Barysheva M.M.,RAS Institute for Physics of Microstructures |
Gribkov B.A.,RAS Institute for Physics of Microstructures |
Vainer Yu.A.,RAS Institute for Physics of Microstructures |
Zorina M.V.,RAS Institute for Physics of Microstructures |
And 5 more authors.
Proceedings of SPIE - The International Society for Optical Engineering | Year: 2011
The requirements for multilayered x-ray elements for diffraction quality imaging optics (EUV - lithography, x-ray microscopy) achieves 0.2-0.3 nm roughness in spatial frequency range 10-3 - 103 mcm -1; it's also true for the substrates. Although, there are plenty of publications on studying a surface, when it comes to angstrom-quality substrates there is still a problem. In some cases we observe, standard methods like x-ray diffuse scattering (XRDS), atomic force microscopy (AFM) and optical interferometric microscopy (OIM) give notably different results in surface characterization. The goal of the attestation procedure is choosing the sample for sputtering a multilayer coating with better reflection properties, that's why it's important to understand the physical causes of the difference and get reliable information about the surface. In this work we discuss the limitation for aforesaid standard methods. OIM is seems to be inapplicable for supersmooth surface investigation because of applying references. It's also shown, that examination substrates with damaged layers in the volume (caused, for example, by ion-beam etching) by XRDS can lead to incorrect results. Imaging systems are composed by nonplanar optical elements with radiuses from 10 mm to 1 meter. That makes impossible using hard x-rays and also limited AFM applicability to high frequencies. Therefore, we propose the diffuse scattering of soft x-rays as an alternative approach. We also describe a new reflectometer, based on soft x-ray and visible light diffuse scattering, which can be used for surface investigation in middle and high spatial frequency ranges for both plane or curved substrates. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).
Huang G.Y.,Baylor College of Medicine |
Kim J.J.,Baylor College of Medicine |
Reger A.S.,Baylor College of Medicine |
Lorenz R.,University of Kassel |
And 11 more authors.
Structure | Year: 2014
Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but the molecular mechanism of cyclic nucleotide selectivity is unknown. Here, we report that the PKG Iβ C-terminal cyclic nucleotide binding domain (CNB-B) is highly selective for cGMP binding, and we have solved crystal structures of CNB-B with and without bound cGMP. These structures, combined with a comprehensive mutagenic analysis, allowed us to identify Leu296 and Arg297 as key residues that mediate cGMP selectivity. In addition, by comparing the cGMP bound and unbound structures, we observed large conformational changes in the C-terminal helices in response to cGMP binding, which were stabilized by recruitment of Tyr351 as a "capping residue" for cGMP. The observed rearrangements of the C-terminal helices provide a mechanical insight into release of the catalytic domain and kinase activation. © 2014 Elsevier Ltd All rights reserved.
Sana B.,Nanyang Technological University |
Johnson E.,Howard Hughes Medical Institute |
Johnson E.,Pfizer |
Magueres P.L.,Rigaku Americas |
And 3 more authors.
Journal of Biological Chemistry | Year: 2013
Archaeoglobus fulgidus ferritin (AfFtn) is the only tetracosameric ferritin known to form a tetrahedral cage, a structure that remains unique in structural biology. As a result of the tetrahedral (2-3) symmetry, four openings (~45 Å in diameter) are formed in the cage. This open tetrahedral assembly contradicts the paradigm of a typical ferritin cage: a closed assembly having octahedral (4-3-2) symmetry. To investigate the molecular mechanism affecting this atypical assembly, amino acid residues Lys-150 and Arg-151 were replaced by alanine. The data presented here shed light on the role that these residues play in shaping the unique structural features and biophysical properties of the AfFtn. The x-ray crystal structure of the K150A/ R151A mutant, solved at 2.1 Å resolution, indicates that replacement of these key residues flips a "symmetry switch." The engineered molecule no longer assembles with tetrahedral symmetry but forms a typical closed octahedral ferritin cage. Small angle x-ray scattering reveals that the overall shape and size of AfFtn and AfFtn-AA in solution are consistent with those observed in their respective crystal structures. Iron binding and release kinetics of the AfFtn and AfFtn-AA were investigated to assess the contribution of cage openings to the kinetics of iron oxidation, mineralization, or reductive iron release. Identical iron binding kinetics for AfFtn and AfFtn-AA suggest that Fe2+ ions do not utilize the triangular pores for access to the catalytic site. In contrast, relatively slow reductive iron release was observed for the closed AfFtn-AA, demonstrating involvement of the large pores in the pathway for iron release. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
PubMed | Lawrence Berkeley National Laboratory, University of Kassel, Rice University, Baylor College of Medicine and 3 more.
Type: Journal Article | Journal: Structure (London, England : 1993) | Year: 2014
Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but the molecular mechanism of cyclic nucleotide selectivity is unknown. Here, we report that the PKG I C-terminal cyclic nucleotide binding domain (CNB-B) is highly selective for cGMP binding, and we have solved crystal structures of CNB-B with and without bound cGMP. These structures, combined with a comprehensive mutagenic analysis, allowed us to identify Leu296 and Arg297 as key residues that mediate cGMP selectivity. In addition, by comparing the cGMP bound and unbound structures, we observed large conformational changes in the C-terminal helices in response to cGMP binding, which were stabilized by recruitment of Tyr351 as acapping residue for cGMP. The observed rearrangements of the C-terminal helices provide a mechanical insight into release of the catalytic domain and kinase activation.
