Journal articles: 'EF structure'

1

Tsuda, K., and M. Tanaka. "Nanometer Crystal Structure Analysis by EF-CBED and EF-Microscopy." Microscopy and Microanalysis 6, S2 (August 2000): 152–53. http://dx.doi.org/10.1017/s1431927600033250.

Full text

Abstract:

Crystal structure refinement by the convergent-beam electron diffraction (CBED) method has the following advantages: (i) Nanometer-size crystal structure refinement: CBED patterns can be obtained from specimen areas of a few nanometer in diameter, (ii) Dynamical diffraction effect: the CBED intensities contain phase information of crystal structure factors through the strong dynamical effect. (iii) Site-selective analysis: the use of Bloch states formed by incident electrons allows structure determination weighted for specific atom sites. Energy-filtering (EF) to revome inelastically scattered background is now getting necessary for such quantitative analysis of CBED patterns. Especially for the determination of atom positions and Debye-Waller factors, the use of energy-filtered higher-order Laue zone (HOLZ) CBED patterns is essential because small displacements of atoms can be sensitively detected using HOLZ reflections with large reciprocal vectors. For this purpose, we developed a new fl-filter transmission electron microscope (JEM-2010FEF) with a high acceptance angle [2] and a new analysis program “mbfit” to refine structural parameters using many-beam Bloch-wave calculations and least-square fitting [1].

APA, Harvard, Vancouver, ISO, and other styles

2

Wang, Yong, Youxing Jiang, Martina Meyering-Voss, Mathias Sprinzl, and Paul B. Sigler. "Crystal structure of the EF-Tu˙EF-Ts complex from Thermus thermophilus." Nature Structural Biology 4, no. 8 (August 1997): 650–56. http://dx.doi.org/10.1038/nsb0897-650.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Merve Çağlar, N., and Erdal Şafak. "Energy Flux Approach for Dynamic Analysis of Structures." Bulletin of the Seismological Society of America 109, no. 5 (July 30, 2019): 1797–811. http://dx.doi.org/10.1785/0120180311.

Full text

Abstract:

Abstract Dynamic response of structures can be analyzed in terms of the propagation of input energy within the structure. Energy propagation is quantified by energy flux (EF), which is the amount of energy transmitted per unit time through a cross section of a medium. The formulation of EF is similar to the formulation of wave propagation in structures. It involves tracking the propagation path of the input energy and the energy loss due to damping within the elements of the structure. The EF approach introduces a new tool to evaluate the dynamic response and the energy absorption capacity of structures, providing an alternative parameter for the design of structures for dynamic loads. This article presents the theoretical basis for the methodology and gives a numerical example for the EF analysis of a plane frame structure under earthquake loads.

APA, Harvard, Vancouver, ISO, and other styles

4

Anderson Jnr, A. G., S. C. Critchlow, L. C. Andrews, and R. D. Haddock. "Structure of dicyclopenta[ef,kl]heptalene (azupyrene)." Acta Crystallographica Section C Crystal Structure Communications 46, no. 3 (March 15, 1990): 439–41. http://dx.doi.org/10.1107/s0108270189007857.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

Mondal, Dibyendu, and Arieh Warshel. "EF-Tu and EF-G are activated by allosteric effects." Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): 3386–91. http://dx.doi.org/10.1073/pnas.1800054115.

Full text

Abstract:

Many cellular processes are controlled by GTPases, and gaining quantitative understanding of the activation of such processes has been a major challenge. In particular, it is crucial to obtain reliable free-energy surfaces for the relevant reaction paths both in solution and in GTPases active sites. Here, we revisit the energetics of the activation of EF-G and EF-Tu by the ribosome and explore the nature of the catalysis of the GTPase reaction. The comparison of EF-Tu to EF-G allows us to explore the impact of possible problems with the available structure of EF-Tu. Additionally, mutational effects are used for a careful validation of the emerging conclusions. It is found that the reaction may proceed by both a two-water mechanism and a one-water (GTP as a base) mechanism. However, in both cases, the activation involves a structural allosteric effect, which is likely to be a general-activation mechanism for all GTPases.

APA, Harvard, Vancouver, ISO, and other styles

6

Kawashima, Takemasa, Carmen Berthet-Colominas, Michael Wulff, Stephen Cusack, and Reuben Leberman. "The structure of the Escherichia coli EF-Tu· EF-Ts complex at 2.5 Å resolution." Nature 379, no. 6565 (February 8, 1996): 511–18. http://dx.doi.org/10.1038/379511a0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Nizhnichenko, Vladimir A., Alexey V. Boyko, Talia T. Ginanova, and Igor Yu Dolmatov. "Muscle Regeneration in Holothurians without the Upregulation of Muscle Genes." International Journal of Molecular Sciences 23, no. 24 (December 16, 2022): 16037. http://dx.doi.org/10.3390/ijms232416037.

Full text

Abstract:

The holothurian Eupentacta fraudatrix is capable of fully restoring its muscles after transverse dissection. Although the regeneration of these structures is well studied at the cellular level, the molecular basis of the process remains poorly understood. To identify genes that may be involved in the regulation of muscle regeneration, the transcriptome of the longitudinal muscle band of E. fraudatrix has been sequenced at different time periods post-injury. An analysis of the map of biological processes and pathways has shown that most genes associated with myogenesis decrease their expression during the regeneration. The only exception is the genes united by the GO term “heart valve development”. This may indicate the antiquity of mechanisms of mesodermal structure transformation, which was co-opted into various morphogeneses in deuterostomes. Two groups of genes that play a key role in the regeneration have been analyzed: transcription factors and matrix metalloproteinases. A total of six transcription factor genes (Ef-HOX5, Ef-ZEB2, Ef-RARB, Ef-RUNX1, Ef-SOX17, and Ef-ZNF318) and seven matrix metalloproteinase genes (Ef-MMP11, Ef-MMP13, Ef-MMP13-1, Ef-MMP16-2, Ef-MMP16-3, Ef-MMP24, and Ef-MMP24-1) showing differential expression during myogenesis have been revealed. The identified genes are assumed to be involved in the muscle regeneration in holothurians.

APA, Harvard, Vancouver, ISO, and other styles

8

Nordenswan, Elisabeth, Eeva-Leena Kataja, Kirby Deater-Deckard, Riikka Korja, Mira Karrasch, Matti Laine, Linnea Karlsson, and Hasse Karlsson. "Latent Structure of Executive Functioning/Learning Tasks in the CogState Computerized Battery." SAGE Open 10, no. 3 (July 2020): 215824402094884. http://dx.doi.org/10.1177/2158244020948846.

