journal
MENU ▼
Read by QxMD icon Read
search

Acta Crystallographica. Section D, Structural Biology

journal
https://www.readbyqxmd.com/read/28876241/structural-insights-into-the-interaction-of-the-conserved-mammalian-proteins-gapr-1-and-beclin-1-a-key-autophagy-protein
#1
Yue Li, Yuting Zhao, Minfei Su, Karen Glover, Srinivas Chakravarthy, Christopher L Colbert, Beth Levine, Sangita C Sinha
Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876240/crystal-structures-of-the-methyltransferase-and-helicase-from-the-zika-1947-mr766-uganda-strain
#2
Malgorzata Bukrejewska, Urszula Derewenda, Malwina Radwanska, Daniel A Engel, Zygmunt S Derewenda
Two nonstructural proteins encoded by Zika virus strain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a bound S-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876239/designing-better-diffracting-crystals-of-biotin-carboxyl-carrier-protein-from-pyrococcus-horikoshii-by-a-mutation-based-on-the-crystal-packing-propensity-of-amino-acids
#3
Kazunori D Yamada, Naoki Kunishima, Yoshinori Matsuura, Koshiro Nakai, Hisashi Naitow, Yoshinori Fukasawa, Kentaro Tomii
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP)...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876238/the-structure-of-the-pfp1-protease-from-the-hyperthermophilic-archaeon-thermococcus-thioreducens-in-two-crystal-forms
#4
Steven B Larson, Alexander McPherson
The Pfp1 protease, a cysteine protease of unknown specificity from the hyperthermophilic archaeon Thermococcus thioreducens, was crystallized in two distinctive crystal forms: from concentrated citrate in one case and PEG in the other. X-ray data were collected from both crystal forms at room temperature to about 1.9 Å resolution using a laboratory source and detector, and the structures were solved by molecular replacement using the Pfp1 protease from Pyrococcus horikoshii as the search model. In the T...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876237/protein-structure-determination-by-electron-diffraction-using-a-single-three-dimensional-nanocrystal
#5
M T B Clabbers, E van Genderen, W Wan, E L Wiegers, T Gruene, J P Abrahams
Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm(3), i.e. no more than 6 × 10(5) unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876236/auspex-a-graphical-tool-for-x-ray-diffraction-data-analysis
#6
Andrea Thorn, James Parkhurst, Paul Emsley, Robert A Nicholls, Melanie Vollmar, Gwyndaf Evans, Garib N Murshudov
In this paper, AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas)...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876235/2017-publication-guidelines-for-structural-modelling-of-small-angle-scattering-data-from-biomolecules-in-solution-an-update
#7
Jill Trewhella, Anthony P Duff, Dominique Durand, Frank Gabel, J Mitchell Guss, Wayne A Hendrickson, Greg L Hura, David A Jacques, Nigel M Kirby, Ann H Kwan, Javier Pérez, Lois Pollack, Timothy M Ryan, Andrej Sali, Dina Schneidman-Duhovny, Torsten Schwede, Dmitri I Svergun, Masaaki Sugiyama, John A Tainer, Patrice Vachette, John Westbrook, Andrew E Whitten
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777085/protein-ligand-complex-structure-from-serial-femtosecond-crystallography-using-soaked-thermolysin-microcrystals-and-comparison-with-structures-from-synchrotron-radiation
#8
Hisashi Naitow, Yoshinori Matsuura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Jun Kobayashi, Eriko Nango, So Iwata, Naoki Kunishima
Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777084/the-role-of-conserved-surface-hydrophobic-residues-in-the-carbapenemase-activity-of-the-class-d-%C3%AE-lactamases
#9
Marta Toth, Clyde A Smith, Nuno T Antunes, Nichole K Stewart, Lauren Maltz, Sergei B Vakulenko
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777083/structural-basis-for-the-regulation-of-chemotaxis-by-mapz-in-the-presence-of-c-di-gmp
#10
Yingxiao Zhu, Zenglin Yuan, Lichuan Gu
The bacterial second messenger cyclic diguanylate monophosphate (c-di-GMP) mediates multiple aspects of bacterial physiology through binding to various effectors. In some cases, these effectors are single-domain proteins which only contain a PilZ domain. It remains largely unknown how single-domain PilZ proteins function and regulate their downstream targets. Recently, a single-domain PilZ protein, MapZ (PA4608), was identified to inhibit the activity of the methyltransferase CheR1. Here, crystal structures of the C-terminal domain of CheR1 containing SAH and of CheR1 in complex with c-di-GMP-bound MapZ are reported...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777082/crystal-structure-of-the-peg-bound-sh3-domain-of-myosin-ib-from-entamoeba-histolytica-reveals-its-mode-of-ligand-recognition
#11
Gunjan Gautam, Syed Arif Abdul Rehman, Preeti Pandey, Samudrala Gourinath
The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777081/binding-of-hydroxycitrate-to-human-atp-citrate-lyase
#12
Jinhong Hu, Aruna Komakula, Marie E Fraser