Sanchez E.J.,Washington State University |
Munske G.R.,Washington State University |
Criswell A.,Rigaku Americas |
Milting H.,Ruhr University Bochum |
And 2 more authors.
Molecular and Cellular Biochemistry | Year: 2011
Both cardiac and skeletal calsequestrin (CASQ2 and CASQ1) serve as a major Ca2+ storage/buffer protein in the sarcoplasmic reticulum (SR) by sequestering and releasing large numbers of Ca2+ ions during each muscular contraction and relaxation cycle. CASQ isolated from various species often exists in a phosphorylated form, but phosphorylation's role is not yet understood. Here, the authors identified two phosphorylation sites, Ser 385 and Ser393, for the first time, in human CASQ2 (hCASQ2) by mass-spectroscopy and evaluated the consequences of such phosphorylation. Substitution of these two serines with phosphoserine-mimicking aspartic-acid residues results in a significant increase in helical content, solubility and Ca2+-binding capacity above 6 mM [Ca2+]. However, neither substitution of Ser385 nor Ser393 alone produce any significant changes. Based on the crystal structures of hCASQ2, Ca2+ binding capacity data, turbidity, and light scattering profiles, it was propose that phosphorylation at these two positions produces a disorder-to-order or coil-to-helix transition of the C-terminus, which in turn provides a more stable network of polyanions. Therefore, considering all the previous reports and the new data, the observed dynamic in vivo phosphorylation of CASQ could provide the basis not only for effective regulation of Ca 2+ buffering capacity, but also for the junctional SR trafficking mechanism. © 2011 Springer Science+Business Media, LLC.
Susner M.A.,Ohio State University |
Susner M.A.,Oak Ridge National Laboratory |
Sumption M.D.,Ohio State University |
Takase A.,Rigaku Americas |
Collings E.W.,Ohio State University
Superconductor Science and Technology | Year: 2014
In an investigation of possible atomic substitution for the Mg site in MgB2, superconducting thin films were deposited by pulsed laser deposition using MgB2 and ZrB2 targets. The resulting c-axis-oriented thin films contained various concentrations of Zr. The structural, chemical, and superconductive properties of these films were investigated. ZrB2 additions were found to increase the a lattice parameter; STEM-based chemical analysis showed Zr to be present within the grains. The superconducting critical temperature was suppressed for the heavily-doped samples. These observations are strong evidence for the substitution of Zr for Mg in the Mg sublattice of MgB2. © 2014 IOP Publishing Ltd.
Patel T.R.,University of Manitoba |
Morris G.A.,University of Nottingham |
Zwolanek D.,University of Cologne |
Keene D.R.,Shriners Hospital for Children |
And 4 more authors.
Matrix Biology | Year: 2010
Laminins are multidomain glycoproteins that play important roles in development and maintenance of the extracellular matrix via their numerous interactions with other proteins. Several receptors for the laminin short arms revealed their importance in network formation and intercellular signaling. However, both the detailed structure of the laminin γ-1 short arm and its organization within the complexes is poorly understood due to the complexity of the molecule and the lack of a high-resolution structure. The presented data provide the first subatomic resolution structure for the laminin γ-1 short arm in solution. This was achieved using an integrated approach that combined a number of complementary biophysical techniques such as small angle X-ray scattering (SAXS), analytical ultracentrifugation, dynamic light scattering and electron microscopy. As a result of this study, we have obtained a significantly improved model for the laminin γ-1 short arm that represents a major step forward in molecular understanding of laminin-mediated complex formations. © 2010.
Patel T.R.,University of Manitoba |
Meier M.,University of Manitoba |
Li J.,Rigaku Americas |
Morris G.,University of Nottingham |
And 3 more authors.
Protein Science | Year: 2011
Agrin is a large heparin sulphate proteoglycan with multiple domains, which is located in the extracellular matrix. The C-terminal G3 domain of agrin is functionally one of the most important domains. It harbors an α-dystroglycan binding site and carries out acetylcholine receptor clustering activities. In the present study, we have fused the G3 domain of agrin to an IgG Fc domain to produce a G3-Fc fusion protein that we intend to use as a tool to investigate new binding partners of agrin. As a first step of the study, we have characterized the recombinant fusion protein using a multidisciplinary approach using dynamic light scattering, analytical ultracentrifugation and small angle X-ray scattering (SAXS). Interestingly, our SAXS analysis using the high-resolution structures of G3 and Fc domain as models indicates that the G3-Fc protein forms a T-shaped molecule with the G3 domains extruding perpendicularly from the Fc scaffold. To validate our models, we have used the program HYDROPRO to calculate the hydrodynamic properties of the solution models. The calculated values are in excellent agreement with those determined experimentally. © 2011 The Protein Society.