Full text

Abstract:

This study tested whether executive functioning (EF)/learning tasks from the CogState computerized test battery show a unitary latent structure. This information is important for the construction of composite measures on these tasks for applied research purposes. Based on earlier factor analytic research, we identified five CogState tasks that have been labeled as EF/learning tasks and examined their intercorrelations in a new sample of Finnish birth cohort mothers ( N = 233). Using confirmatory factor analyses, we compared two single-factor EF/learning models. The first model included the recommended summative scores for each task. The second model exchanged summative scores for first test round results for the three tasks providing these data, as initial task performance is expected to load more heavily on EF. A single-factor solution provided a good fit for the present five EF/learning tasks. The second model, which was hypothesized to tap more onto EF, had slightly better fit indices, χ2(5) = 1.37, p = .93, standardized root mean square residual (SRMR) = .02, root mean square error of approximation (RMSEA) = .00, 90% CI = [.00–.03], comparative fit index (CFI) = 1.00, and more even factor loadings (.30–.56) than the first model, χ2(5) = 4.56, p = .47, SRMR = .03, RMSEA = .00, 90% CI = [.00–.09], CFI = 1.00, factor loadings (.20–.74), which was hypothesized to tap more onto learning. We conclude that the present CogState sum scores can be used for studying EF/learning in healthy adult samples, but call for further research to validate these sum scores against other EF tests.

APA, Harvard, Vancouver, ISO, and other styles

9

Himi, Samsad Afrin, Markus Bühner, and Sven Hilbert. "Advancing the Understanding of the Factor Structure of Executive Functioning." Journal of Intelligence 9, no. 1 (March 16, 2021): 16. http://dx.doi.org/10.3390/jintelligence9010016.

Full text

Abstract:

There has been considerable debate and interest regarding the factor structure of executive functioning (EF). Therefore, the aim of the current study was to delve into this issue differently, by investigating EF and other cognitive constructs, such as working memory capacity (WMC), relational integration, and divided attention, which may contribute to EF. Here, we examined whether it is possible to provide evidence for a definite model of EF containing the components of updating, shifting, and inhibition. For this purpose, 202 young adults completed a battery of EF, three WMC tests, three relational integration tests, and two divided attention tests. A confirmatory factor analysis on all the cognitive abilities produced a five-factor structure, which included one factor predominately containing shifting tasks, the next factor containing two updating tasks, the third one predominately representing WMC, the fourth factor consisting of relational integration and antisaccade tasks, and finally, the last factor consisting of the divided attention and stop signal tasks. Lastly, a subsequent hierarchical model supported a higher-order factor, thereby representing general cognitive ability.

APA, Harvard, Vancouver, ISO, and other styles

10

Hirano, Yu, Kana Tsukamoto, Shingo Ariki, Yuki Naka, Mitsuhiro Ueda, and Taro Tamada. "X-ray crystallographic structural studies of α-amylase I from Eisenia fetida." Acta Crystallographica Section D Structural Biology 76, no. 9 (August 25, 2020): 834–44. http://dx.doi.org/10.1107/s2059798320010165.

Full text

Abstract:

The earthworm Eisenia fetida possesses several cold-active enzymes, including α-amylase, β-glucanase and β-mannanase. E. fetida possesses two isoforms of α-amylase (Ef-Amy I and II) to digest raw starch. Ef-Amy I retains its catalytic activity at temperatures below 10°C. To identify the molecular properties of Ef-Amy I, X-ray crystal structures were determined of the wild type and of the inactive E249Q mutant. Ef-Amy I has structural similarities to mammalian α-amylases, including the porcine pancreatic and human pancreatic α-amylases. Structural comparisons of the overall structures as well as of the Ca2+-binding sites of Ef-Amy I and the mammalian α-amylases indicate that Ef-Amy I has increased structural flexibility and more solvent-exposed acidic residues. These structural features of Ef-Amy I may contribute to its observed catalytic activity at low temperatures, as many cold-adapted enzymes have similar structural properties. The structure of the substrate complex of the inactive mutant of Ef-Amy I shows that a maltohexaose molecule is bound in the active site and a maltotetraose molecule is bound in the cleft between the N- and C-terminal domains. The recognition of substrate molecules by Ef-Amy I exhibits some differences from that observed in structures of human pancreatic α-amylase. This result provides insights into the structural modulation of the recognition of substrates and inhibitors.

APA, Harvard, Vancouver, ISO, and other styles

11

Kawashima, Takemasa, Carmen Berthet-Colominas, Michael Wulff, Stephen Cusack, and Reuben Leberman. "Correction: The structure of the Escherichia coli EF-Tu. EF-Ts complex at 2.5 Å resolution." Nature 381, no. 6578 (May 1996): 172. http://dx.doi.org/10.1038/381172b0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Samsonova, M. G., S. G. Inge-Vechtomov, and P. Taylor. "Structure comparison and evolutionary relations between elongation factors EF-Tu (EF-1?) and SUP 2 proteins." Genetica 85, no. 1 (1991): 35–44. http://dx.doi.org/10.1007/bf00056104.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

CRISAN, V., A. VERNES, V. POPESCU, L. DULCA, and D. KAPUSI. "ELECTRONIC STRUCTURE OF YBa2(Cu1−xFex)3O7." International Journal of Modern Physics B 07, no. 01n03 (January 1993): 170–73. http://dx.doi.org/10.1142/s021797929300038x.

Full text

Abstract:

The density of states (DOS) at the Fermi level, (EF), for the 123 superconductor doped with iron was computed. The LCAO model hamiltonian and the Haydock recursive method were used. The iron atoms were located only in one of the copper atom positions Cu1 or Cu2 or in both of them with the same probability. The substitution of Fe in Cu1 positions increased the DOS at the Fermi level as x increased but the substitutions in the Cu2 positions had an opposite effect. In both cases the O2 and O3 positions are inequivalent. When the replacement of copper atoms is produced with the same probability in Cu1 and Cu2 positions the DOS at EF decreases as x increases. The DOS at EF and the electron orbital occupation numbers for O2 and O3 have the same behaviour as the lattice parameters, a and b.

APA, Harvard, Vancouver, ISO, and other styles

14

Wray, Charlotte, Alysse Kowalski, Feziwe Mpondo, Laura Ochaeta, Delia Belleza, Ann DiGirolamo, Rachel Waford, et al. "Executive functions form a single construct and are associated with schooling: Evidence from three low- and middle- income countries." PLOS ONE 15, no. 11 (November 30, 2020): e0242936. http://dx.doi.org/10.1371/journal.pone.0242936.

Full text

Abstract:

Measuring executive function (EF) among adults is important, as the cognitive processes involved in EF are critical to academic achievement, job success and mental health. Current evidence on measurement and structure of EF largely come from Western, Educated, Industrialized, Rich and Democratic (WEIRD) countries. However, measuring EF in low-and-middle-income countries (LMICs) is challenging, because of the dearth of EF measures validated across LMICs, particularly measures that do not require extensive training, expensive equipment, or professional administration. This paper uses data from three LMIC cohorts to test the feasibility, validity and reliability of EF assessment in adults using three sub-tests (representing key components of EF) of the NIH Toolbox Cognitive battery. For each cohort, all three EF measures (inhibition, flexibility and working memory) loaded well onto a unidimensional latent factor of EF. Factor scores related well to measures of fluid intelligence, processing speed and schooling. All measures showed good test-retest reliability across countries. This study provides evidence for a set of sound measures of EF that could be used across different cultural, language and socio-economic backgrounds in future LMIC research. Furthermore, our findings extend conclusions on the structure of EF beyond those drawn from WEIRD countries.

