scholarly journals Secondary structural features of the bacteriophage Mu-encoded A and B transposition proteins

1989 ◽  
Vol 263 (1) ◽  
pp. 19-23 ◽  
Author(s):  
G Chaconas ◽  
W D McCubbin ◽  
C M Kay
Keyword(s):  
Biochemical Characterization ◽  
Alpha Helix ◽  
Structural Features ◽  
Random Coil ◽  
Beta Sheet ◽  
Bacteriophage Mu ◽  
Intensive Study ◽  
Beta Turn ◽  
Biochemical Level

The role of the bacteriophage Mu-encoded A and B proteins is to direct the transposition of Mu DNA. These are the first active DNA transposition proteins to have been purified and their mechanism of action at the biochemical level is under intensive study. Structural studies on these proteins, however, have lagged behind their biochemical characterization. We report here near- and far-u.v. c.d. spectra for these proteins and their secondary structural features derived from these data. The Mu A protein appears to be composed of primarily beta-sheet (40%) with 24% alpha-helix, 9% beta-turn and 27% random coil. In contrast, the Mu B protein contains 55% alpha-helix with only 13% beta-sheet and 3+ beta-turn and 29% random coil. The near-u.v. c.d. spectrum of the A protein was not unusual; however, the profile of the B protein suggested either buried or restricted chromophores within the protein or short-range interactions between aromatic residues.

scholarly journals Multiple native-like conformations trapped via self-association-induced hydrophobic collapse of the 33-residue β-sheet domain from platelet factor 4

1995 ◽  
Vol 306 (2) ◽  
pp. 407-419 ◽  
Author(s):  
E Ilyina ◽  
K H Mayo
Keyword(s):  
Electrostatic Interactions ◽  
Nuclear Overhauser Effect ◽  
Alpha Helix ◽  
Platelet Factor 4 ◽  
Random Coil ◽  
Beta Sheet ◽  
Platelet Factor ◽  
Hydrophobic Collapse ◽  
Low Dielectric ◽  
Self Association

Native platelet factor 4 (PF4) (70 residues) has a hydrophobic three-stranded anti-parallel beta-sheet domain on to which is folded an amphipathic C-terminal alpha-helix and an aperiodic N-terminal domain. The 33-amino acid beta-sheet domain from PF4 (residues 23-55) has been synthesized and studied by c.d. and n.m.r. At 10 degrees C and low concentration, peptide 23-55 appears to exist in aqueous solution in a random-coil distribution of highly flexible conformational states. Some preferred conformation, however, is observed, particularly within a relatively stable chain reversal from Leu-45 to Arg-49. As the peptide concentration and/or temperature is increased, a new conformational state(s) appears and intensifies as slowly exchanging (600 MHz 1H-n.m.r. chemical-shift time scale) random-coil resonances disappear. Hill plots of the concentration-dependence indicated mostly tetramer formation as found in native PF4. Although apparent resonance linewidths in aggregate state(s) are of the order of 100 Hz, sequence-specific assignments for most resonances could be made. N.m.r./nuclear Overhauser effect structural analysis indicates the formation of multiple native-like anti-parallel beta-sheet conformations, kinetically trapped via subunit-association-induced hydrophobic collapse and stabilized by low-dielectric electrostatic interactions among/between Gly-28 and Lys-50 in opposing subunits. Results are discussed in terms of protein folding.

scholarly journals In Silico prediction and Comparative Modeling of proteins in Creeping Fig (Ficus pumila) plant

2021 ◽  
Vol 23 (08) ◽  
pp. 898-905
Author(s):  
P. Revathi ◽  
◽  
K. Nirubama ◽  
G. Thamotharan ◽  
M. Beutline Malgija ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Transmembrane Helix ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Comparative Modeling ◽  
Structural Features ◽  
Vital Role ◽  
Random Coil ◽  
Dimensional Structure ◽  
Grand Average

