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Journal articles on the topic 'Proteins crystal structure'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Banerjee, Sanchari, Nathan P. Coussens, François-Xavier Gallat, et al. "Structure of a heterogeneous, glycosylated, lipid-bound,in vivo-grown protein crystal at atomic resolution from the viviparous cockroachDiploptera punctata." IUCrJ 3, no. 4 (2016): 282–93. http://dx.doi.org/10.1107/s2052252516008903.

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Macromolecular crystals for X-ray diffraction studies are typically grownin vitrofrom pure and homogeneous samples; however, there are examples of protein crystals that have been identifiedin vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grownin cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. Thesein vivo-grown crystals were isolated from the midg

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Tarique, K. F., S. Devi, S. A. Abdul Rehman, and S. Gourinath. "Crystal structure of HINT fromHelicobacter pylori." Acta Crystallographica Section F Structural Biology Communications 72, no. 1 (2016): 42–48. http://dx.doi.org/10.1107/s2053230x15023316.

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Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which

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3

Priestle, John P. "Improved dihedral-angle restraints for protein structure refinement." Journal of Applied Crystallography 36, no. 1 (2003): 34–42. http://dx.doi.org/10.1107/s0021889802018265.

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Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better

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Sprenger, Janina, Jannette Carey, Alexander Schulz, et al. "Guest-protein incorporation into solvent channels of a protein host crystal (hostal)." Acta Crystallographica Section D Structural Biology 77, no. 4 (2021): 471–85. http://dx.doi.org/10.1107/s2059798321001078.

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Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge

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Nguyen, Van Dat, Ekaterina Biterova, Mikko Salin, Rik K. Wierenga, and Lloyd W. Ruddock. "Crystal structure of human anterior gradient protein 3." Acta Crystallographica Section F Structural Biology Communications 74, no. 7 (2018): 425–30. http://dx.doi.org/10.1107/s2053230x18009093.

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Oxidative protein folding in the endoplasmic reticulum is catalyzed by the protein disulfide isomerase family of proteins. Of the 20 recognized human family members, the structures of eight have been deposited in the PDB along with domains from six more. Three members of this family, ERp18, anterior gradient protein 2 (AGR2) and anterior gradient protein 3 (AGR3), are single-domain proteins which share sequence similarity. While ERp18 has a canonical active-site motif and is involved in native disulfide-bond formation, AGR2 and AGR3 lack elements of the active-site motif found in other family

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Conrad, Chelsie E., Shibom Basu, Daniel James, et al. "A novel inert crystal delivery medium for serial femtosecond crystallography." IUCrJ 2, no. 4 (2015): 421–30. http://dx.doi.org/10.1107/s2052252515009811.

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Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the prot

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Melville, Zephan, Ehson Aligholizadeh, Laura E. McKnight, Dylan J. Weber, Edwin Pozharski, and David J. Weber. "X-ray crystal structure of human calcium-bound S100A1." Acta Crystallographica Section F Structural Biology Communications 73, no. 4 (2017): 215–21. http://dx.doi.org/10.1107/s2053230x17003983.

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S100A1 is a member of the S100 family of Ca2+-binding proteins and regulates several cellular processes, including those involved in Ca2+signaling and cardiac and skeletal muscle function. In Alzheimer's disease, brain S100A1 is overexpressed and gives rise to disease pathologies, making it a potential therapeutic target. The 2.25 Å resolution crystal structure of Ca2+-S100A1 is solved here and is compared with the structures of other S100 proteins, most notably S100B, which is a highly homologous S100-family member that is implicated in the progression of malignant melanoma. The observed stru

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8

HARATA, Kazuaki. "Crystal Structure as a Snapshot of Dynamic Structure of Proteins." Nihon Kessho Gakkaishi 36, no. 4 (1994): 270–75. http://dx.doi.org/10.5940/jcrsj.36.270.

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9

Jung, James, Ghader Bashiri, Jodie Johnston, Alistair Brown, David Ackerley, and Edward Baker. "Crystal structure of M. tuberculosis phosphopantetheinyl transferase PptT." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C815. http://dx.doi.org/10.1107/s2053273314091840.