APA, Harvard, Vancouver, ISO, and other styles

15

Gagnon, Matthieu G., Jinzhong Lin, and Thomas A. Steitz. "Elongation factor 4 remodels the A-site tRNA on the ribosome." Proceedings of the National Academy of Sciences 113, no. 18 (April 18, 2016): 4994–99. http://dx.doi.org/10.1073/pnas.1522932113.

Full text

Abstract:

During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5′-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.

APA, Harvard, Vancouver, ISO, and other styles

16

Jang, Hyunseok, Sunghark Kwon, Chang-Sook Jeong, Chang Woo Lee, Jisub Hwang, Kyoung Ho Jung, Jun Hyuck Lee, and Hyun Ho Park. "Structural analysis of a novel substrate-free form of the aminoglycoside 6′-N-acetyltransferase from Enterococcus faecium." Acta Crystallographica Section F Structural Biology Communications 76, no. 8 (July 28, 2020): 364–71. http://dx.doi.org/10.1107/s2053230x20009735.

Full text

Abstract:

Aminoglycoside acetyltransferases (AACs) catalyze the transfer of an acetyl group between acetyl-CoA and an aminoglycoside, producing CoA and an acetylated aminoglycoside. AAC(6′)-Ii enzymes target the amino group linked to the 6′ C atom in an aminoglycoside. Several structures of the AAC(6′)-Ii from Enterococcus faecium [Ef-AAC(6′)-Ii] have been reported to date. However, the detailed mechanism of its enzymatic function remains elusive. In this study, the crystal structure of Ef-AAC(6′)-Ii was determined in a novel substrate-free form. Based on structural analysis, it is proposed that Ef-AAC(6′)-Ii sequentially undergoes conformational selection and induced fit for substrate binding. These results therefore provide a novel viewpoint on the mechanism of action of Ef-AAC(6′)-Ii.

APA, Harvard, Vancouver, ISO, and other styles

17

Wei, Guoke, Jinliang Wang, and Yu Chen. "Electromagnetic enhancement of ordered silver nanorod arrays evaluated by discrete dipole approximation." Beilstein Journal of Nanotechnology 6 (March 9, 2015): 686–96. http://dx.doi.org/10.3762/bjnano.6.69.

Full text

Abstract:

The enhancement factor (EF) of surface-enhanced Raman scattering (SERS) from two-dimensional (2D) hexagonal silver nanorod (AgNR) arrays were investigated in terms of electromagnetic (EM) mechanism by using the discrete dipole approximation (DDA) method. The dependence of EF on several parameters, i.e., structure, length, excitation wavelength, incident angle and polarization, and gap size has been investigated. “Hotspots” were found distributed in the gaps between adjacent nanorods. Simulations of AgNR arrays of different lengths revealed that increasing the rod length from 374 to 937 nm (aspect ratio from 2.0 to 5.0) generated more “hotspots” but not necessarily increased EF under both 514 and 532 nm excitation. A narrow lateral gap (in the incident plane) was found to result in strong EF, while the dependence of EF on the diagonal gap (out of the incident plane) showed an oscillating behavior. The EF of the array was highly dependent on the angle and polarization of the incident light. The structure of AgNR and the excitation wavelength were also found to affect the EF. The EF of random arrays was stronger than that of an ordered one with the same average gap of 21 nm, which could be explained by the exponential dependence of EF on the lateral gap size. Our results also suggested that absorption rather than extinction or scattering could be a good indicator of EM enhancement. It is expected that the understanding of the dependence of local field enhancement on the structure of the nanoarrays and incident excitations will shine light on the optimal design of efficient SERS substrates and improved performance.

APA, Harvard, Vancouver, ISO, and other styles

18

Li, James J., Tammy A. Chung, Michael M. Vanyukov, D. Scott Wood, Robert Ferrell, and Duncan B. Clark. "A Hierarchical Factor Model of Executive Functions in Adolescents: Evidence of Gene-Environment Interplay." Journal of the International Neuropsychological Society 21, no. 1 (December 15, 2014): 62–73. http://dx.doi.org/10.1017/s1355617714001039.

Full text

Abstract:

AbstractExecutive functions (EF) are a complex set of neurodevelopmental, higher-ordered processes that are especially salient during adolescence. Disruptions to these processes are predictive of psychiatric problems in later adolescence and adulthood. The objectives of the current study were to characterize the latent structure of EF using bifactor analysis and to investigate the independent and interactive effects of genes and environments on EF during adolescence. Using a representative young adolescent sample, we tested the interaction of a polymorphism in the serotonin transporter gene (5-HTTLPR) and parental supervision for EF through hierarchical linear regression. To account for the possibility of a hierarchical factor structure for EF, a bifactor analysis was conducted on the eight subtests of the Delis-Kaplan Executive Functions System (D-KEFS). The bifactor analysis revealed the presence of a general EF construct and three EF subdomains (i.e., conceptual flexibility, inhibition, and fluency). A significant5-HTTLPRby parental supervision interaction was found for conceptual flexibility, but not for general EF, fluency or inhibition. Specifically, youth with the L/L genotype had significantly lower conceptual flexibility scores compared to youth with S/S or S/L genotypes given low levels of parental supervision. Our findings indicate that adolescents with the L/L genotype were especially vulnerable to poor parental supervision on EF. This vulnerability may be amenable to preventive interventions. (JINS, 2014,20, 62–73)

APA, Harvard, Vancouver, ISO, and other styles

19

Han, Yong, Bingjia Wei, Xiaoqiang Guo, and Tifeng Jiao. "Influence of Electrostatic Field on Mixed Aqueous Solution of Calcium and Ferrous Ions: Insights from Molecular Dynamics Simulations." Coatings 12, no. 8 (August 12, 2022): 1165. http://dx.doi.org/10.3390/coatings12081165.

Full text

Abstract:

In order to investigate the anti-scaling and anti-corrosion characteristics of an electrostatic anti-fouling system in the application process, the influence of an electrostatic field (EF) on the structure and dynamics of hydrated Ca2+ and hydrated Fe2+ in a mixed aqueous system was studied through the calculation and analysis of the radial distribution function (RDF), self-diffusion coefficients, viscosity, and hydrogen bond structure by using molecular dynamics simulation. The study results show that the EF can decrease the radius of the first water shell of hydrated Ca2+ but increase that of Fe2+, which will reduce the possibility of forming calcite. The EF can make water molecules and Fe2+ more active, which can hinder iron release and thus decrease iron corrosion products. In addition, the EF can enhance the hydrogen structure of water molecules in the aqueous solution.

APA, Harvard, Vancouver, ISO, and other styles

20

Gifford, Jessica L., Michael P. Walsh, and Hans J. Vogel. "Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs." Biochemical Journal 405, no. 2 (June 27, 2007): 199–221. http://dx.doi.org/10.1042/bj20070255.

