) produces enhanced acetylcholine-gated currents. Here, we investigate structural changes that underlie the opposite effects of MTSET+ and MMTS using acetylcholine-binding protein (AChBP), a homolog of the extracellular domain of the nAChR. Crystal structures of Y53C AChBP show that MT-SET+-modification stabilizes loop C in an extended conformation that resembles the antagonist-bound state, which parallels our observation that MTSET+ produces unresponsive W55C nAChRs. The MMTS-modified mutant in complex with acetylcholine is characterized by a contracted C-loop, similar to other agonist-bound complexes. Surprisingly, we find two acetylcholine molecules bound in the ligand-binding site, which might explain the potentiating effect of MMTS modification in W55C nAChRs. Unexpectedly, we observed in the MMTS-Y53C structure that ten phosphate ions arranged in two rings at adjacent sites are bound in the vestibule of AChBP. We mutated homologous residues in the vestibule of alpha 1 GlyR and observed a reduction in the single channel conductance, suggesting a role of this site in ion permeation. Taken together, our results demonstrate that targeted modification of a conserved aromatic residue in loop D is sufficient for a conformational switch of AChBP and that a defined region in the vestibule of the extracellular domain contributes to ion conduction in an-ion-selective Cys-loop receptors. ispartof: Journal of Biological Chemistry vol:286 issue:6 pages:4420-4428 ispartof: location:United States status: published

The potential of glycoside hydrolase family (GH) 8 xylanases in biotechnological applications is virtually unexplored. Therefore, the substrate preference and hydrolysis product profiles of two GH8 xylanases were evaluated to investigate their activities and substrate specificities. A GH8 xylanase from an uncultured bacterium (rXyn8) shows endo action but very selectively releases xylotriose from its substrates. It has a higher activity than the Pseudoalteromonas haloplanktis GH8 endo-xylanase (PhXyl) on xylononaose and smaller xylo-oligosaccharides. PhXyl preferably degrades xylan substrates with a high degree of polymerization. It is sterically more hindered by arabinose substituents than rXyn8, producing larger end hydrolysis products. The specificities of rXyn8 and PhXyl differ completely from these of the previously described GH8 xylanases from Bifidobacterium adolescentis (BaRexA) and Bacillus halodurans (BhRex). As reducing-end xylose-releasing exo-oligoxylanases, they selectively release xylose from the reducing end of small xylo-oligosaccharides. The findings of this study show that GH8 xylanases have a narrow substrate specificity, but also one that strongly varies between family members and is distinct from that of GH10 and GH11 xylanases. Structural comparison of rXyn8, PhXyl, BaRexA, and BhRex showed that subtle amino acid changes in the glycon as well as the aglycon subsites probably form the basis of the observed differences between GH8 xylanases. GH8 xylanases, therefore, are an interesting group of enzymes, with potential towards engineering and applications.

Lens epithelium-derived growth factor (LEDGF/p75) is a cellular cofactor of HIV-1 integrase that promotes viral integration by tethering the preintegration complex to the chromatin. By virtue of its crucial role in the early steps of HIV replication, the interaction between LEDGF/p75 and integrase represents an attractive target for antiviral therapy. We have rationally designed a series of 2-(quinolin-3-yl)acetic acid derivatives (LEDGINs) that act as potent inhibitors of the LEDGF/p75-integrase interaction and HIV-1 replication at submicromolar concentration by blocking the integration step. A 1.84-A resolution crystal structure corroborates the binding of the inhibitor in the LEDGF/p75-binding pocket of integrase. Together with the lack of cross-resistance with two clinical integrase inhibitors, these findings define the 2-(quinolin-3-yl)acetic acid derivatives as the first genuine allosteric HIV-1 integrase inhibitors. Our work demonstrates the feasibility of rational design of small molecules inhibiting the protein-protein interaction between a viral protein and a cellular host factor.

Diamond, with its exceptionally high optical nuclear potential and low absorption cross-section, is a unique material for a series of applications in VCN (very cold neutron) physics and techniques. In particular, powder of diamond nanoparticles provides the best reflector for neutrons in the complete VCN energy range. It allowed also the first observation of quasi-specular reflection of cold neutrons (CN) from disordered medium. Effective critical velocity for such a quasi-specular reflection is higher than that for the best super-mirror. Nano-diamonds survive in high radiation fluxes; therefore they could be used, under certain conditions, in the vicinity of intense neutron sources.