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Phosphopantetheinyl transferases (PPTases) are essential enzymes that catalyze covalent attachment of the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to a conserved serine residue on acyl (ACP) and peptidyl carrier proteins (PCP) [1]. This post-translational modification converts the inactive apo-carrier proteins to the functional form, shuttling the intermediates of biosynthetic reactions catalyzed by fatty acid synthases (FAS), polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPSs). In Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB)

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10

Zhang, Fajun, Georg Zocher, Andrea Sauter, Thilo Stehle, and Frank Schreiber. "Novel approach to controlled protein crystallization through ligandation of yttrium cations." Journal of Applied Crystallography 44, no. 4 (2011): 755–62. http://dx.doi.org/10.1107/s0021889811017997.

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Crystal structure determination of macromolecules is often hampered by the lack of crystals suitable for diffraction experiments. This article describes a protocol to crystallize the acidic protein bovine β-lactoglobulin in the presence of yttrium to yield high-quality crystals that belong to a new space group. The yttrium ions not only are used to engineer the crystallization, but are an integral part of the crystal lattice and can therefore be used to solve the phase problem using anomalous dispersion methods. Protein crystallization conditions were first optimized using an experimental phas

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11

Roznowski, Aaron P., та Bentley A. Fane. "Structure-Function Analysis of the ϕX174 DNA-Piloting Protein Using Length-Altering Mutations". Journal of Virology 90, № 17 (2016): 7956–66. http://dx.doi.org/10.1128/jvi.00914-16.

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ABSTRACTAlthough the ϕX174 H protein is monomeric during procapsid morphogenesis, 10 proteins oligomerize to form a DNA translocating conduit (H-tube) for penetration. However, the timing and location of H-tube formation are unknown. The H-tube's highly repetitive primary and quaternary structures made it amenable to a genetic analysis using in-frame insertions and deletions. Length-altered proteins were characterized for the ability to perform the protein's three known functions: participation in particle assembly, genome translocation, and stimulation of viral protein synthesis. Insertion mu

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Ishchenko, Andrii, Benjamin Stauch, Gye Won Han, et al. "Toward G protein-coupled receptor structure-based drug design using X-ray lasers." IUCrJ 6, no. 6 (2019): 1106–19. http://dx.doi.org/10.1107/s2052252519013137.

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Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking adva

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13

Pelz, Jann-Patrick, Hermann Schindelin, Katharina van Pee, et al. "Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project." Acta Crystallographica Section D Biological Crystallography 71, no. 10 (2015): 2040–53. http://dx.doi.org/10.1107/s1399004715014832.

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The small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/6 and U5 are major constituents of the pre-mRNA processing spliceosome. They contain a common RNP core that is formed by the ordered binding of Sm proteins onto the single-stranded Sm site of the snRNA. Although spontaneousin vitro, assembly of the Sm core requires assistance from the PRMT5 and SMN complexesin vivo. To gain insight into the key steps of the assembly process, the crystal structures of two assembly intermediates of U snRNPs termed the 6S and 8S complexes have recently been reported. These multimeric protein complexes could

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14

Karthikeyan, Subramanian, Murugan Paramasivam, Savita Yadav, Alagiri Srinivasan, and Tej P. Singh. "Structure of buffalo lactoferrin at 2.5 Å resolution using crystals grown at 303 K shows different orientations of the N and C lobes." Acta Crystallographica Section D Biological Crystallography 55, no. 11 (1999): 1805–13. http://dx.doi.org/10.1107/s0907444999010951.

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The structure of buffalo lactoferrin has been determined at 303 K. The crystals belong to orthorhombic space group P212121, with unit-cell parameters a = 77.5, b = 91.0, c = 131.5 Å and Z = 4. The structure has been refined to an R factor of 0.187. The overall structure of the protein is similar to its structure determined at 277 K in a different crystal form. However, the lobe orientations in the two structures differ by 9.0°, suggesting significant inter-lobe flexibility in this family of proteins. The inter-lobe interactions are predominantly hydrophobic and could act as a cushion for a cha

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15

Lanza, Arianna, Eleonora Margheritis, Enrico Mugnaioli, Valentina Cappello, Gianpiero Garau, and Mauro Gemmi. "Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme." IUCrJ 6, no. 2 (2019): 178–88. http://dx.doi.org/10.1107/s2052252518017657.

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Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting

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16

Purushotham, Sangeetha, Matthew Larson, Jeffrey Banas, and Champion Deivanayagam. "Structure/Function studies on Glucan Binding Protein C of Streptococcus mutans." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1639. http://dx.doi.org/10.1107/s2053273314083600.

