scholarly journals EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

2020 ◽  
Vol 48 (W1) ◽  
pp. W104-W109 ◽  
Author(s):  
Jiri Hon ◽  
Simeon Borko ◽  
Jan Stourac ◽  
Zbynek Prokop ◽  
Jaroslav Zendulka ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
Data Gathering ◽  
Soluble Form ◽  
Web Interface ◽  
Solubility Prediction ◽  
Genomic Databases ◽  
Wet Lab ◽  
Automated Screening ◽  
Soluble Enzymes ◽  
Selection Of

Abstract Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner—a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https://loschmidt.chemi.muni.cz/enzymeminer/.

Scanning Tunneling Microscopy and Atomic Force Microscopy of Enzymes and Enzyme Complexes

1990 ◽  
Vol 48 (3) ◽  
pp. 174-175
Author(s):  
Ronald D. Edstrom ◽  
Xiuru Yang ◽  
Mary E. Gurnack ◽  
Marcia A. Miller ◽  
Rui Yang ◽  
...  
Keyword(s):  
Cell Biology ◽  
Inorganic Ions ◽  
Bulk Liquid ◽  
Soluble Form ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Metabolic Channeling ◽  
Simplistic Notion ◽  
Soluble Enzymes

Many of the questions in biochemistry and cell biology are concerned with the relationships of proteins and other macromolecules in complex arrays which are responsible for carrying out metabolic sequences. The simplistic notion that the enzymes we isolate in soluble form from the cytoplasm were also soluble in vivo is being replaced by the concept that these enzymes occur in organized systems within the cell. In this newer view, the cytoplasm is organized and the “soluble enzymes” are in fact fixed in the cellular space and the only soluble components of the cell are small metabolites, inorganic ions etc. Further support for the concept of metabolic organization is provided by the evidence of metabolic channeling. It has been shown that for some metabolic pathways, the intermediates are not in free diffusion equilibrium with the bulk liquid in the cell but are passed along, more or less directly, from one enzyme to the next.

Pola Bimbingan Orang Tua Asuh dalam Menumbuhkan Kecerdasan Emosional Remaja

2019 ◽  
Vol 7 (3) ◽  
pp. 311-330
Author(s):  
Iva Faridha Azahro ◽  
Nanih Machendrawaty ◽  
Hajir Tajiri
Keyword(s):  
Emotional Intelligence ◽  
Foster Care ◽  
Research Method ◽  
Foster Parents ◽  
Data Gathering ◽  
Qualitative Approach ◽  
Research Results ◽  
Descriptive Research ◽  
Selection Of

Tujuan dari peneliti ini yaitu untuk mengetahui (1) karakteristik kecerdasan emosional remaja di RPSAA Ciumbuleuit Bandung; (2) pola bimbingan orang tua asuh dalam menumbuhkan kecerdasan emosional remaja di RPSAA Ciumbuleuit Bandung; (3) hasil pola bimbingan orang tua asuh dalam menumbuhkan kecerdasan emosional remaja di RPSAA Ciumbuleuit Bandung. Penelitian ini menggunakan pendekatan kualitatif dengan metode penelitian deskriptif, pemilihan subjek dan informan dengan cara acak dan teknik pengumpulan datanya melalui observasi, dokumentasi dan wawancara terhadap enam orang anak asuh dan tiga orang tua asuh. Hasil penelitian yang diperoleh peneliti menyimpulkan bahwa anak sebelum memperoleh pengasuhan dari orang tua asuh di RPSAA memiliki karakteristik kecerdasan emosional rendah. Pola pengasuhan yang diterapkan di RPSAA kepada anak asuh adalah pola asuh demokratis. Sedangkan hasil pengasuhan dalam menumbuhkan kecerdasan emosional remaja di RPSAA Ciumbuleuit Bandung menyimpulkan bahwa anak asuh usia remaja telah memiliki kecerdasan emosional yang cukup baik, yaitu terlihat dari bagaimana cara mereka mampu mengendalikan segala perasaan yang pada dirinya, meskipun ada remaja yang belum sepenuhnya memenuhi aspek kecerdasan emosional.   The goal of these researchers is to figure out (1) characteristics of the emotional intelligence of teenagers in RPSAA Ciumbuleuit Bandung; (2) foster parents guidance pattern in fostering emotional intelligence RPSAA Ciumbuleuit Bandung in adolescents; (3) results foster parents guidance pattern in fostering emotional intelligence RPSAA Ciumbuleuit Bandung in teens. This research used the qualitative approach with descriptive research method, the selection of subjects and informants by means of random and data gathering techniques through observation, interview and documentation against six people and three foster care parents foster care. The research results obtained by researchers concluded that child before obtaining care of foster parents in RPSAA has the characteristic of low emotional intelligence. Parenting patterns are applied in the RPSAA to foster care parenting is democratic. While parenting results in fostering emotional intelligence RPSAA Ciumbuleuit Bandung teenager in concluding that foster care teens have had a pretty good emotional intelligence, that is visible from how they are able to control all the feelings on him, even though there are teenagers who do not yet fully meet aspects of emotional intelligence.