Full text

Abstract:

The ‘EF-hand’ Ca2+-binding motif plays an essential role in eukaryotic cellular signalling, and the proteins containing this motif constitute a large and functionally diverse family. The EF-hand is defined by its helix–loop–helix secondary structure as well as the ligands presented by the loop to bind the Ca2+ ion. The identity of these ligands is semi-conserved in the most common (the ‘canonical’) EF-hand; however, several non-canonical EF-hands exist that bind Ca2+ by a different co-ordination mechanism. EF-hands tend to occur in pairs, which form a discrete domain so that most family members have two, four or six EF-hands. This pairing also enables communication, and many EF-hands display positive co-operativity, thereby minimizing the Ca2+ signal required to reach protein saturation. The conformational effects of Ca2+ binding are varied, function-dependent and, in some cases, minimal, but can lead to the creation of a protein target interaction site or structure formation from a molten-globule apo state. EF-hand proteins exhibit various sensitivities to Ca2+, reflecting the intrinsic binding ability of the EF-hand as well as the degree of co-operativity in Ca2+ binding to paired EF-hands. Two additional factors can influence the ability of an EF-hand to bind Ca2+: selectivity over Mg2+ (a cation with very similar chemical properties to Ca2+ and with a cytoplasmic concentration several orders of magnitude higher) and interaction with a protein target. A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities.

APA, Harvard, Vancouver, ISO, and other styles

21

Sanders, J., M. Brandsma, G. M. Janssen, J. Dijk, and W. Moller. "Immunofluorescence studies of human fibroblasts demonstrate the presence of the complex of elongation factor-1 beta gamma delta in the endoplasmic reticulum." Journal of Cell Science 109, no. 5 (May 1, 1996): 1113–17. http://dx.doi.org/10.1242/jcs.109.5.1113.

Full text

Abstract:

The eukaryotic elongation factor-1 (EF-1) consists of four subunits, EF-1 alpha, EF-1 beta, EF-1 gamma and EF-1 delta which induce efficient transfer of aminoacyl-tRNA to the ribosome. In this process EF-1 alpha.GTP acts as the carrier of the aminoacyl-tRNA on its way to the ribosome. After release of aminoacyl-tRNA to the ribosome under concomitant hydrolysis of GTP, the inactive EF-1 alpha.GDP form is recycled to EF-1 alpha.GTP by EF-1 beta gamma delta. In eukaryotic cells the concentration of EF-1 alpha exceeds that of the complex beta gamma delta by a factor of 5–10. In order to delineate the intracellular localization of the different subunits of EF-1, antibodies against the EF-1 subunits have been elicited and indirect immunofluorescence microscopy experiments were performed. In human fibroblasts, the guanine nucleotide exchange part of EF-1, EF-1 beta gamma delta, was found to co-localize with the endoplasmic reticulum (ER), displaying a distinct fine-structure in its staining pattern. The guanine nucleotide-binding subunit of EF-1, EF-1 alpha, shows a more diffuse distribution throughout the cytoplasm and is, in addition, associated with the nucleus.

APA, Harvard, Vancouver, ISO, and other styles

22

Luo, Haiqiong, Wei Lan, Qingfeng Chen, Zhiqiang Wang, Zhixian Liu, Xiaofeng Yue, and Lingzhi Zhu. "Inferring microRNA-Environmental Factor Interactions Based on Multiple Biological Information Fusion." Molecules 23, no. 10 (September 24, 2018): 2439. http://dx.doi.org/10.3390/molecules23102439.

Full text

Abstract:

Accumulated studies have shown that environmental factors (EFs) can regulate the expression of microRNA (miRNA) which is closely associated with several diseases. Therefore, identifying miRNA-EF associations can facilitate the study of diseases. Recently, several computational methods have been proposed to explore miRNA-EF interactions. In this paper, a novel computational method, MEI-BRWMLL, is proposed to uncover the relationship between miRNA and EF. The similarities of miRNA-miRNA are calculated by using miRNA sequence, miRNA-EF interaction, and the similarities of EF-EF are calculated based on the anatomical therapeutic chemical information, chemical structure and miRNA-EF interaction. The similarity network fusion is used to fuse the similarity between miRNA and the similarity between EF, respectively. Further, the multiple-label learning and bi-random walk are employed to identify the association between miRNA and EF. The experimental results show that our method outperforms the state-of-the-art algorithms.

APA, Harvard, Vancouver, ISO, and other styles

23

Gao, Yonggui. "Structural basis of bacterial protein translation elongation." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C199. http://dx.doi.org/10.1107/s2053273314098003.

Full text

Abstract:

Recently, better understanding of ribosome function has been achieved through structural determination. These results provided a wealth of information on how genetic codes are precisely translated into proteins that control life, as well as established the platform to put ribosome as one of the richest validated targets for antibacterial drug discovery. We discovered a new ribosome crystal form obtained from ribosome lacking subunit L9, which allows crystallization of the ribosome in the presence of elongation factors Tu and G (EF-Tu/EF-G), trapped by antibiotics kirromycin and fusidic acid, respectively. These structures for the first time at atomic level offer insight into the molecular mechanism of protein elongation, which lies at the heart of translation. In each elongation cycle, EF-G facilitates the movement of tRNA-mRNA by one codon, which is coupled to the ratchet-like rotation of the ribosome complex and is triggered by EF-G-mediated GTP hydrolysis. The structure of pre-translocational ribosome bound to EF-G trapped with a GTP analogue, sheds light on how the positioning of the catalytic residue His87 into the active site is coupled to the hydrophobic gate opening which involves the sarcin-ricin loop (SRL) and domain III of EF-G. These results provide the structural basis for the GTPase activation of EF-G. After translocation, a cognate deacylated tRNA can only move together with the codon into the ribosomal E site. We also determined the structure of a cognate tRNA bound to the ribosomal E site, representing an authentic ribosome elongation complex. Quality control in protein translation by bacterial toxin has been associated with ribosome stalling and rescue system that is critical for cell to adapt environmental stress. Finally, I will introduce our structural progress on bacterial toxin bound to ribosome towards understanding of a classical acid-base catalysis mechanism.

APA, Harvard, Vancouver, ISO, and other styles

24

Kim, Min-Kyu, Ji-Hye Kim, Ji-Sun Kim, and Sa-Ouk Kang. "Structure of the 34 kDa F-actin-bundling protein ABP34 fromDictyostelium discoideum." Acta Crystallographica Section D Biological Crystallography 71, no. 9 (August 25, 2015): 1835–49. http://dx.doi.org/10.1107/s139900471501264x.

Full text

Abstract:

The crystal structure of the 34 kDa F-actin-bundling protein ABP34 fromDictyostelium discoideumwas solved by Ca2+/S-SAD phasing and refined at 1.89 Å resolution. ABP34 is a calcium-regulated actin-binding protein that cross-links actin filaments into bundles. Itsin vitroF-actin-binding and F-actin-bundling activities were confirmed by a co-sedimentation assay and transmission electron microscopy. The co-localization of ABP34 with actin in cells was also verified. ABP34 adopts a two-domain structure with an EF-hand-containing N-domain and an actin-binding C-domain, but has no reported overall structural homologues. The EF-hand is occupied by a calcium ion with a pentagonal bipyramidal coordination as in the canonical EF-hand. The C-domain structure resembles a three-helical bundle and superposes well onto the rod-shaped helical structures of some cytoskeletal proteins. Residues 216–244 in the C-domain form part of the strongest actin-binding sites (193–254) and exhibit a conserved sequence with the actin-binding region of α-actinin and ABP120. Furthermore, the second helical region of the C-domain is kinked by a proline break, offering a convex surface towards the solvent area which is implicated in actin binding. The F-actin-binding model suggests that ABP34 binds to the side of the actin filament and residues 216–244 fit into a pocket between actin subdomains −1 and −2 through hydrophobic interactions. These studies provide insights into the calcium coordination in the EF-hand and F-actin-binding site in the C-domain of ABP34, which are associated through interdomain interactions.