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Streptococcus mutans is a known etiological agent in dental caries. In the past several years, we have taken a concerted effort toward understanding the adhesion mechanisms adopted by the surface proteins S. mutans. The Glucan Binding Protein C (GBPC) is a LPXTG anchored surface protein on S. mutans that has been widely implicated to play a significant role in biofilm formation. GBPC displays limited homology to the V-region of Antigen I/II (AgI/II), another surface protein of S. mutans (1,2). We undertook to crystallize and resolve the structure of GBPC. Recombinant GbpC111-552 (residues enco

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17

Kumar, Adarsh, and Subramanian Karthikeyan. "Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis." Acta Crystallographica Section F Structural Biology Communications 74, no. 3 (2018): 166–73. http://dx.doi.org/10.1107/s2053230x18002236.

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TheMSMEG_4306gene fromMycobacterium smegmatisencodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two simil

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18

Caldararu, Octav, Majda Misini Ignjatović, Esko Oksanen, and Ulf Ryde. "Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures." RSC Advances 10, no. 14 (2020): 8435–43. http://dx.doi.org/10.1039/c9ra09601a.

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19

Im, Ha Na, and Se Won Suh. "Crystal structure of Rv2258c, a putative SAM-dependent methyltransferase." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1651. http://dx.doi.org/10.1107/s205327331408348x.

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The Mycobacterium tuberculosis protein Rv2258c belongs to a large family of putative S-adenosylmethionine (SAM)-dependent methyltransferases in mycobacteria. As part of a laboratory-scale structural genomics project on conserved hypothetical proteins in pathogenic bacteria, we have determined the crystal structure of Rv2258c from M. tuberculosis H37Rv at 1.8 Å resolution. The crystals of apo Rv2258c belong to space group C2, with unit cell parameters a = 109.2 Å, b = 140.6 Å, c = 97.2 Å, and β = 98.50. Assuming that three monomers are present in the asymmetric unit, the Matthews parameter and

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Reddy, Vijay, and Glen Nemerow. "Structure and function of cement proteins in human adenovirus." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1603. http://dx.doi.org/10.1107/s205327331408396x.

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Human adenoviruses (HAdVs) are large (~150nm in diameter, 150MDa) nonenveloped double-stranded DNA (dsDNA) viruses that cause respiratory, ocular, and enteric diseases. The capsid shell of adenovirus (Ad) comprises multiple copies of three major capsid proteins (MCP: hexon, penton base and fiber) and four minor/cement proteins (IIIa, VI, VIII and IX) that are organized with pseudo T=25 icosahedral symmetry. In addition, six other proteins (V, VII, μ, IVa2, terminal protein and protease) are encapsidated along with the 36Kb dsDNA genome inside the capsid. The crystal structures of all three MCP

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Martynowycz, Michael W., Farha Khan, Johan Hattne, Jeff Abramson, and Tamir Gonen. "MicroED structure of lipid-embedded mammalian mitochondrial voltage-dependent anion channel." Proceedings of the National Academy of Sciences 117, no. 51 (2020): 32380–85. http://dx.doi.org/10.1073/pnas.2020010117.

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A structure of the murine voltage-dependent anion channel (VDAC) was determined by microcrystal electron diffraction (MicroED). Microcrystals of an essential mutant of VDAC grew in a viscous bicelle suspension, making it unsuitable for conventional X-ray crystallography. Thin, plate-like crystals were identified using scanning-electron microscopy (SEM). Crystals were milled into thin lamellae using a focused-ion beam (FIB). MicroED data were collected from three crystal lamellae and merged for completeness. The refined structure revealed unmodeled densities between protein monomers, indicative

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Carugo, Oliviero. "Identification of domains in protein crystal structures." Journal of Applied Crystallography 40, no. 4 (2007): 778–81. http://dx.doi.org/10.1107/s0021889807023874.

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Large proteins are often composed of two or more domains, the identification of which can allow one to determine their crystal structures at higher resolution. The computer program described here is intended to assist the user in the identification of the structural domains, defined as compact ensembles of residues, on the basis of the crystal structure of the protein that contains them.

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Billeter, Martin. "Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals." Quarterly Reviews of Biophysics 25, no. 3 (1992): 325–77. http://dx.doi.org/10.1017/s0033583500004261.