scholarly journals Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor

2020 ◽  
Vol 19 (10) ◽  
pp. 1602-1618 ◽  
Author(s):  
Thibault Robin ◽  
Julien Mariethoz ◽  
Frédérique Lisacek
Keyword(s):  
Search Engine ◽  
Posttranslational Modifications ◽  
Search Engines ◽  
Web Application ◽  
Contextual Information ◽  
Fine Tuning ◽  
Data Sources ◽  
Web Interface ◽  
Definition Of ◽  
Selection Of

A key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing MS data. We introduce here a glycan composition visualizing and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It offers a web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarizing information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. They also confirm the consistency of a set of compositions based on the content of the GlyConnect database. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application. It is also directly accessible from the GlyConnect database.

scholarly journals Toward Best Practices in Quantitative, Qualitative, and Mixed- Method Research: A Social Justice Perspective

2013 ◽  
Vol 5 (2) ◽  
pp. 69-83 ◽  
Author(s):  
Ruth Fassinger ◽  
Susan L. Morrow
Keyword(s):  
Social Justice ◽  
Best Practices ◽  
Mixed Method ◽  
Research Method ◽  
Data Gathering ◽  
Team Formation ◽  
Mixed Method Research ◽  
Special Issue ◽  
Selection Of

Various research methods can be appropriate for social justice aims. Quantitative, qualitative, and mixed-method approaches offer different kinds of strengths in advancing a social justice agenda. This article recaptures and expands upon the ideas presented by the authors of this special issue, recommending best practices in research for social justice in the following areas: (a) cultural competence and the role of the researcher(s); (b) formulating the focus of the research; (c) selection of the underlying paradigm and research method/design; (d) the research team: formation, process, and issues of power; (e) power and relationship with research participants; and (f) data gathering, analysis, and reporting.

scholarly journals A novel DNA helicase with strand-annealing activity from the crenarchaeon Sulfolobus solfataricus

2007 ◽  
Vol 408 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Mariarita De Felice ◽  
Valentina Aria ◽  
Luca Esposito ◽  
Mariarosaria De Falco ◽  
Biagio Pucci ◽  
...  
Keyword(s):  
High Efficiency ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Sulfolobus Solfataricus ◽  
Genetic Material ◽  
Dna Helicase ◽  
Soluble Form ◽  
Monomeric Form ◽  
Genome Database ◽  
Strand Annealing

To protect their genetic material cells adopt different mechanisms linked to DNA replication, recombination and repair. Several proteins function at the interface of these DNA transactions. In the present study, we report on the identification of a novel archaeal DNA helicase. BlastP searches of the Sulfolobus solfataricus genome database allowed us to identify an open reading frame (SSO0112, 875 amino acid residues) having sequence similarity with the human RecQ5β. The corresponding protein, termed Hel112 by us, was produced in Escherichia coli in soluble form, purified to homogeneity and characterized. Gel-filtration chromatography and glycerol-gradient sedimentation analyses revealed that Hel112 forms monomers and dimers in solution. Biochemical characterization of the two oligomeric species revealed that only the monomeric form has an ATP-dependent 3′–5′ DNA-helicase activity, whereas, unexpectedly, both the monomeric and dimeric forms possess DNA strand-annealing capability. The Hel112 monomeric form is able to unwind forked and 3′-tailed DNA structures with high efficiency, whereas it is almost inactive on blunt-ended duplexes and bubble-containing molecules. This analysis reveals that S. solfataricus Hel112 shares some enzymatic features with the RecQ-like DNA helicases and suggests potential cellular functions of this protein.