The Big Gravitational Spectrometer (BGS) takes advantage of the strong influence of the Earth’s gravity on the motion of ultracold neutrons (UCNs) that makes it possible to shape and measure UCN spectra. We optimized the BGS to investigate the “small heating” of UCNs, that is, the inelastic reflection of UCNs from a surface accompanied by an energy change comparable with the initial UCN energy. UCNs whose energy increases are referred to as “Vaporized UCNs” (VUCNs). The BGS provides the narrowest UCN spectra of a few cm and the broadest “visible” VUCN energy range of up to ∼150 cm (UCN energy is given in units of its maximum height in the Earth’s gravitational field, where 1.00 cm ≈ 1.02 neV). The dead-zone between the UCN and VUCN spectra is the narrowest ever achieved (a few cm). We performed measurements with and without samples without breaking vacuum. BGS provides the broadest range of temperatures (77-600 K) and the highest sensitivity to the small heating effect, up to ∼10−8 per bounce, i.e., two o...

Usually Ultra Cold Neutrons (UCN) and Very Cold Neutrons (VCN) are not efficiently scattered by individual atoms in matter due to their large wavelength. On the contrary, such neutrons are coherently scattered by nanoparticles, providing a powerful tool, in particular for VCN reflectors, for VCN storage in closed traps, probably for ‘quasi-specular’ reflectors for cold neutrons, and for cooling VCN to the UCN energy range. On the other hand, quasi-elastic scattering of UCN at nanoparticles and large molecules (as those of Fomblin oil) in all presently used UCN trap wall materials causes false effects in the neutron lifetime measurements because of poorly controlled spectrum evolution.

A study of treatment of molten metal under industrial conditions in nonstationary electromagnetic field of a low-power generator is performed and data on improvement of the structure and rising of the mechanical characteristics of the cast metal are obtained. The design of a generator equipped with guided emitter of electromagnetic oscillation, which is mounted against the melting furnace at a distance of up to 10 m is presented. The physical mechanisms of the action of the radiation of the generator on the volume of the melt are described in brief.

Intermediate filaments (IFs) are major constituents of the cytoskeleton and nuclear boundary in animal cells. They are of prime importance for the functional organization of structural elements. Depending on the cell type, morphologically similar but biochemically distinct proteins form highly viscoelastic filament networks with multiple nanomechanical functions. Besides their primary role in cell plasticity and their established function as cellular stress absorbers, recently discovered gene defects have elucidated that structural alterations of IFs can affect their involvement both in signaling and in controlling gene regulatory networks. Here, we highlight the basic structural and functional properties of IFs and derive a concept of how mutations may affect cellular architecture and thereby tissue construction and physiology. ispartof: Journal of Clinical Investigation vol:119 issue:7 pages:1772-1783 ispartof: location:United States status: published

AXHs (arabinoxylan arabinofuranohydrolases) are alpha-L-arabinofuranosidases that specifically hydrolyse the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Bacillus subtilis was recently shown to produce an AXH that cleaves arabinose units from O-2- or O-3-mono-substituted xylose residues: BsAXH-m2,3 (B. subtilis AXH-m2,3). Crystallographic analysis reveals a two-domain structure for this enzyme: a catalytic domain displaying a five-bladed beta-propeller fold characteristic of GH (glycoside hydrolase) family 43 and a CBM (carbohydrate-binding module) with a beta-sandwich fold belonging to CBM family 6. Binding of substrate to BsAXH-m2,3 is largely based on hydrophobic stacking interactions, which probably allow the positional flexibility needed to hydrolyse both arabinose substituents at the O-2 or O-3 position of the xylose unit. Superposition of the BsAXH-m2,3 structure with known structures of the GH family 43 exo-acting enzymes, beta-xylosidase and alpha-L-arabinanase, each in complex with their substrate, reveals a different orientation of the sugar backbone.

We suggest a new measure to find similarity between ordered histograms. In our approach the similarity is related to the closeness of positions and shapes of peaks in the compared histograms. Using this measure for comparison of a big number of histograms we obtain results that agree reasonably well with the expert decisions. Applying our peak matching algorithm for studies of the histogram series obtained from experimental data, we reproduce a phenomenon that was found earlier using the expert decisions on the histogram similarity, but was not reproduced with the computer histogram analysis utilized in earlier studies.

The structural analog of liquid-crystalline adducts of lanthanides containing nitroxyl radicals in the bipyridine moiety was synthesized. The distances between the radicals in the ligand and adduct were determined by the pulse ESR technique. The obtained data were used as a criterion for the adequate choice of the parameters of the semiempirical quantum chemical calculation of the structures of the LnIII coordination compounds containing paramagnetic centers.