APA, Harvard, Vancouver, ISO, and other styles

25

Tuckwell, D. S., A. Brass, and M. J. Humphries. "Homology modelling of integrin EF-hands. Evidence for widespread use of a conserved cation-binding site." Biochemical Journal 285, no. 1 (July 1, 1992): 325–31. http://dx.doi.org/10.1042/bj2850325.

Full text

Abstract:

Integrin alpha-subunits contain three or four peptide sequences that are similar to the EF-hand, a 13-residue bivalent cation-binding motif found in calmodulin and parvalbumin. The integrin sequences differ from classical EF-hands in that they lack a co-ordinating residue at position 12. One hypothesis to explain integrin-ligand binding is that aspartate-containing recognition sequences in integrin ligands, which bind at or near to the EF-hand-like sequences, may take the place of the missing residue and co-ordinate directly to the bound cation. In this report, homology modelling of integrin EF-hand-like sequences has been performed using the X-ray structure of calmodulin as a template in order to assess the functional activity of the integrin sequences. In the calmodulin-integrin hybrid structures, integrin EF-hand-like sequences were able to retain cations whereas control sequences did not. Structural analyses demonstrated that the integrin sequences in the hybrid proteins closely resembled conventional EF-hands. The integrin sequences are therefore highly likely to bind Ca2+ ions in vivo, a prerequisite for the ligand-binding model. Database searching with a matrix derived from known integrin EF-hand-like sequences has been used to identify other proteins containing the integrin EF-hand-like motif. Annexin V (anchorin CII), atrial natriuretic peptide receptors and the 70 kDa heat-shock protein were identified by the matrix; the functions of these proteins are known from previous studies to be bivalent cation-dependent. These findings suggest that the integrin EF-hand-like sequence may be a more common motif than originally thought.

APA, Harvard, Vancouver, ISO, and other styles

26

Yadira, Agung, T. Thyrhaya Zein, and Eddy Setia. "The Analysis Schematic Structure of Research Article from Journal Indexed by Sinta." East Asian Journal of Multidisciplinary Research 1, no. 5 (June 28, 2022): 825–42. http://dx.doi.org/10.55927/eajmr.v1i5.572.

Full text

Abstract:

This study analyzes the schematic structure of Sinta's indexed research articles. The object of this research is in the form of fifteen indexed research articles of Sinta ranked 1 and 2. The schematic structure of this research article is then analyzed using SLF theory because this study is a study of the SFL genre. The researcher integrates the concept of Huang & Chen (2018). In conducting data analysis, this study adapted the interactive model of Miles, Huberman & Saldana (2014). It was found in this study that there are two structures in the research article, namely the mandatory structure and the optional structure. There are three mandatory structures, namely Reporting Findings (RF), Interpreting Findings (IF), and Literature Compare (LC), while Accounting Findings (AF) is not a mandatory phase. The rest are optional, namely; Explanation of Context (CE), Order of Presentation (SP), Restatement Analysis Procedure (RAP), Summarizing Findings (SF), Evaluation of Findings (EF), Recommending Further Research (RFS), Providing Pedagogical Implications (PI), Providing Pedagogical Implications (ISA). The analysis yielded (RAP)^(SF)^(CE)^(SP)^[[RF.IF]n.LC]^(AF)^(EF)^(RFS)^(PI)^(ISA).

APA, Harvard, Vancouver, ISO, and other styles

27

Wang, Zhen Hui, Qing Feng Zeng, Feng Xia Guo, Dong Pu Xu, and Hao Wang. "A Study of the Electrostatic Field Networking in Three Isolated Thunderstorms." Applied Mechanics and Materials 239-240 (December 2012): 775–84. http://dx.doi.org/10.4028/www.scientific.net/amm.239-240.775.

Full text

Abstract:

This work presents an analysis of atmospheric electrostatic field (EF) networking using radar and sounding data base on a quasi-normal charge distribution model in isolated storm cells. The charge distribution parameters of the thundercloud are first estimated and inversed with the model, and then the networked EF of the ground can be recalculated using the obtained parameters. The method was used to analyze three isolated thunderstorms that passed through the experiment site in 2009. It was found that the EF networking and the charge distribution were concordant with the location of lightning and radar echo. It is revealed that the method for EF networking using radar and sounding data is feasible. It was also found out that the charge structures of three thunderstorms were similar, i.e., the charge structure was dipole in the development, tripole in the mature stage and dipole in the extinct stage. The charge structures at different stages, charge space-distribution around cloud-ground (CG) lightning occurrence may be conducive for electrostatic characteristics research and lightning forecasting.

APA, Harvard, Vancouver, ISO, and other styles

28

Chen, Yun, Shu Feng, Veerendra Kumar, Rya Ero, and Yong-Gui Gao. "Structure of EF-G–ribosome complex in a pretranslocation state." Nature Structural & Molecular Biology 20, no. 9 (August 4, 2013): 1077–84. http://dx.doi.org/10.1038/nsmb.2645.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Ekblad, Bie, Panagiota K. Kyriakou, Camilla Oppegård, Jon Nissen-Meyer, Yiannis N. Kaznessis, and Per Eugen Kristiansen. "Structure–Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF." Biochemistry 55, no. 36 (August 31, 2016): 5106–16. http://dx.doi.org/10.1021/acs.biochem.6b00588.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Okazaki, H., T. Yokoya, J. Nakamura, N. Yamada, T. Nakamura, T. Muro, Y. Tamenori, et al. "Near EF electronic structure of heavily boron-doped superconducting diamond." Journal of Physics and Chemistry of Solids 69, no. 12 (December 2008): 2978–81. http://dx.doi.org/10.1016/j.jpcs.2008.06.006.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Miloushev, Vesselin Z., Joshua A. Levine, Mark A. Arbing, John F. Hunt, Geoffrey S. Pitt, and Arthur G. Palmer. "Solution Structure of the NaV1.2 C-terminal EF-hand Domain." Journal of Biological Chemistry 284, no. 10 (January 7, 2009): 6446–54. http://dx.doi.org/10.1074/jbc.m807401200.