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Following the first determinations of protein structures in the late 1950s and the early 1960s (see for example Kendrewet al.1960; Perutz, 1964), the three-dimensional structures of several hundred proteins have been elucidated by X-ray diffraction on single crystals. By the end of 1991, approximately 150 entries of proteins with substantially different sequences and a well resolved structure (Hobohmet al.1992) were deposited in the Protein Data Bank (Bernsteinet al.1977; Abolaet al.1987). In addition, many structures of homologous proteins or of mutants have been described, bringing the total

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Guo, Youzhong. "Be Cautious with Crystal Structures of Membrane Proteins or Complexes Prepared in Detergents." Crystals 10, no. 2 (2020): 86. http://dx.doi.org/10.3390/cryst10020086.

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Membrane proteins are an important class of macromolecules found in all living organisms and many of them serve as important drug targets. In order to understand their biological and biochemical functions and to exploit them for structure-based drug design, high-resolution and accurate structures of membrane proteins are needed, but are still rarely available, e.g., predominantly from X-ray crystallography, and more recently from single particle cryo-EM — an increasingly powerful tool for membrane protein structure determination. However, while protein-lipid interactions play crucial roles for

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Ye, Qilu, Robert Eves, Robert L. Campbell, and Peter L. Davies. "Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface." Biochemical Journal 477, no. 17 (2020): 3271–86. http://dx.doi.org/10.1042/bcj20200539.

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Antifreeze proteins (AFPs) are characterized by their ability to adsorb to the surface of ice crystals and prevent any further crystal growth. AFPs have independently evolved for this purpose in a variety of organisms that encounter the threat of freezing, including many species of polar fish, insects, plants and microorganisms. Despite their diverse origins and structures, it has been suggested that all AFPs can organize ice-like water patterns on one side of the protein (the ice-binding site) that helps bind the AFP to ice. Here, to test this hypothesis, we have solved the crystal structure

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Śledź, Paweł, Radosław Kamiński, Maksymilian Chruszcz, Matthew D. Zimmerman, Wladek Minor, and Krzysztof Woźniak. "An experimental charge density of HEPES." Acta Crystallographica Section B Structural Science 66, no. 4 (2010): 482–92. http://dx.doi.org/10.1107/s0108768110023025.

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We report the experimental charge density of HEPES [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], which is a common buffering agent. The structure was refined using the Hansen–Coppens formalism. The ability of the HEPES molecule to form stable intermolecular interactions and intermolecular hydrogen bonds in the crystal structure is discussed in terms of its buffering properties. The protonation mode observed in the crystal structure is different from that expected in solution, suggesting that additional factors must be taken into consideration in order to explain the solution properties

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Arakaki, Atsushi, Daiki Kikuchi, Masayoshi Tanaka, Ayana Yamagishi, Takuto Yoda, and Tadashi Matsunaga. "Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals." Journal of Bacteriology 198, no. 20 (2016): 2794–802. http://dx.doi.org/10.1128/jb.00280-16.

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ABSTRACTThe magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-l

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Hansen, Simon, Christian Reichen, Chaithanya Madhurantakam, Markus Grütter, Andreas Plückthun, and Peer Mittl. "Structure-based engineering of designed armadillo repeat proteins." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1153. http://dx.doi.org/10.1107/s2053273314088469.

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The specific recognition of macromolecules is key for many applications in biochemical research, medical diagnostics and disease treatment. Currently the development of new recognition molecules depends on the immunization of lab animals or combinatorial biochemistry techniques. Since both approaches are elaborate and require the availability of sufficient amounts of stable target molecules we are developing a modular system that allows a rational design of peptide recognition modules. This system is based on the armadillo repeat scaffold, because natural armadillo repeat proteins bind their t

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Wang, Meitian. "Advancing Native-SAD Phasing at Synchrotron with 13 Real-life Case Studies." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C601. http://dx.doi.org/10.1107/s205327331409398x.

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The key step in elucidating de novo 3D X-ray structures relies on the incorporation of heavy elements into proteins or crystals. Selenomethionine incorporation or heavy metal derivatization are however not always possible and require additional efforts. Exploiting anomalous signals from intrinsically present elements like S, P, and Ca2+ from proteins and nucleic acids, as well as Cl-, SO42-, and PO42- from crystallization solutions, is therefore an appealing alternative. Such a method has been shown to be valid by collecting data from several crystals and combining them(1). Recent developments

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Bettati, Stefano, Elisa Pasqualetto, Graziano Lolli, Barbara Campanini, and Roberto Battistutta. "Structure and single crystal spectroscopy of Green Fluorescent Proteins." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814, no. 6 (2011): 824–33. http://dx.doi.org/10.1016/j.bbapap.2010.10.002.