This study provides insights into the role of nuclear lamins in DNA replication. Our data demonstrate that the Ig-fold motif located in the lamin C terminus binds directly to proliferating cell nuclear antigen (PCNA), the processivity factor necessary for the chain elongation phase of DNA replication. We find that the introduction of a mutation in the Ig-fold, which alters its structure and causes human muscular dystrophy, inhibits PCNA binding. Studies of nuclear assembly and DNA replication show that lamins, PCNA, and chromatin are closely associated in situ. Exposure of replicating nuclei to an excess of the lamin domain containing the Ig-fold inhibits DNA replication in a concentration-dependent fashion. This inhibitory effect is significantly diminished in nuclei exposed to the same domain bearing the Ig-fold mutation. Using the crystal structures of the lamin Ig-fold and PCNA, molecular docking simulations suggest probable interaction sites. These findings also provide insights into the mechanisms underlying the numerous disease-causing mutations located within the lamin Ig-fold. ispartof: Journal of Cell Biology vol:181 issue:2 pages:269-280 ispartof: location:United States status: published

We studied the phenomenon of relatively small changes in the energy of ultracold neutrons (UCN) (when compared to thermal motion energy) when these are reflected on a surface. The changes observed involved both increases in UCN energy (their heating) and decreases (cooling) of the order of ~ 10-7 eV. The probability values of this process on various surfaces ranged between 10-8 and 10-5 per one collision; the probability of such a small heating was many times larger than that of such a small cooling. We measured the spectra of such heated neutrons and the dependence of small heating probability on the temperature of sample out-gazing. We found that out-gazing of samples in vacuum at a temperature of 500–600 K could increase the small heating probability on stainless steel surface by a factor of ~ 100; and on copper surface by a factor of ~ 10. We observed, for the first time, extremely intensive small heating of UCN on powder of diamond nanoparticles. Neither small heating of UCN, nor nanoparticles could be found on a sapphire single crystal surface. This set of experimental data indicates that the inelastic scattering of UCN on weakly bound nanoparticles at a surface in a state of thermal motion is responsible for the process investigated.

The main goal of this work is to explore feasibility of a new method for producing high density of ultra cold neutrons. The method proposed consists in the cooling of very cold neutrons owing to their many collisions with ultracold nanoparticles made of low adsorbing materials (heavy water, deuterium) down to the temperature of this particles during the diffusion motion of neutrons through a macroscopically large ensemble of nanoparticles—a sample of high porous impurity gel in superfluid He-II. At the first stage of this experimental program we have studied propagation and small angle scattering of cold neutrons in the gel samples cooled down to 1.6 K. The results obtained look very encouraging: estimated characteristic dimensions of impurity clusters are 3≤d≤150 nm for as-prepared deuterium gel sample and d≤15 nm for heavy-water gel samples. In the next series of experiments we plan to study the inelastic scattering of cold neutrons in the bulk of deuterium and heavy water gel samples.

The formation and evolution dynamics of the laser plasma produced in the microvolumes of gases (air, nitrogen, argon, and helium) upon their multiple ionisation by high-intensity (4×1016 W cm-2) tightly focused (to a region 1.7 μm in diameter) 400-nm, 100-fs second-harmonic pulses from a Ti:sapphire laser is studied. The spatiotemporal distribution profiles of the refractive index and electron microplasma density were recorded by ultrahigh-speed interferometry. The postionisation of a femtosecond laser plasma, i.e. the growth of the electron density known after the end of the exciting laser pulse, is detected for the first time. A theoretical model is proposed, which describes the mechanism of plasma postionisation by hot photoelectrons. The results of electron density calculations are in good agreement with experimental data.

The self-organization of the poly(ethylene glycol)(10)monododecyl ether (C12EO10)/poly(ethyleneimine) (PEI)/La(III)/water multicomponent system has been examined in the micellar and liquid-crystalline ranges. A step-by-step investigation of the catalytic effect toward the cleavage of phosphorus acid esters was performed for the following series: single C12EO10 micelles → ternary C12EO10/PEI/water micellar system → quaternary C12EO10/PEI/La(III)/water micellar system → liquid-crystalline mesophase. The quaternary system was found to be an effective nanosized catalyst, demonstrating the complex mechanism of the catalytic action under mild conditions (25 °C, pH ≈ 8.0) and the substrate specificity toward the more hydrophobic phosphonate. A marked (ca. 1000-fold) acceleration of the reaction studied as compared to the basic hydrolysis of the substrates was achieved.

The approach we have proposed earlier for a large increase in ultracold neutron density was based on equilibrium thermalization of cold neutrons during their diffusive motion in a large sample of an impurity-helium gel which consists of weakly bounded deuterium or heavy water nanoclusters in He-II cooled below a few mK. It is clear that the nanoparticles should provide a sufficiently large cross-section of coherent scattering of cold neutrons, but the scattering of neutrons on impurity gel samples in He-II has been never investigated earlier. In this paper we present results of the first observations of the scattering of a beam of cold neutrons with mean velocities from 30 to 160 m/s on heavy water and deuterium gel samples in He-II at temperatures T∼1.6 K. It has been observed that the beam transmission through the heavy water gel sample has been changed from ∼0% to ∼50% upon increasing the neutron velocity from 30 to 160 m/s, and that the neutron transmission trough the deuterium gel sample is less than 5% at all velocities. The angular distribution of the neutron scattering changes with variations in the neutron velocity: for both the gels at large neutron energies the scattering is directed in a front hemisphere mainly, and at low energies the angular distribution of scattered neutrons is close to uniform.