Full text

APA, Harvard, Vancouver, ISO, and other styles

32

Kjeldgaard, Morten, and Jens Nyborg. "Refined structure of elongation factor EF-Tu from Escherichia coli." Journal of Molecular Biology 223, no. 3 (February 1992): 721–42. http://dx.doi.org/10.1016/0022-2836(92)90986-t.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Kenworthy, Lauren, Andrew Freeman, Allison Ratto, Katerina Dudley, Kelly K. Powell, Cara E. Pugliese, John F. Strang, Alyssa Verbalis, and Laura G. Anthony. "Preliminary Psychometrics for the Executive Function Challenge Task: A Novel, “Hot” Flexibility, and Planning Task for Youth." Journal of the International Neuropsychological Society 26, no. 7 (March 17, 2020): 725–32. http://dx.doi.org/10.1017/s135561772000017x.

Full text

Abstract:

AbstractObjective:Executive functions (EF) drive health and educational outcomes and therefore are increasingly common treatment targets. Most treatment trials rely on questionnaires to capture meaningful change because ecologically valid, pediatric performance-based EF tasks are lacking. The Executive Function Challenge Task (EFCT) is a standardized, treatment-sensitive, objective measure which assesses flexibility and planning in the context of provocative social interactions, making it a “hot” EF task.Method:We investigate the structure, reliability, and validity of the EFCT in youth with autism (Autism Spectrum Disorder; n = 129), or attention deficit hyperactivity disorder with flexibility problems (n = 93), and typically developing (TD; n = 52) youth.Results:The EFCT can be coded reliably, has a two-factor structure (flexibility and planning), and adequate internal consistency and consistency across forms. Unlike a traditional performance-based EF task (verbal fluency), it shows significant correlations with parent-reported EF, indicating ecological validity. EFCT performance distinguishes youth with known EF problems from TD youth and is not significantly related to visual pattern recognition, or social communication/understanding in autistic children.Conclusions:The EFCT demonstrates adequate reliability and validity and may provide developmentally appropriate, treatment-sensitive, and ecologically valid assessment of “hot” EF in youth. It can be administered in controlled settings by masked administrators.

APA, Harvard, Vancouver, ISO, and other styles

34

Guo, Xiaohu, Kristin Peisker, Kristina Bäckbro, Yang Chen, Ravi Kiran Koripella, Chandra Sekhar Mandava, Suparna Sanyal, and Maria Selmer. "Structure and function of FusB: an elongation factor G-binding fusidic acid resistance protein active in ribosomal translocation and recycling." Open Biology 2, no. 3 (March 2012): 120016. http://dx.doi.org/10.1098/rsob.120016.

Full text

Abstract:

Fusidic acid (FA) is a bacteriostatic antibiotic that locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis during elongation and ribosome recycling. The plasmid pUB101-encoded protein FusB causes FA resistance in clinical isolates of Staphylococcus aureus through an interaction with EF-G. Here, we report 1.6 and 2.3 Å crystal structures of FusB. We show that FusB is a two-domain protein lacking homology to known structures, where the N-terminal domain is a four-helix bundle and the C-terminal domain has an alpha/beta fold containing a C4 treble clef zinc finger motif and two loop regions with conserved basic residues. Using hybrid constructs between S. aureus EF-G that binds to FusB and Escherichia coli EF-G that does not, we show that the sequence determinants for FusB recognition reside in domain IV and involve the C-terminal helix of S. aureus EF-G. Further, using kinetic assays in a reconstituted translation system, we demonstrate that FusB can rescue FA inhibition of tRNA translocation as well as ribosome recycling. We propose that FusB rescues S. aureus from FA inhibition by preventing formation or facilitating dissociation of the FA-locked EF-G–ribosome complex.

APA, Harvard, Vancouver, ISO, and other styles

35

Wu, Decun, and Jinping Liu. "Threshold Effects of Restraining Factors on China’s Provincial Ecological Footprint in the Process of Urbanization." International Journal of Environmental Research and Public Health 17, no. 7 (April 2, 2020): 2407. http://dx.doi.org/10.3390/ijerph17072407.

Full text

Abstract:

This study uses a panel threshold model to explore the nonlinear relationship between restraining factors and ecological footprint (EF) evolution from 2003 to 2015 in China. In addition, the heterogeneity of the environmental Kuznets curve (EKC) hypothesis is identified. The results show that the four regime-dependent variables, i.e., technology level, openness, industrial structure and energy efficiency, have significant single-threshold effects on the EF in China, and the negative correlations between these variables and EF are significantly enhanced when the threshold variable urbanization exceeds 86.20%, 68.71%, 86.20% and 47.51%, respectively. As the urbanization level increases, more factors begin to play a high restraining role on the EF. The single-threshold effects on the EKC are significant under the threshold variables of urbanization and industrial structure. Meanwhile, the significant inverted-U relationship trends emerge when the two variables exceed the thresholds of 86.2% and 69.1%, respectively. Based on an empirical study, to restrain the EF of China’s 30 provinces more effectively, the urbanization process should be accelerated, while energy efficiency, foreign capital investment, technology level and service sector proportion should be promoted according to the urbanization level. Compared to other studies, this study is more focused on EF restraining factors and it contributes to the identification of the heterogeneity of EF’s restraining factors and EKC hypothesis, which would be useful for the EF reduction policy in the case of China.

APA, Harvard, Vancouver, ISO, and other styles

36

Zheng, Chunlei, Hui-hui Liu, Jiahai Zhou, and Bin Zhang. "EF-hand domains of MCFD2 mediate interactions with both LMAN1 and coagulation factor V or VIII." Blood 115, no. 5 (February 4, 2010): 1081–87. http://dx.doi.org/10.1182/blood-2009-09-241877.

Full text

Abstract:

Abstract Combined deficiency of factor V and factor VIII (F5F8D) is a bleeding disorder caused by mutations in either LMAN1 or MCFD2. LMAN1 (ERGIC-53) and MCFD2 form a Ca2+-dependent cargo receptor that cycles between the endoplasmic reticulum (ER) and the ER-Golgi intermediate compartment for efficient transport of FV/FVIII from the ER to the Golgi. Here we show that the C-terminal EF-hand domains are both necessary and sufficient for MCFD2 to interact with LMAN1. MCFD2 with a deletion of the entire N-terminal non-EF hand region still retains the LMAN1-binding function. Deletions that disrupt core structure of the EF-hand domains abolish LMAN1 binding. Circular dichroism spectroscopy studies on missense mutations localized to different structural elements of the EF-hand domains suggest that Ca2+-induced folding is important for LMAN1 interaction. The EF-hand domains also mediate the interaction with FV and FVIII. However, mutations in MCFD2 that disrupt the tertiary structure and abolish LMAN1 binding still retain the FV/FVIII binding activities, suggesting that this interaction is independent of Ca2+-induced folding of the protein. Our results suggest that the EF-hand domains of MCFD2 contain separate binding sites for LMAN1 and FV/FVIII that are essential for cargo receptor formation and cargo loading in the ER.

APA, Harvard, Vancouver, ISO, and other styles

37

Ansari, M. "Implications of One-Loop Quantum Correction in the Background Geometry of 5-Dimensional Kaluza-Klein Cosmology." Journal of the Tensor Society 4, no. 01 (June 30, 2007): 77–86. http://dx.doi.org/10.56424/jts.v4i01.10421.

