Molecular Visualization of the Yeast Dmc1 Protein Ring and Dmc1−ssDNA Nucleoprotein Complex†

Biochemistry ◽  
2005 ◽  
Vol 44 (16) ◽  
pp. 6052-6058 ◽  
Author(s):  
Yuan-Chih Chang ◽  
Yu-Hui Lo ◽  
Ming-Hui Lee ◽  
Chih-Hsiang Leng ◽  
Su-Ming Hu ◽  
...  
Keyword(s):  
Molecular Visualization ◽  
Nucleoprotein Complex

scholarly journals Interactions between Integrase and Excisionase in the Phage Lambda Excisive Nucleoprotein Complex

2002 ◽  
Vol 184 (18) ◽  
pp. 5200-5203 ◽  
Author(s):  
Eun Hee Cho ◽  
Richard I. Gumport ◽  
Jeffrey F. Gardner
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Mobility Shift ◽  
Host Chromosome ◽  
Amino Terminal ◽  
Nucleoprotein Complex ◽  
Carboxyl Terminal ◽  
Α Helix ◽  
Gel Mobility Shift ◽  
Amino Terminal Domain

ABSTRACT Bacteriophage lambda site-specific recombination comprises two overall reactions, integration into and excision from the host chromosome. Lambda integrase (Int) carries out both reactions. During excision, excisionase (Xis) helps Int to bind DNA and introduces a bend in the DNA that facilitates formation of the proper excisive nucleoprotein complex. The carboxyl-terminal α-helix of Xis is thought to interact with Int through direct protein-protein interactions. In this study, we used gel mobility shift assays to show that the amino-terminal domain of Int maintained cooperative interactions with Xis. This finding indicates that the amino-terminal arm-type DNA binding domain of Int interacts with Xis.

scholarly journals Nucleoprotein complex intermediates in HIV-1 integration

Methods ◽  
2009 ◽  
Vol 47 (4) ◽  
pp. 237-242 ◽  
Author(s):  
Min Li ◽  
Robert Craigie
Keyword(s):  
Nucleoprotein Complex ◽  
Hiv 1

An Iron–Copper–Nucleoprotein Complex in Animal Tissue

Nature ◽  
1941 ◽  
Vol 148 (3759) ◽  
pp. 595-596 ◽  
Author(s):  
K. C. SAHA ◽  
B. C. GUHA
Keyword(s):  
Animal Tissue ◽  
Iron Copper ◽  
Nucleoprotein Complex

scholarly journals FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

2020 ◽  
Author(s):  
Xavier Martinez ◽  
Marc Baaden
Keyword(s):  
Virtual Reality ◽  
Structural Data ◽  
Molecular Data ◽  
Molecular Visualization ◽  
Related Data ◽  
Broad Audience ◽  
Collaborative Virtual Reality ◽  
3D Environments ◽  
Fair Principles ◽  
Collaborative Exploration

AbstractMotivated by the current Covid-19 pandemic that has spurred a substantial flow of structural data we describe how molecular visualization experiences can be used to make these datasets accessible to a broad audience. Using a variety of technology vectors related to the cloud, 3D- and virtual reality gear, we examine how to share curated visualizations of structural biology, modeling and/or bioinformatics datasets for interactive and collaborative exploration. We discuss F.A.I.R. as overarching principle for sharing such visualizations. We provide four initial example scenes related to recent Covid-19 structural data together with a ready-to-use (and share) implementation in the UnityMol software.SynopsisVisualization renders structural molecular data accessible to a broad audience. We describe an approach to share molecular visualization experiences based on FAIR principles. Our workflow is exemplified with recent Covid-19 related data.

scholarly journals Isolation and some properties of the nucleoprotein complex of Propionibacterium freudenreichii subsp.shermanii

1999 ◽  
Vol 79 (1) ◽  
pp. 187-196 ◽  
Author(s):  
Lena Vorobjeva ◽  
Aleksei Zinchenko ◽  
Evgeni Khodjaev ◽  
Galina Ponomareva ◽  
Elena Gordeeva
Keyword(s):  
Propionibacterium Freudenreichii ◽  
Nucleoprotein Complex

scholarly journals Development of Guided Inquiry based E-Learning Teaching Material on the Intermolecular Forces Enriched with Molview