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ADACHI, Shin-ichi, and Nobuhisa WATANABE. "Time-Resolved X-ray Crystal Structure Analysis of Proteins." Seibutsu Butsuri 35, no. 6 (1995): 245–48. http://dx.doi.org/10.2142/biophys.35.245.

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Kudlinzki, Denis, Verena L. Linhard, Krishna Saxena, et al. "High-resolution crystal structure of cAMP-dependent protein kinase fromCricetulus griseus." Acta Crystallographica Section F Structural Biology Communications 71, no. 8 (2015): 1088–93. http://dx.doi.org/10.1107/s2053230x1501242x.

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Protein kinases (PKs) are dynamic regulators of numerous cellular processes. Their phosphorylation activity is determined by the conserved kinase core structure, which is maintained by the interaction and dynamics with associated domains or interacting proteins. The prototype enzyme for investigations to understand the activity and regulation of PKs is the catalytic subunit of cAMP-dependent protein kinase (PKAc). Major effects of functional regulation and ligand binding are driven by only minor structural modulations in protein–protein interactions. In order to resolve such minor structural d

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Lee, Sang Jae, Chao Ma, Bong-Jin Lee, and Se Won Suh. "Crystal structure of PhoU from Pseudomonas aeruginosa." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C825. http://dx.doi.org/10.1107/s2053273314091748.

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The PhoU protein in bacteria plays a role in maintaining phosphate homeostasis by regulating the Pho regulon. Recent studies showed that PhoU is essential for normal growth and is also involved in persister formation. PhoU is a potential target for overcoming drug tolerance of pathogenic bacteria. However, the exact mechanism of PhoU functions is still unknown. Here we have determined the crystal structure of PhoU from Pseudomonas aeruginosa at 2.28 Å resolution by Se SAD method. P. aeruginosa PhoU exists as a dimer in the crystals. A monomer of P. aeruginosa PhoU consists of six alpha-helices

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Oganesyan, Vaheh, Natalia Oganesyan, Paul D. Adams, et al. "Crystal Structure of the “PhoU-Like” Phosphate Uptake Regulator from Aquifex aeolicus." Journal of Bacteriology 187, no. 12 (2005): 4238–44. http://dx.doi.org/10.1128/jb.187.12.4238-4244.2005.

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ABSTRACT The phoU gene of Aquifex aeolicus encodes a protein called PHOU_AQUAE with sequence similarity to the PhoU protein of Escherichia coli. Despite the fact that there is a large number of family members (more than 300) attributed to almost all known bacteria and despite PHOU_AQUAE's association with the regulation of genes for phosphate metabolism, the nature of its regulatory function is not well understood. Nearly one-half of these PhoU-like proteins, including both PHOU_AQUAE and the one from E. coli, form a subfamily with an apparent dimer structure of two PhoU domains on the basis o

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Scicluna, Kristen, Grant Dewson, Peter E. Czabotar, and Richard W. Birkinshaw. "A new crystal form of GABARAPL2." Acta Crystallographica Section F Structural Biology Communications 77, no. 5 (2021): 140–47. http://dx.doi.org/10.1107/s2053230x21004489.

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The Atg8 protein family comprises the GABA type A receptor-associated proteins (GABARAPs) and microtubule-associated protein 1 light chains 3 (MAP1LC3s) that are essential mediators of autophagy. The LC3-interacting region (LIR) motifs of autophagy receptors and adaptors bind Atg8 proteins to promote autophagosome formation, cargo recruitment, and autophagosome closure and fusion to lysosomes. A crystal structure of human GABARAPL2 has been published [PDB entry 4co7; Ma et al. (2015), Biochemistry, 54, 5469–5479]. This was crystallized in space group P21 with a monoclinic angle of 90° and show

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Fukuhara, Satoshi, Takanori Nakane, Keitaro Yamashita, Ryohei Ishii, Ryuichiro Ishitani, and Osamu Nureki. "Crystal structure of the Agrobacterium tumefaciens type VI effector–immunity complex." Acta Crystallographica Section F Structural Biology Communications 74, no. 12 (2018): 810–16. http://dx.doi.org/10.1107/s2053230x18016369.