Full text

Abstract:

Through dimensional reduction and one-loop quantum correction of scalar and spinor fields, time-dependent cosmological constant Λef f , effective gravitational constant Gef f and fine structure constant are derived in 5-dimensional Kaluza-Klein model for cosmology. If the internal manifold contracts with time and stabilizes itself at some later time, one possibility gets fine-structure constant equal to (1/137) , G_{ef f} ~ GN and Λ_{ef f} ~ 0 .

APA, Harvard, Vancouver, ISO, and other styles

38

Koyama, Tomohiro, Yoshinobu Nakatani, Jun’ichi Ieda, and Daichi Chiba. "Electric field control of magnetic domain wall motion via modulation of the Dzyaloshinskii-Moriya interaction." Science Advances 4, no. 12 (December 2018): eaav0265. http://dx.doi.org/10.1126/sciadv.aav0265.

Full text

Abstract:

We show that the electric field (EF) can control the domain wall (DW) velocity in a Pt/Co/Pd asymmetric structure. With the application of a gate voltage, a substantial change in DW velocity up to 50 m/s is observed, which is much greater than that observed in previous studies. Moreover, modulation of a DW velocity exceeding 100 m/s is demonstrated in this study. An EF-induced change in the interfacial Dzyaloshinskii-Moriya interaction (DMI) up to several percent is found to be the origin of the velocity modulation. The DMI-mediated velocity change shown here is a fundamentally different mechanism from that caused by EF-induced anisotropy modulation. Our results will pave the way for the electrical manipulation of spin structures and dynamics via DMI control, which can enhance the performance of spintronic devices.

APA, Harvard, Vancouver, ISO, and other styles

39

Mizokawa, T., A. Ino, T. Yoshida, A. Fujimori, C. Kim, H. Eisaki, Z. X. Shen, et al. "ARPES study of LSCO and PBCO: Electronic structure of the stripe phase and the 1/4-filled Cu-O chains." International Journal of Modern Physics B 14, no. 29n31 (December 20, 2000): 3602–9. http://dx.doi.org/10.1142/s021797920000412x.

Full text

Abstract:

We have studied the electronic structure of the stripe phase in La 2-x Sr x CuO 4 (LSCO) and the Cu-O chains in PrBa 2 Cu 3 O 7 (Pr123) and PrBa 2 Cu 4 O 8 (Pr124) using angle-resolved photoemission spectroscopy (ARPES). In LSCO with x=0.12, the spectral feature near the Fermi level (EF) is almost flat from (π, 0) to (π, π/4), namely, along the stripe direction in LSCO. While the 1/4-filled chain in Pr123 has a band gap because of charge ordering, the metallic chain in Pr124 shows a dispersive feature which reaches EF at ~(π, π/4) and a flat feature near EF which is similar to that observed in the stripe phase of LSCO. Although Pr124 shows spectral-weight suppression near EF due to the instability toward charge ordering, the suppression is imperfect and Pr124 has a substantial spectral weight at EF probably due to the chain-chain coupling. This is in sharp contrast to LSCO with the perfect gap opening near (π, π/4). The difference between the stripe phase in LSCO and the coupled chains of Pr124 would be derived from the interaction between the stripe and the neighboring Cu spins which suppresses the charge ordering along the stripe.

APA, Harvard, Vancouver, ISO, and other styles

40

Tomlinson, Jennifer H., Arnout P. Kalverda, and Antonio N. Calabrese. "Fusidic acid resistance through changes in the dynamics of the drug target." Proceedings of the National Academy of Sciences 117, no. 41 (September 30, 2020): 25523–31. http://dx.doi.org/10.1073/pnas.2008577117.

Full text

Abstract:

Antibiotic resistance in clinically important bacteria can be mediated by target protection mechanisms, whereby a protein binds to the drug target and protects it from the inhibitory effects of the antibiotic. The most prevalent source of clinical resistance to the antibiotic fusidic acid (FA) is expression of the FusB family of proteins that bind to the drug target (Elongation factor G [EF-G]) and promote dissociation of EF-G from FA-stalled ribosome complexes. FusB binding causes changes in both the structure and conformational flexibility of EF-G, but which of these changes drives FA resistance was not understood. We present here detailed characterization of changes in the conformational flexibility of EF-G in response to FusB binding and show that these changes are responsible for conferring FA resistance. Binding of FusB to EF-G causes a significant change in the dynamics of domain III of EF-GC3that leads to an increase in a minor, more disordered state of EF-G domain III. This is sufficient to overcome the steric block of transmission of conformational changes within EF-G by which FA prevents release of EF-G from the ribosome. This study has identified an antibiotic resistance mechanism mediated by allosteric effects on the dynamics of the drug target.

APA, Harvard, Vancouver, ISO, and other styles

41

Opron, Kristopher, and Zachary Burton. "Ribosome Structure, Function, and Early Evolution." International Journal of Molecular Sciences 20, no. 1 (December 21, 2018): 40. http://dx.doi.org/10.3390/ijms20010040.

Full text

Abstract:

Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S–50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.

APA, Harvard, Vancouver, ISO, and other styles

42

Bitto, Eduard, Craig A. Bingman, Lenka Bittova, Ronnie O. Frederick, Brian G. Fox, and George N. Phillips. "X-ray structure ofDanio reriosecretagogin: A hexa-EF-hand calcium sensor." Proteins: Structure, Function, and Bioinformatics 76, no. 2 (August 1, 2009): 477–83. http://dx.doi.org/10.1002/prot.22362.

Full text

APA, Harvard, Vancouver, ISO, and other styles

43

Chataigner, Lucas, Jingxu Guo, Peter T. Erskine, Alun R. Coker, Steve P. Wood, Zoltan Gombos, and Jonathan B. Cooper. "Binding of Gd3+to the neuronal signalling protein calexcitin identifies an exchangeable Ca2+-binding site." Acta Crystallographica Section F Structural Biology Communications 72, no. 4 (March 16, 2016): 276–81. http://dx.doi.org/10.1107/s2053230x16003526.

Full text

Abstract:

Calexcitin was first identified in the marine snailHermissenda crassicornisas a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg2+and Ca2+, while EF-3 is likely to bind only Ca2+. The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd3+in the presence of trace Ca2+, EF-1 was shown to become fully occupied by Gd3+ions, while the other two sites remain fully occupied by Ca2+. The structure of the Gd3+–calexcitin complex has been refined to anRfactor of 21.5% and anRfreeof 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca2+-binding site with the lowest selectivity for Ca2+, and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.

APA, Harvard, Vancouver, ISO, and other styles

44

Rodnina, Marina V., Frank Peske, Bee-Zen Peng, Riccardo Belardinelli, and Wolfgang Wintermeyer. "Converting GTP hydrolysis into motion: versatile translational elongation factor G." Biological Chemistry 401, no. 1 (December 18, 2019): 131–42. http://dx.doi.org/10.1515/hsz-2019-0313.