scholarly journals Biochemical characterization and essentiality ofPlasmodiumfumarate hydratase

2017 ◽  
Author(s):  
Vijay Jayaraman ◽  
Arpitha Suryavanshi ◽  
Pavithra Kalale ◽  
Jyothirmai Kunala ◽  
Hemalatha Balaram
Keyword(s):  
Biochemical Characterization ◽  
Tricarboxylic Acid Cycle ◽  
Fumarate Hydratase ◽  
Class I ◽  
Iron Sulfur Cluster ◽  
Mercaptosuccinic Acid ◽  
Nanomolar Range ◽  
Strain Dependent ◽  
Selection Of

ABSTRACTPlasmodium falciparum(Pf), the causative agent of malaria has an iron-sulfur cluster-containing class I fumarate hydratase (FH) that catalyzes the interconversion of fumarate to malate, a well-known reaction in the tricarboxylic acid cycle. In humans, the same reaction is catalyzed by class II FH that has no sequence or structural homology with the class I enzyme. Fumarate, generated in large quantities in the parasite as a byproduct of AMP synthesis is converted to malate by the action of FH, and subsequently used in the generation of the key metabolites oxaloacetate, aspartate and pyruvate. Here we report on the kinetic characterization of purified recombinant PfFH, functional complementation offhdeficiency inEscherichia coliand mitochondrial localization in the parasite. The substrate analog, mercaptosuccinic acid was found to be a potent inhibitor of PfFH with a Kivalue in the nanomolar range. Knockout of thefhgene was not possible inP. bergheiwhen drug-selection of the transfectants was performed in BALB/c mice while the gene was amenable to knockout when C57BL/6 mice were used as host, thereby indicating mouse-strain dependent essentiality of thefhgene to the parasite.

Development and application of efficient methods for the forward propagation of epistemic uncertainty and sensitivity analysis within complex broad-scale flood risk system modelsThis article is one of a selection of papers published in this Special Issue on Hydrotechnical Engineering.

2010 ◽  
Vol 37 (7) ◽  
pp. 955-967 ◽  
Author(s):  
B. P. Gouldby ◽  
P. B. Sayers ◽  
M. C. Panzeri ◽  
J. E. Lanyon
Keyword(s):  
Sensitivity Analysis ◽  
Flood Risk ◽  
Large Scale ◽  
Epistemic Uncertainty ◽  
Data Gathering ◽  
Future Research ◽  
Special Issue ◽  
Flood Probability ◽  
Output Quantity ◽  
Selection Of

Increasingly, an understanding of flood risk across regions and nations, and an ability to explore how these might change in time, is seen as a prerequisite to effective and efficient flood risk management. In response, specific flood risk analysis methods have been developed that are both accurate and fast to run. Although widely acknowledged as desirable, it has not previously been possible to quantify the uncertainty associated with the assessed flood probability, consequence, or risk. To help overcome this deficiency, an efficient method for the propagation of epistemic uncertainties through large-scale flood risk system models has been developed and trialed for three pilot catchments. The approach is allied to an efficient sensitivity analysis that enables the influence of individual uncertainties on the output quantity of risk to be isolated, enabling future research, development, and data-gathering efforts to be focused.

Molecular and biochemical characterization of a new thermostable bacterial laccase from Meiothermus ruber DSM 1279

RSC Advances ◽  
2016 ◽  
Vol 6 (5) ◽  
pp. 3910-3918 ◽  
Author(s):  
D. C. Kalyani ◽  
L. Munk ◽  
J. D. Mikkelsen ◽  
A. S. Meyer
Keyword(s):  
Escherichia Coli ◽  
Biochemical Characterization ◽  
Soluble Form ◽  
Laccase Gene ◽  
Bacterial Laccase ◽  
Meiothermus Ruber ◽  
Chaperone Protein

A new bacterial laccase gene (mrlac) fromMeiothermus ruberDSM 1279 was successfully overexpressed to produce a laccase (Mrlac) in soluble form inEscherichia coliduring simultaneous overexpression of a chaperone protein (GroEL/ES).

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