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The type VI secretion system (T6SS) comprises needle-shaped multisubunit complexes that play a role in the microbial defense systems of Gram-negative bacteria. Some Gram-negative bacteria harboring a T6SS deliver toxic effector proteins into the cytoplasm or periplasm of competing bacteria in order to lyse and kill them. To avoid self-cell disruption, these bacteria have cognate immunity proteins that inhibit their toxic effector proteins. T6SS amidase effector protein 4 (Tae4) and T6SS amidase immunity protein 4 (Tai4) are a representative of the toxic effector–immunity pairs of the T6SS. Her

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Bhardwaj, Anshul, Sherwood R. Casjens, and Gino Cingolani. "Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography." Acta Crystallographica Section D Biological Crystallography 70, no. 2 (2014): 342–53. http://dx.doi.org/10.1107/s1399004713027685.

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Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the t

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García-Nafría, Javier, and Christopher G. Tate. "Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development." Annual Review of Pharmacology and Toxicology 60, no. 1 (2020): 51–71. http://dx.doi.org/10.1146/annurev-pharmtox-010919-023545.

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Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiolog

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Padyana, Anil K., Bhamini Vaidialingam, David B. Hayes, Priyanka Gupta, Michael Franti, and Neil A. Farrow. "Crystal structure of human GDF11." Acta Crystallographica Section F Structural Biology Communications 72, no. 3 (2016): 160–64. http://dx.doi.org/10.1107/s2053230x16001588.

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Members of the TGF-β family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94

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Chirgadze, Yuri N., Teresa E. Clarke, Vladimir Romanov, et al. "The structure of SAV1646 fromStaphylococcus aureusbelonging to a new `ribosome-associated' subfamily of bacterial proteins." Acta Crystallographica Section D Biological Crystallography 71, no. 2 (2015): 332–37. http://dx.doi.org/10.1107/s1399004714025619.

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The crystal structure of the SAV1646 protein from the pathogenic microorganismStaphylococcus aureushas been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genom

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Vives-Adrián, Laia, Damià Garriga, Mònica Buxaderas, et al. "Structural Basis for Host Membrane Remodeling Induced by Protein 2B of Hepatitis A Virus." Journal of Virology 89, no. 7 (2015): 3648–58. http://dx.doi.org/10.1128/jvi.02881-14.

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ABSTRACTThe complexity of viral RNA synthesis and the numerous participating factors require a mechanism to topologically coordinate and concentrate these multiple viral and cellular components, ensuring a concerted function. Similarly to all other positive-strand RNA viruses, picornaviruses induce rearrangements of host intracellular membranes to create structures that act as functional scaffolds for genome replication. The membrane-targeting proteins 2B and 2C, their precursor 2BC, and protein 3A appear to be primarily involved in membrane remodeling. Little is known about the structure of t

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Perkins, S. J., and K. F. Smith. "Identity of the putative serine-proteinase fold in proteins of the complement system with nine relevant crystal structures." Biochemical Journal 295, no. 1 (1993): 109–14. http://dx.doi.org/10.1042/bj2950109.

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The serine-proteinase domain is responsible for the proteolytic events that occur during complement activation. The sequences of nine serine proteinases of known crystal structure were compared with the serine-proteinase sequences in the six complement proteins C1r, C1s, C2, factor B, factor I and factor D to assess the degree of structural homology of the latter with the crystal structures. All sequence insertions and deletions were readily located at the protein surface. The internal location of disulphide bridges and the surface location of putative glycosylation sites are compatible with t

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Nybakken, Grant E., Christopher A. Nelson, Beverly R. Chen, Michael S. Diamond, and Daved H. Fremont. "Crystal Structure of the West Nile Virus Envelope Glycoprotein." Journal of Virology 80, no. 23 (2006): 11467–74. http://dx.doi.org/10.1128/jvi.01125-06.

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ABSTRACT The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-Å crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylatio

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Lahey-Rudolph, J. Mia, Robert Schönherr, Miriam Barthelmess, et al. "Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals." IUCrJ 8, no. 4 (2021): 665–77. http://dx.doi.org/10.1107/s2052252521005297.

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The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approac

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Schumacher, Benjamin, Malgorzata Skwarczynska, Rolf Rose та Christian Ottmann. "Structure of a 14-3-3σ–YAP phosphopeptide complex at 1.15 Å resolution". Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, № 9 (2010): 978–84. http://dx.doi.org/10.1107/s1744309110025479.

