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Related Concept Videos

Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Protein Networks02:26

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Protein-protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Nucleic acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
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Analyzing and Building Nucleic Acid Structures with 3DNA
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NuProPlot: nucleic acid and protein interaction analysis and plotting program.

Lagnajeet Pradhan1, Hyun Joo Nam1

  • 1Department of Bioengineering, University of Texas at Dallas, 800 W. Campbell Road RL10, Richardson, TX 75080, USA.

Acta Crystallographica. Section D, Biological Crystallography
|March 12, 2015
PubMed
Summary
This summary is machine-generated.

NuProPlot is a new web-based tool that simplifies the analysis and visualization of protein-nucleic acid interactions. It automatically identifies and plots various interaction types, improving presentation of complex structural data.

Keywords:
NuProPlotprotein–nucleic acid complexes

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Increasing availability of complex protein-nucleic acid structures necessitates advanced analysis tools.
  • Current visualization software for these interactions is limited in scope and user-friendliness.
  • Analyzing three-dimensional interactions in protein-nucleic acid complexes presents significant challenges.

Purpose of the Study:

  • To develop an automated, interactive web-based program for analyzing protein-nucleic acid interactions.
  • To provide a user-friendly platform for visualizing hydrogen, electrostatic, and van der Waals interactions.
  • To improve the presentation of complex protein-DNA and protein-RNA interaction data.

Main Methods:

  • Development of an interactive web-based program, NuProPlot.
  • Automated identification of hydrogen, electrostatic, and van der Waals interactions.
  • Generation of 2D schematic plots with interactive drawing and customization options.

Main Results:

  • NuProPlot successfully identifies and visualizes protein-DNA and protein-RNA interactions.
  • The program automatically generates plots of all identified interactions.
  • Interactive features allow users to customize plots for clarity and legibility.

Conclusions:

  • NuProPlot offers a significant improvement for the analysis and presentation of protein-nucleic acid interactions.
  • The automated and user-friendly nature of NuProPlot enhances accessibility for researchers.
  • This tool addresses limitations of existing software for visualizing complex structural data.