In the present study, the Ficus pumila have taken to analyze the proteins by their preliminary characters from the database and predicted vital role of different sequences. The F. pumila (Creeping fig) is a prostrate/climbing shrub, experiments proved various active phytochemicals and antioxidant, antimicrobial, antimutagenic, analgesic, anti-inflammatory, antiproliferative, hypoglycemic, hypolipidemic, antihyperprolactinemic, anticholinesterase, nephroprotective properties. In addition to all metabolites, it also constitutes specific proteins that were evaluated through insilico homology modeling. Though it is considered as a poisonous weed, the protein present in this plant is evaluated by physicochemical, phylogeny and amino acid proportions by protparam, Swiss model, SOPMA, Clustal omega tools to describe its structural features and to understand molecular function. The computed theoretical isoelectric point (pI) found to be more than 7 indicates basic nature of proteins. The aliphatic index ranges 67-113 indicates thermal stability of proteins. The predicted Grand average hydropathy(GRAVY) shows possibilities of enhanced interaction of these proteins with water by lowest value. Functional analysis of these proteins was performed by SOSUI server which predicted transmembrane helix and solubility. Secondary structure analysis was carried out by SOPMA revealed that Alpha helix and random coil dominated followed by extended strand, and beta turns among secondary structure elements. The modelling of three-dimensional structure of proteins was performed by Swiss model. The model was validated using protein structure checking tool- VADAR. Particularly, NAD(P)H –quinoneoxidoreductase and Glyceraldehyde-3-phosphate dehydrogenase structures were analysed by phylogenetic analysis to trace relationship and reported. The results suggesting its possible role in cellular and metabolic functions.

scholarly journals High-throughput mutagenesis reveals unique structural features of human ADAR1

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
SeHee Park ◽  
Erin E. Doherty ◽  
Yixuan Xie ◽  
Anil K. Padyana ◽  
Fang Fang ◽  
...  
Keyword(s):  
High Throughput ◽  
Rational Design ◽  
Biochemical Characterization ◽  
Structural Information ◽  
Structural Features ◽  
Adenosine Deaminases ◽  
Zinc Binding Site ◽  
Editing Activity ◽  
Deaminase Domain

Abstract Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1.

scholarly journals Lopap, a prothrombin activator from Lonomia obliqua belonging to the lipocalin family: recombinant production, biochemical characterization and structure–function insights

2006 ◽  
Vol 398 (2) ◽  
pp. 295-302 ◽  
Author(s):  
Cleyson Valença Reis ◽  
Sonia Aparecida Andrade ◽  
Oscar Henrique Pereira Ramos ◽  
Celso Raul Romero Ramos ◽  
Paulo Lee Ho ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Serine Protease ◽  
Calcium Binding ◽  
Biochemical Characterization ◽  
Structural Features ◽  
Reading Frame ◽  
Molecular Features ◽  
Recombinant Production ◽  
Lonomia Obliqua

Using a cDNA library made from Lonomia obliqua caterpillar bristles, we identified a transcript with a 603 bp open reading frame. The deduced protein corresponds to Lopap, a prothrombin activator previously isolated by our group from the bristles of this species. The mature protein is composed by 185 amino acids and shares similarity with members of the lipocalin family. The cDNA encoding the mature form was amplified by PCR, subcloned into pAE vector and used to transform Escherichia coli BL21(DE3) cells. As for the native Lopap, the recombinant fusion protein shows enzymatic activity, promotes prothrombin hydrolysis, generates fragments similar to prethrombin-2 and fragment 1.2 as intermediates, and generates thrombin as the final product. In addition, structural bioinformatics studies indicated several interesting molecular features, including the residues that could be responsible for Lopap's serine protease-like activity and the role of calcium binding in this context. Such catalytic activity has never been found in other members of the lipocalin family. This is the first report describing the recombinant production and biochemical characterization of a Lonomia obliqua lipocalin, as well as the structural features that could be responsible for its serine protease-like catalytic activity.