Hydroxycitrate from the fruit of Garcinia cambogia [i.e. (2S,3S)-2-hydroxycitrate] is the best-known inhibitor of ATP-citrate lyase. Well diffracting crystals showing how the inhibitor binds to human ATP-citrate lyase were grown by modifying the protein. The protein was modified by introducing cleavage sites for Tobacco etch virus protease on either side of a disordered linker. The protein crystallized consisted of residues 2-425-ENLYFQ and S-488-810 of human ATP-citrate lyase. (2S,3S)-2-Hydroxycitrate binds in the same orientation as citrate, but the citrate-binding domain (residues 248-421) adopts a different orientation with respect to the rest of the protein (residues 4-247, 490-746 and 748-809) from that previously seen...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777080/toscana-virus-nucleoprotein-oligomer-organization-observed-in-solution
#13
Amal Baklouti, Adeline Goulet, Julie Lichière, Bruno Canard, Rémi N Charrel, François Ferron, Bruno Coutard, Nicolas Papageorgiou
Toscana virus (TOSV) is an arthropod-borne virus belonging to the Phlebovirus genus within the Bunyaviridae family. As in other bunyaviruses, the genome of TOSV is made up of three RNA segments. They are encapsidated by the nucleoprotein (N), which also plays an essential role in virus replication. To date, crystallographic structures of phlebovirus N have systematically revealed closed-ring organizations which do not fully match the filamentous organization of the ribonucleoprotein (RNP) complex observed by electron microscopy...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777079/activity-inhibition-and-crystal-polymorphism-induced-by-active-site-metal-swapping
#14
Elsie Yekwa, Joelle Khourieh, Bruno Canard, Nicolas Papageorgiou, François Ferron
The Arenaviridae family is one of the two RNA viral families that encode a 3'-5' exonuclease in their genome. An exonuclease domain is found in the Arenaviridae nucleoprotein and targets dsRNA specifically. This domain is directly involved in suppression of innate immunity in the host cell. Like most phosphate-processing enzymes, it requires a divalent metal ion such as Mg(2+) (or Mn(2+)) as a cofactor to catalyse nucleotide-cleavage and nucleotide-transfer reactions. On the other hand, calcium (Ca(2+)) inhibits this enzymatic activity, in spite of the fact that Mg(2+) and Ca(2+) present comparable binding affinities and biological availabilities...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777078/an-overview-of-comparative-modelling-and-resources-dedicated-to-large-scale-modelling-of-genome-sequences
#15
Su Datt Lam, Sayoni Das, Ian Sillitoe, Christine Orengo
Computational modelling of proteins has been a major catalyst in structural biology. Bioinformatics groups have exploited the repositories of known structures to predict high-quality structural models with high efficiency at low cost. This article provides an overview of comparative modelling, reviews recent developments and describes resources dedicated to large-scale comparative modelling of genome sequences. The value of subclustering protein domain superfamilies to guide the template-selection process is investigated...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695862/factors-affecting-the-amplitude-of-the-%C3%AF-angle-in-proteins-a-revisitation
#16
Nicole Balasco, Luciana Esposito, Luigi Vitagliano
The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N-C(α)-C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695861/seeing-but-not-believing-the-structure-of-glycerol-dehydrogenase-initially-assumed-to-be-the-structure-of-a-survival-protein-from-salmonella-typhimurium
#17
Kaushik Hatti, Yamuna Kalyani Mathiharan, Narayanaswamy Srinivasan, Mathur R N Murthy
The determination of the crystal structure of a mutant protein using phases based on a previously determined crystal structure of the wild-type protein is often a straightforward molecular-replacement protocol. Such a structure determination may be difficult if there are large-scale structural differences between the wild-type and mutant proteins. In this manuscript, an interesting case is presented of the unintentional crystallization of a contaminant protein which shared some structural features with the presumed target protein, leading to difficulties in obtaining a completely satisfactory molecular-replacement structure solution...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695860/dna-conformational-transitions-inferred-from-re-evaluation-of-m-fo-d-fc-electron-density-maps
#18
Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695859/octamer-formation-in-lysozyme-solutions-at-the-initial-crystallization-stage-detected-by-small-angle-neutron-scattering
#19
Anastasiia S Boikova, Yulia A Dyakova, Kseniia B Ilina, Petr V Konarev, Alyona E Kryukova, Alexandr I Kuklin, Margarita A Marchenkova, Boris V Nabatov, Alexandr E Blagov, Yurii V Pisarevsky, Mikhail V Kovalchuk
Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml(-1) with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695858/rapid-cadmium-sad-phasing-at-the-standard-wavelength-1%C3%A2-%C3%A3
#20
Saravanan Panneerselvam, Esa Pekka Kumpula, Inari Kursula, Anja Burkhardt, Alke Meents
Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
journal
journal
52882
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"