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The 14-3-3 proteins are a class of eukaryotic acidic adapter proteins, with seven isoforms in humans. 14-3-3 proteins mediate their biological function by binding to target proteins and influencing their activity. They are involved in pivotal pathways in the cell such as signal transduction, gene expression, enzyme activation, cell division and apoptosis. The Yes-associated protein (YAP) is a WW-domain protein that exists in two transcript variants of 48 and 54 kDa in humans. By transducing signals from the cytoplasm to the nucleus, YAP is important for transcriptional regulation. In both vari

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Tian, Yu, Matthew Tirrell, Carley Davis, and Jeffrey A. Wesson. "Protein primary structure correlates with calcium oxalate stone matrix preference." PLOS ONE 16, no. 9 (2021): e0257515. http://dx.doi.org/10.1371/journal.pone.0257515.

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Despite the apparent importance of matrix proteins in calcium oxalate kidney stone formation, the complexity of the protein mixture continues to elude explanation. Based on a series of experiments, we have proposed a model where protein aggregates formed from a mixture containing both strongly charged polyanions and strongly charged polycations could initiate calcium oxalate crystal formation and crystal aggregation to create a stone. These protein aggregates also preferentially adsorb many weakly charged proteins from the urine to create a complex protein mixture that mimics the protein distr

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Dörner, Katerina, Jose Martin-Garcia, Christopher Kupitz, Rebekka Wachter, and Petra Fromme. "Detection of protein nanocrystals based on the reversibility of crystallization." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1147. http://dx.doi.org/10.1107/s2053273314088524.

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A prerequisite for conventional X-ray protein structure analysis is the growth of crystals with a sufficient size in the range of several µm. This is a time consuming and not always successful process, challenging especially when working with membrane proteins. The recently developed technique of femtosecond X-ray crystallography enables structure analysis of crystals with a size in the nm range, thus the process of growing large single crystals can be avoided. Moreover femtosecond X-ray nanocrystallography is a potential method to overcome the radiation damage problem and to perform time-reso

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Perkins, Stephen J., and Alexandra Bonner. "Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling." Biochemical Society Transactions 36, no. 1 (2008): 37–42. http://dx.doi.org/10.1042/bst0360037.

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X-ray and neutron scattering and analytical ultracentrifugation provide multiparameter structural and compositional information on proteins that complements high-resolution protein crystallography and NMR studies. They are ideal methods to use when either a large protein cannot be crystallized, when scattering provides the only means to obtain a solution structure, or the protein crystal structure has been determined and it is necessary to validate this. Once these results have been obtained, we apply automated constrained modelling methods based on known subunit crystal structures to identify

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Nishitani, Yuichi, Jan-Robert Simons, Tamotsu Kanai, Haruyuki Atomi, and Kunio Miki. "Crystal structure of the TK2203 protein fromThermococcus kodakarensis, a putative extradiol dioxygenase." Acta Crystallographica Section F Structural Biology Communications 72, no. 6 (2016): 427–33. http://dx.doi.org/10.1107/s2053230x16006920.

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The TK2203 protein from the hyperthermophilic archaeonThermococcus kodakarensisKOD1 (262 residues, 29 kDa) is a putative extradiol dioxygenase catalyzing the cleavage of C–C bonds in catechol derivatives. It contains three metal-binding residues, but has no significant sequence similarity to proteins for which structures have been determined. Here, the first crystal structure of the TK2203 protein was determined at 1.41 Å resolution to investigate its functional role. Structure analysis reveals that this protein shares the same fold and catalytic residues as other extradiol dioxygenases, stron

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Yao, Min, Keisuke Komoda, Naofumi Sakurai, et al. "Increasing the probability of successful crystallization by using symmetric tag." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1159. http://dx.doi.org/10.1107/s2053273314088408.

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Recent progress in the techniques of bio-macromolecular crystallography makes crystal structure analysis more powerful and useful for life science. The structure analysis of huge super-molecular (eukaryotic Ribosome, Vault etc.) and membrane proteins related to diseases were successful. Moreover, the structure/fragment drug design using crystal structure analysis method is also becoming reliable. However, crystallization still remains as a major bottleneck for determining bio-macromolecular structures, although many methods have been developed such as crystallization kits, crystallization robo

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