2021 ◽  
Vol 2 (2) ◽  
pp. 80
Author(s):  
Nur Indah Agustina ◽  
Munzil Munzil ◽  
Habiddin Habiddin ◽  
M. Muchson
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Intermolecular Forces ◽  
School Curriculum ◽  
Teaching Material ◽  
Guided Inquiry ◽  
Chemistry Teaching ◽  
Molecular Visualization ◽  
High School Curriculum ◽  
E Learning

The intermolecular force is one of the chemistry topics covered in the high school curriculum in Indonesia. As the characteristics of chemistry concepts in general, intermolecular forces concepts can be presented in the three levels of chemical representations (microscopic, symbolic, and macroscopic).  Currently, chemistry teaching materials are available in Indonesian schools mostly have limited support for helping students to visualize the molecular aspect of intermolecular forces concepts mainly in the form of three-dimensional space (3D). This study aimed to produce an E-Learning teaching material enriched with 3D Molecular Visualization. The product (teaching material) in this study is presented by considering the syntax of guided inquiry-based learning. The product was developed with the procedure adopted from Lee and Owens, including assessment/analysis, need assessment, front-end analysis, design, and development. The product is valid and suitable to be applied in online chemistry teaching. However, further study to investigate the effectiveness of this product empirically need to be explored in the future.

scholarly journals SlyA and H-NS Regulate Transcription of the Escherichia coli K5 Capsule Gene Cluster, and Expression of slyA in Escherichia coli Is Temperature-dependent, Positively Autoregulated, and Independent of H-NS

2007 ◽  
Vol 282 (46) ◽  
pp. 33326-33335 ◽  
Author(s):  
David Corbett ◽  
Hayley J. Bennett ◽  
Hamdia Askar ◽  
Jeffrey Green ◽  
Ian S. Roberts
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Regulation Of Transcription ◽  
Temperature Dependent ◽  
Mobility Shift ◽  
E Coli ◽  
Dnase I Footprinting ◽  
Nucleoprotein Complex ◽  
Electrophoretic Mobility Shift Assays

In this paper, we present the first evidence of a role for the transcriptional regulator SlyA in the regulation of transcription of the Escherichia coli K5 capsule gene cluster and demonstrate, using a combination of reporter gene fusions, DNase I footprinting, and electrophoretic mobility shift assays, the dependence of transcription on the functional interplay between H-NS and SlyA. Both SlyA and H-NS bind to multiple overlapping sites within the promoter in vitro, but their binding is not mutually exclusive, resulting in a remodeled nucleoprotein complex. In addition, we show that expression of the E. coli slyA gene is temperature-regulated, positively autoregulated, and independent of H-NS.

Molecular Visualization with Supports of Interaction, Immersion, and Collaboration among Geographically Separated Research Groups

2013 ◽  
pp. 252-269
Author(s):  
Moacyr Francischetti-Corrêa
Keyword(s):  
High Performance ◽  
Collaborative Work ◽  
Receptor Interaction ◽  
Research Groups ◽  
Negative Effects ◽  
Molecular Visualization ◽  
Geographically Dispersed ◽  
Communication Techniques ◽  
Time Interaction ◽  
Drug Receptor

In the search for new drug and medication discovery, especially related to drug-receptor interaction, the importance of interaction among researchers is essential, either within the same room or dispersed throughout the world. The interaction in an online environment through the molecule shared view and information and ideas exchange via text and/or voice enable researchers to discuss molecule aspects under study, increasing the chances of reaching the new compound’s identification. In subsequent sections an architecture that uses concepts of Distributed Multiuser Virtual Reality, Computer-Supported Collaborative Work, and world-wide network communication techniques for creating a high performance system that allows real-time interaction among various geographically dispersed research groups studying molecular visualization and using hardware systems ranging from desktop to immersive systems as CAVEs is presented. Its construction was made possible by defining a structure based on local servers to each group, which communicate with each other on a remote network, and creating a protocol for communication among these servers that seeks agility to minimize the negative effects of packet loss and delay delivery, Internet characteristic problems.

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