9 results match your criteria Acta crystallographica. Section D Structural biology[Journal]

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FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments.

Acta Crystallogr D Struct Biol 2020 Feb 24;76(Pt 2):102-117. Epub 2020 Jan 24.

Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA.

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. Read More

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http://dx.doi.org/10.1107/S2059798319015961DOI Listing
February 2020

Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes.

Acta Crystallogr D Struct Biol 2019 Jan 7;75(Pt 1):56-69. Epub 2019 Jan 7.

Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.

Structures of a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides (BbKI) complexed with bovine trypsin were determined in two crystal forms. The crystal structure with the L55R mutant of BbKI was determined in space group P6 at 1.94 Å resolution and that with native BbKI in the monoclinic space group P2 at 3. Read More

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http://dx.doi.org/10.1107/S2059798318016492DOI Listing
January 2019
3 Reads

Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity.

Acta Crystallogr D Struct Biol 2018 Dec 30;74(Pt 12):1219-1232. Epub 2018 Nov 30.

Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA.

Neutron reflectivity (NR) has emerged as a powerful technique to study the structure and behavior of membrane proteins at planar lipid interfaces. Integral membrane proteins (IMPs) remain a significant challenge for NR owing to the difficulty of forming complete bilayers with sufficient protein density for scattering techniques. One strategy to achieve high protein density on a solid substrate is the capture of detergent-stabilized, affinity-tagged IMPs on a nitrilotriacetic acid (NTA)-functionalized self-assembled monolayer (SAM), followed by reconstitution into the lipids of interest. Read More

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http://dx.doi.org/10.1107/S2059798318011749DOI Listing
December 2018
11 Reads

Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer.

Acta Crystallogr D Struct Biol 2018 Nov 29;74(Pt 11):1041-1052. Epub 2018 Oct 29.

Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.

The STARGazer data-processing software is used for neutron time-of-flight (TOF) single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC). This software creates hkl intensity data from three-dimensional (x, y, TOF) diffraction data. STARGazer is composed of a data-processing component and a data-visualization component. Read More

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http://dx.doi.org/10.1107/S2059798318012081DOI Listing
November 2018
6 Reads

Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank.

Acta Crystallogr D Struct Biol 2018 Sep 5;74(Pt 9):939-945. Epub 2018 Sep 5.

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

The Protein Data Bank (PDB) constitutes a collection of the available atomic models of macromolecules and their complexes obtained by various methods used in structural biology, but chiefly by crystallography. It is an indispensable resource for all branches of science that deal with the structures of biologically active molecules, such as structural biology, bioinformatics, the design of novel drugs etc. Since not all users of the PDB are familiar with the methods of crystallography, it is important to present the results of crystallographic analyses in a form that is easy to interpret by nonspecialists. Read More

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http://dx.doi.org/10.1107/S2059798318009828DOI Listing
September 2018
4 Reads

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) extend the repertoire of crystal structures of Z-DNA.

Acta Crystallogr D Struct Biol 2017 Nov 30;73(Pt 11):940-951. Epub 2017 Oct 30.

Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) duplexes are described here. Read More

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http://dx.doi.org/10.1107/S2059798317014954DOI Listing
November 2017
24 Reads

Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C.

Acta Crystallogr D Struct Biol 2016 11 28;72(Pt 11):1194-1202. Epub 2016 Oct 28.

Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden.

Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described. Read More

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http://dx.doi.org/10.1107/S2059798316015540DOI Listing
November 2016
25 Reads

Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.

Acta Crystallogr D Struct Biol 2016 08 13;72(Pt 8):922-32. Epub 2016 Jul 13.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.

The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). Read More

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http://dx.doi.org/10.1107/S205979831601038XDOI Listing
August 2016
27 Reads

Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

Acta Crystallogr D Struct Biol 2016 06 25;72(Pt 6):770-9. Epub 2016 May 25.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. Read More

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http://dx.doi.org/10.1107/S2059798316006355DOI Listing
June 2016
7 Reads
3 Citations
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