Full text

Abstract:

Abstract Elongation factor G (EF-G) is a translational GTPase that acts at several stages of protein synthesis. Its canonical function is to catalyze tRNA movement during translation elongation, but it also acts at the last step of translation to promote ribosome recycling. Moreover, EF-G has additional functions, such as helping the ribosome to maintain the mRNA reading frame or to slide over non-coding stretches of the mRNA. EF-G has an unconventional GTPase cycle that couples the energy of GTP hydrolysis to movement. EF-G facilitates movement in the GDP-Pi form. To convert the energy of hydrolysis to movement, it requires various ligands in the A site, such as a tRNA in translocation, an mRNA secondary structure element in ribosome sliding, or ribosome recycling factor in post-termination complex disassembly. The ligand defines the direction and timing of EF-G-facilitated motion. In this review, we summarize recent advances in understanding the mechanism of EF-G action as a remarkable force-generating GTPase.

APA, Harvard, Vancouver, ISO, and other styles

45

Gardill, Bernd R., Ricardo E. Rivera-Acevedo, Ching-Chieh Tung, and Filip Van Petegem. "Crystal structures of Ca2+–calmodulin bound to NaV C-terminal regions suggest role for EF-hand domain in binding and inactivation." Proceedings of the National Academy of Sciences 116, no. 22 (May 9, 2019): 10763–72. http://dx.doi.org/10.1073/pnas.1818618116.

Full text

Abstract:

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

APA, Harvard, Vancouver, ISO, and other styles

46

Fabre, Lucien, Eugenio Santelli, Driss Mountassif, Annemarie Donoghue, Aviroop Biswas, Rikard Blunck, Dorit Hanein, Niels Volkmann, Robert Liddington, and Isabelle Rouiller. "Structure of anthrax lethal toxin prepore complex suggests a pathway for efficient cell entry." Journal of General Physiology 148, no. 4 (September 26, 2016): 313–24. http://dx.doi.org/10.1085/jgp.201611617.

Full text

Abstract:

Anthrax toxin comprises three soluble proteins: protective antigen (PA), lethal factor (LF), and edema factor (EF). PA must be cleaved by host proteases before it oligomerizes and forms a prepore, to which LF and EF bind. After endocytosis of this tripartite complex, the prepore transforms into a narrow transmembrane pore that delivers unfolded LF and EF into the host cytosol. Here, we find that translocation of multiple 90-kD LF molecules is rapid and efficient. To probe the molecular basis of this translocation, we calculated a three-dimensional map of the fully loaded (PA63)7–(LF)3 prepore complex by cryo–electron microscopy (cryo-EM). The map shows three LFs bound in a similar way to one another, via their N-terminal domains, to the surface of the PA heptamer. The model also reveals contacts between the N- and C-terminal domains of adjacent LF molecules. We propose that this molecular arrangement plays an important role in the maintenance of translocation efficiency through the narrow PA pore.

APA, Harvard, Vancouver, ISO, and other styles

47

Ziatdinov, Albert M., Vladimir V. Kainara, and Nikita S. Saenko. "The Effect of Adsorbed Molecules on Electronic Structure and Magnetic Properties of Nanographites." Solid State Phenomena 247 (March 2016): 111–17. http://dx.doi.org/10.4028/www.scientific.net/ssp.247.111.

Full text

Abstract:

The results of investigation of changes in electronic structure and magnetic properties of multilayer graphene nanoclusters (nanographites) occurring during their interaction with adsorbed chlorine molecules are presented. The found reversible decrease in the density of states of current carriers D(EF) at the Fermi energy EF can be explained by the spin-splitting of edge π-electron states in nanographites induced by the enhancement of electron-electron interactions due to increase of the D(EF) at partial transfer of the electron density from nanographites to chlorine adatoms. The revealed irreversible decrease in the concentration of localized spins indicates that the electron spins of 3p-orbitals of chlorine and unpaired (dundling) σ-orbitals of edge carbon atoms are coupled also at this interaction, i.e. the edge covalent compound of nanographite with chlorine forms. Character of changes in the spin-relaxation rate of π-electrons depending on the amount of adsorbed chlorine molecules and on temperature in chlorinated samples are also consistent with the above model of nanographite-chlorine interaction.

APA, Harvard, Vancouver, ISO, and other styles

48

Wade, Mark, Heather Prime, Thomas J. Hoffmann, Louis A. Schmidt, Thomas G. O'Connor, and Jennifer M. Jenkins. "Birth weight interacts with a functional variant of the oxytocin receptor gene (OXTR) to predict executive functioning in children." Development and Psychopathology 30, no. 1 (May 17, 2017): 203–11. http://dx.doi.org/10.1017/s0954579417000578.

Full text

Abstract:

AbstractGenetic variation in the oxytocin receptor gene (OXTR) is associated with several psychiatric conditions characterized by deficits in executive functioning (EF). A specific OXTR variant, rs2254298, has previously been associated with brain functioning in regions implicated in EF. Moreover, birth weight variation across the entire range is associated with individual differences in cortical structure and function that underlie EF. This is the first study to examine the main and interactive effect between rs2254298 and birth weight on EF in children. The sample consisted of 310 children from an ongoing longitudinal study. EF was measured at age 4.5 using observational tasks indexing working memory, cognitive flexibility, and inhibitory control. A family-based design that controlled for population admixture, stratification, and nongenomic confounds was employed. A significant genetic association between rs2254298 and EF was observed, with more copies of the major allele (G) associated with higher EF. There was also a significant interaction between rs2254298 and birth weight, such that more copies of the major allele in combination with higher birth weight predicted better EF. Findings suggest that OXTR may be associated with discrete neurocognitive abilities in childhood, and these effects may be modulated by intrauterine conditions related to fetal growth and development.

APA, Harvard, Vancouver, ISO, and other styles

49

Boiadjieva, Tz, D. Kovacheva, K. Petrov, S. Hardcastle, A. Sklyarov, and M. Monev. "Electrodeposition, composition and structure of Zn–Cr alloys." Journal of Applied Electrochemistry 34, no. 3 (March 2004): 315–21. http://dx.doi.org/10.1023/b:jach.0000015609.43585.ef.

Full text

APA, Harvard, Vancouver, ISO, and other styles

50

Gupta, Susmita, Abhik Gupta, and V. Benno Meyer-Rochow. "Cuticular microstructures of abdominal tergites and sternites of Cloeon sp. (Ephemeroptera; Baetidae) during post-embryonic development." Entomologica Fennica 10, no. 1 (January 1, 1999): 51–59. http://dx.doi.org/10.33338/ef.83999.

Full text

Abstract:

The postembryonic changes of the external microstructure of the cuticle on the abdominal tergites and stemites of Cloeon sp. (Ephemeroptera:Baetidae) are described. An inventory of the structures as the aquatic nymph grows and becomes transformed into a terrestrial subimago and then an imago, is provided. It is found that sensillar diversity on nymphal tergites increases with development, but remains unchanged on the stemites. While nymphs and subimago possess various types of sensilla trichoidea, sensilla basiconica are apparent on the imaginal abdomen only. Furthermore, the scaled and spiny cuticle of the nymph becomes relatively smooth in the adult stages. The distinct changes which structure and distribution of the scales as well as marginal spines on the abdominal tergites and stemites of the nymphs undergo during development, must find a reflection in behavioural changes of the larvae. Finally, the taxonomic implications of the observed changes are discussed.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'EF structure'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles