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Journal of Structural Biology

Hiroki Yamaguchi, Akiko Kamegawa, Kunio Nakata, Tatsuki Kashiwagi, Toshimi Mizukoshi, Yoshinori Fujiyoshi, Kazutoshi Tani
Leucine dehydrogenase (LDH, EC is a NAD+ -dependent oxidoreductase that catalyzes the deamination of branched-chain L-amino acids (BCAAs). LDH of Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has been applied for the quantification or production of BCAAs. Here the cryo-electron microscopy (cryo-EM) structures of apo and NAD+ -bound LDH are reported at 3.0 and 3.2 Å resolution, respectively. On comparing the structures, the two overall structures are almost identical, but it was observed that the partial conformational change was triggered by the interaction between Ser147 and the nicotinamide moiety of NAD+ ...
December 10, 2018: Journal of Structural Biology
Kailash Ramlaul, Colin M Palmer, Christopher H S Aylett
We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM. Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps...
November 28, 2018: Journal of Structural Biology
José Malanho Silva, Linda Cerofolini, Stefano Giuntini, Vito Calderone, Carlos F G C Geraldes, Anjos L Macedo, Giacomo Parigi, Marco Fragai, Enrico Ravera, Claudio Luchinat
Solid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the electronic properties of different metal centers affect the quality of their SSNMR spectra differently, and not all systems turn out to be equally easy to approach by this technique...
November 28, 2018: Journal of Structural Biology
Min Su
Preferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient...
November 26, 2018: Journal of Structural Biology
Horst Kierdorf, Friederike Breuer, Carsten Witzel, Uwe Kierdorf
The nature and periodicity of incremental markings in pig enamel is currently debated. To broaden the basis for a correct interpretation of growth marks in pig enamel, we analyzed their periodicity in teeth of wild boars and domestic pigs. For that, the numbers of enamel incremental markings were recorded in ground sections and compared with crown formation times for the respective teeth derived from literature data on tooth development and eruption in Sus scrofa. Our study revealed that laminations with a daily periodicity are the dominant incremental feature of pig enamel...
November 22, 2018: Journal of Structural Biology
Sandra L Koch, Mark D Shriver, Nina G Jablonski
Human scalp hairs are often examined microscopically to study the variation and diversity among a range of visible morphological traits. In this study, we focused on the ultrastructure of human scalp hair within its keratinized matrix, emphasizing, the density and distribution of melanosomes, variation in cuticle thickness within populations, and the relationship of hair fiber ultrastructure with biogeographic ancestry. We used transmission electron microscopy (TEM) to visualize hair cross-sections and generate micron-scale resolution images for analysis of particle morphology and the layered hair matrix...
November 22, 2018: Journal of Structural Biology
Bao-Di Gou, Yang Liu, Yu-Xi Gao, Kun Tang, Lei Zheng, Yi-Dong Zhao, Tian-Lan Zhang
The total calcium (tCa) in blood serum comprises free Ca2+ ions (fCa), protein-bound calcium (prCa), and complexed calcium by small anions (cCa). The cCa fraction, in addition to fCa, has been indicated to have some physiological activity. However, there is little evidence for the structure of its constituents. Here we report an ex vivo detection of the cCa constituents by synchrotron X-ray absorption near-edge structure spectroscopy. We collected the data directly on rat blood serum and, by making use of the reference samples, derived a spectrum that exhibits the features of cCa constituents...
November 22, 2018: Journal of Structural Biology
Prerana Gogoi, Prerana Mordina, Shankar Prasad Kanaujia
Methylthioribose-1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of methylthioribose-1-phosphate (MTR-1-P) to methylthioribulose-1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins such as ribose-1,5-bisphosphate isomerase (R15Pi) and the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B)...
November 21, 2018: Journal of Structural Biology
Olga I Antimonova, Dmitry V Lebedev, Yana A Zabrodskaya, Natalia A Grudinina, Andrey L Timkovsky, Edward Ramsay, Michael M Shavlovsky, Vladimir V Egorov
In a number of conformational diseases, intracellular accumulation of proteins bearing non-native conformations occurs. The search for compounds that are capable of hindering the formation and accumulation of toxic protein aggregates and fibrils is an urgent task. Present fluorescent methods of fibrils' detection prevent simple real-time observations. We suppose to use green fluorescent protein fused with target protein and fluorescence lifetime measurement technique for this purpose. The recombinant proteins analyzed were produced in E...
November 17, 2018: Journal of Structural Biology
Patrícia T Borges, Célia V Romão, Lígia M Saraiva, Vera L Gonçalves, Maria A Carrondo, Miguel Teixeira, Carlos Frazão
Flavodiiron proteins (FDPs) play key roles in biological response mechanisms against oxygen and/or nitric oxide; in particular they are present in oxygenic phototrophs (including cyanobacteria and gymnosperms). Two conserved domains define the core of this family of proteins: a N-terminal metallo-β-lactamase-like domain followed by a C-terminal flavodoxin-like one, containing the catalytic diiron centre and a FMN cofactor, respectively. Members of the FDP family may present extra modules in the C-terminus, and were classified into several classes according to their distribution and composition...
November 14, 2018: Journal of Structural Biology
Tomohiko Matsuzawa, Masahiro Watanabe, Yusuke Nakamichi, Zui Fujimoto, Katsuro Yaoi
Isoprimeverose-producing enzymes (IPases) release isoprimeverose (α-d-xylopyranosyl-(1→6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. Aspergillus oryzae IPase (IpeA) is classified as a member of the glycoside hydrolase family 3 (GH3); however, it has unusual substrate specificity compared with other GH3 enzymes. Xylopyranosyl branching at the non-reducing ends of xyloglucan oligosaccharides is vital for IpeA activity. We solved the crystal structure of IpeA with isoprimeverose at 2...