The Role of Archpriest Eugene Popov in Enhancing of the Anglican-Orthodox Dialog

2020 ◽  
pp. 71-84
Author(s):  
Ярослав Очканов
Keyword(s):  
State Level ◽  
Structural Features ◽  
Russian Orthodox ◽  
Church Community ◽  
Anglican Church ◽  
Current State ◽  
The Church

Статья посвящена исследованию малоизученной стороны деятельности видного русского священнослужителя протоиерея Евгения Попова, бывшего с 1842 по 1875 гг. настоятелем русской посольской церкви в Лондоне. Его служение на Английской земле совпало с углублением диалога между Русской Православной и Англиканской церквами, явившегося следствием религиозных преобразований в Англии в 1830 - 1840-е гг. Отец Евгений в рассматриваемый период фактически стал связующим звеном между русским церковноначалием и англиканами - инициаторами единения двух Церквей. Он проделал огромную работу по популяризации православия в Англии и много сделал для ознакомления русской церковной общественности с вероучением и структурными особенностями англиканства. Материалом для исследования послужили, прежде всего, письма протоиерея Евгения Попова обер-прокурорам Святейшего Синода Н. А. Протасову и А. П. Толстому. Эти документы являются своеобразными отчётами о современном состоянии Англиканской Церкви, о религиозных течениях в ней и усилиях, предпринимаемых определёнными церковными кругами в Англии по сближению с православием. Результаты его деятельности имели важное значение в последующие десятилетия, когда англикано-православный диалог вышел на церковно-государственный уровень. The article is devoted to the insufficiently studied aspects of Russian prominent cleric Archpriest Eugene Popov, rector of Russian Embassy Church in London from 1842 to 1875. His Ministry on the English soil coincided with the deepening of the dialogue between the Russian Orthodox and Anglican Churches, which was the result of religious transformations in England in the 1830s and 1840s. Father Eugene in the period under consideration actually became a connecting link between the Russian Church authorities and the anglicans-initiators of the union of the two Churches. He had done a great job by popularizing Orthodoxy in England and by familiarizing the Russian Church community with the doctrine and structural features of Anglicanism. The study, first of all, is based the letters of Archpriest Yevgeny Popov to the chief prosecutors of the Holy Synod N. A. Protasov and A. P. Tolstoy, which were original reports on the current state of the Anglican Church, it’s religious trends, and the efforts made by certain Church circles in England to get closer to Orthodoxy. The fruits of his activities were important in the following decades, when the Anglican-Orthodox dialogue reached the Church-state level.

THE USE OF THE TRANSLATION METHOD IN MASTERING THE TERMS

2019 ◽  
pp. 87-95
Keyword(s):  
International Relations ◽  
English Language ◽  
Structural Features ◽  
Point Of View ◽  
General Classification ◽  
Optimal Methods ◽  
Foreign Companies ◽  
The Social ◽  
Problems Of Translation

The article is devoted to the role of Tourism terminology in linguistics and the issue of general classification, peculiarities in the expression and translation of terms related to tourism in English into Uzbek and Russian, as well as the choice of the most optimal methods for translating terms in accordance with the requirements of this professional sphere. The terminology of the English language tourism is distinguished by its brightness, versatility. Tourism terms are formed under the influence of a generalized lexical layer of language and perform a specific functional function.Tourism terms are formed through the affixation method (prefixation, suffixation, circumphixation) and get rich through the process.The terminology of English Tourism is distinguished by its content and structural features, forming a part of the language vocabulary from the linguistic point of view. Texts in the field of Tourism take into their composition concepts of Tourism and interpret them in their content. They will be mainly in the form of advertising, as well as enlighten information about a particular region or place, create informational precedents and ensure their manifestation in the social cultural presence. The relevance of the study of the problems of translation of terms in the field of tourism has been investigated, mainly due to the development of international relations, expansion of cooperation between local and foreign companies, as well as the increase in this area of communication.

