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Related Concept Videos

Protein Networks02:26

Protein Networks

4.7K
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-protein Interfaces02:04

Protein-protein Interfaces

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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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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Nucleic Acid Structure01:25

Nucleic Acid Structure

10.5K
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.
DNA Structure
DNA...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.

V Suresh1, Liang Liu1, Donald Adjeroh2

  • 1Department of Radiology, Wake Forest University Health Science, Medical Center Boulevard, Winston-Salem, NC 27157, USA.

Nucleic Acids Research
|January 23, 2015
PubMed
Summary
This summary is machine-generated.

RPI-Pred accurately predicts RNA-protein interactions using sequence and structure data. This computational method enhances understanding of gene regulation and aids in constructing ncRNA-protein networks.

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA-protein complexes are crucial for cellular processes like transport and localization.
  • ncRNA-protein interactions regulate gene expression post-transcriptionally, affecting mRNA stability, localization, splicing, and translation.
  • Experimental prediction of RNA-protein interactions is costly and time-intensive.

Purpose of the Study:

  • To develop an accurate and efficient computational method for predicting RNA-protein interactions.
  • To utilize sequence and structural information for improved prediction accuracy.
  • To facilitate the construction of RNA-protein interaction networks.

Main Methods:

  • Development of RPI-Pred, a support-vector machine-based prediction tool.
  • Input features include RNA and protein sequences and structures.
  • Validation using experimentally determined and predicted structural data.

Main Results:

  • RPI-Pred achieved approximately 94% accuracy using experimental structures and sequences.
  • Achieved approximately 83% accuracy using predicted structures and sequences.
  • Outperformed existing methods in predicting experimentally validated ncRNA-protein interactions across diverse organisms.

Conclusions:

  • RPI-Pred offers a highly accurate and efficient approach for predicting RNA-protein interactions.
  • The method's performance supports its application in constructing reliable ncRNA-protein interaction networks.
  • RPI-Pred is publicly available, promoting further research in RNA-protein interactions.