November 13, 2018: Journal of Structural Biology
Matthew B Connell, Michael J Y Lee, Jerry Li, William C Plaxton, Zongchao Jia
Phosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5.3 Å) and interactions between citrate and specific residues were identified...
November 9, 2018: Journal of Structural Biology
Liuqing Chen, Yong Zhang, Yan Feng
Sterol glycosyltransferases catalyze the formation of a variety of glycosylated sterol derivatives and are involved in producing a plethora of bioactive natural products. To understand the molecular mechanism of sterol glycosyltransferases, we determined crystal structures of a sterol glycosyltransferase UGT51 from Saccharomyces cerevisiae. The structures of the UGT51 and its complex with uridine diphosphate glucose (UDPG) were solved at resolutions of 2.77 Å and 1.9 Å, respectively. The structural analysis revealed that a long hydrophobic cavity, 9...
November 2, 2018: Journal of Structural Biology
Tobias Raisch, Felix Sandmeir, Oliver Weichenrieder, Eugene Valkov, Elisa Izaurralde
The CCR4-NOT complex plays a central role in the regulation of gene expression and degradation of messenger RNAs. The multisubunit complex assembles on the NOT1 protein, which acts as a 'scaffold' and is highly conserved in eukaryotes. NOT1 consists of a series of helical domains that serve as docking sites for other CCR4-NOT subunits. We describe a crystal structure of a connector domain of NOT1 from the thermophilic fungus Chaetomium thermophilum (Ct). Comparative structural analysis indicates that this domain adopts a MIF4G-like fold and we have termed it the MIF4G-C domain...
October 24, 2018: Journal of Structural Biology
Amy E McGrath, Alexander P Martyn, Louise R Whittell, Fay E Dawes, Jennifer L Beck, Nicholas E Dixon, Michael J Kelso, Aaron J Oakley
Bacterial sliding clamps bind to DNA and act as protein-protein interaction hubs for several proteins involved in DNA replication and repair. The partner proteins all bind to a common pocket on sliding clamps via conserved linear peptide sequence motifs, which suggest the pocket as an attractive target for development of new antibiotics. Herein we report the X-ray crystal structures and biochemical characterization of β sliding clamps from the Gram-negative pathogens Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae...
October 23, 2018: Journal of Structural Biology
Mohamed E A Abdellatif, Christian Sinzger, Paul Walther
Human cytomegalovirus (HCMV) entry into susceptible cells is a fast intricate process that is not fully understood. Although, previous studies explored different aspects of this process by means of biochemical and inhibitors assays, a clear morphological characterization of its steps at the ultrastructural level is still lacking. We attempted to characterize those intermediates involved during HCMV entry by developing a methodological approach that resulted in optimal ultrastructure preservation and allowed for 3D imaging...
October 20, 2018: Journal of Structural Biology
Nebojša Bogdanović, Lavanya Sundararaman, Neelagandan Kamariah, Anu Tyagi, Shashi Bhushan, Priya Ragunathan, Joon Shin, Thomas Dick, Gerhard Grüber
The Mycobacterium tuberculosis (Mtb) F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) is an essential enzyme that supplies energy for both the aerobic growing and the hypoxic dormant stage of the mycobacterial life cycle. Employing the heterologous F-ATP synthase model system αchi 3 :β3 :γ we showed previously, that transfer of the C-terminal domain (CTD) of Mtb subunit α (Mtα514-549 ) to a standard F-ATP synthase α subunit suppresses ATPase activity. Here we determined the 3D reconstruction from electron micrographs of the αchi 3 :β3 :γ complex reconstituted with the Mtb subunit ε (Mtε), which has been shown to crosstalk with the CTD of Mtα...
October 17, 2018: Journal of Structural Biology
Damien M Rasmussen, Ross W Soens, Timothy J Davie, Cody K Vaneerd, Basudeb Bhattacharyya, John F May
DcrB is an 18 kDa lipoprotein that contains a single domain of unknown function. DcrB is found within Enterobacteriaceae, a family of Gram-negative bacteria which includes pathogens that can cause food-borne illness and hospital-acquired infections. In Salmonella enterica serovar Typhimurium, DcrB is up-regulated by conditions that promote the production of known virulence factors. We determined the structure of a truncated form of DcrB from Salmonella to 1.92 Å resolution by X-ray crystallography. This truncated form, DcrBΔ37, contains the entire domain of unknown function but lacks the lipoprotein signal sequence (residues 1-20) as well as residues 21-37...
October 16, 2018: Journal of Structural Biology
Nutan Agadi, Sheeja Vasudevan, Ashutosh Kumar
Structural characterization of BMAP-28(1-18), a potent bovine myeloid antimicrobial peptide can aid in understanding its mechanism of action at molecular level. We report NMR structure of the BMAP-28(1-18) and its mutated analogue mutBMAP18 in SDS micelles. Structural comparison of the peptides bound to SDS micelles and POPE-POPG vesicles using circular dichroism, suggest that structures in the two lipid preparations are similar. Antimicrobial assays show that even though both these peptides adopt helical conformation, BMAP-28(1-18) is more potent than mutBMAP18 in killing bacterial cells...
October 15, 2018: Journal of Structural Biology
Catherine L Lawson, Wah Chiu
No abstract text is available yet for this article.
October 13, 2018: Journal of Structural Biology
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