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

Are All Lockdown Teams Created Equally? Work Characteristics and Team Perceived Virtuality

2021 ◽  
pp. 104649642199789
Author(s):  
Patrícia L. Costa ◽  
Lisa Handke ◽  
Thomas A. O’Neill
Keyword(s):  
Virtual Teams ◽  
Organizational Support ◽  
Latent Profile Analysis ◽  
Profile Analysis ◽  
Structural Features ◽  
Pivotal Role ◽  
Work Characteristics ◽  
Team Members ◽  
Latent Profile

Team virtuality has been mostly conceptualized as structural features, such as the percentage of time team members communicate via technology. However, the perception of distance and of information deficits (team perceived virtuality, TPV) may be an indispensable construct to understand virtual teams’ functioning. The lockdowns imposed on most countries due to COVID-19 created virtual teams with high degrees of structural virtuality. With structural virtuality held constant among teams, we explore configurations of work characteristics (autonomy, interdependence, and organizational support) that influence TPV. With a sample of 296 multinational workers, a Latent Profile Analysis identified four distinct profiles of those work characteristics. Those profiles related differently to TPV. Contrary to previous findings, interdependence seems to play an important role in these teams high in structural virtuality when their autonomy is also high, highlighting the pivotal role of frequent interaction among team members, under conditions of high structural virtuality.

scholarly journals Cloning, expression, and analysis of the group 2 allergen from Dermatophagoides farinae from China

2010 ◽  
Vol 82 (4) ◽  
pp. 941-951 ◽  
Author(s):  
Cui Yu-bao ◽  
Ying Zhou ◽  
Shi Weihong ◽  
Ma Guifang ◽  
Li Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Alpha Helix ◽  
Random Coil ◽  
Reference Sequence ◽  
Scale Production ◽  
Dermatophagoides Farinae ◽  
E Coli ◽  
Large Scale Production ◽  
Solid Foundation ◽  
Group 2

To obtain the recombinant group 2 allergen product of Dermatophagoides farinae (Der f 2), the Der f 2 gene was synthesized by RT-PCR. The full-length cDNA comprised 441 nucleotides and was 99.3% identical to the reference sequence (GenBank AB195580). The cDNA was bound to vector pET28a to construct plasmid pET28a(+)-Der f 2, which was transformed into E. coli BL21 and induced by IPTG. SDS-PAGE showed a specific band of about 14kDa in the hole cell lysate. s estiated by chroatography, about 3.86 g of the recobinant product as obtained, which conjugated with serum IgE from asthmatic children. The protein had a signal peptide of 17 amino acids. Its secondary structure comprised an alpha helix (19.86%), an extended strand (30.82%), and a random coil (49.32%). The subcellular localization of this allergen was predicted to be at mitochondria. Furthermore, its function was shown to be associated with an MD-2-related lipid-recognition (ML) domain. The results of this study provide a solid foundation for large-scale production of the allergen for clinical diagnosis and treatent of allergic disorders.

scholarly journals Role of the Ser-287-Asn Replacement in the Hydrolysis Spectrum Extension of AmpC β-Lactamases in Escherichia coli

2008 ◽  
Vol 53 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Hedi Mammeri ◽  
Moreno Galleni ◽  
Patrice Nordmann
Keyword(s):  
Escherichia Coli ◽  
Biochemical Characterization ◽  
Catalytic Efficiency ◽  
Phylogenetic Groups ◽  
Extended Spectrum ◽  
Group A

ABSTRACT Two AmpC variants harboring the S287N substitution were obtained by mutagenesis from cephalosporinases representative of the phylogenetic groups A and B2 of Escherichia coli. Their biochemical characterization revealed that the S287N replacement led to an important increase in the catalytic efficiency toward extended-spectrum cephalosporins in the AmpC β-lactamase of group A only.

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