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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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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.
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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.
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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Web tools support predicting protein-nucleic acid complexes stability with affinity changes.

Xiao Zhang1, Long-Can Mei2, Yang-Yang Gao1

  • 1National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China.

Wiley Interdisciplinary Reviews. RNA
|January 24, 2023
PubMed
Summary
This summary is machine-generated.

This review synthesizes databases and web tools for protein-nucleic acid interactions (PNIs). It aims to integrate dispersed resources to better understand PNI binding stability and recognition mechanisms.

Keywords:
affinities and stabilitiesmutationsprotein-nucleic acid interactionsstructural bioinformatics

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Protein-nucleic acid interactions (PNIs) are crucial for fundamental biological processes like transcription, replication, and translation.
  • Assessing the binding stability of protein-nucleic acid complexes is essential for understanding PNI mechanisms.
  • Existing web-based tools and databases for PNI stability prediction are fragmented, hindering comprehensive analysis.

Purpose of the Study:

  • To review and evaluate existing databases for protein-nucleic acid binding stability.
  • To compare and contrast web tools used for predicting interaction energies in protein-nucleic acid complexes.
  • To discuss the potential of integrated models for advancing the study of PNIs.

Main Methods:

  • Systematic literature review of databases and web tools related to protein-nucleic acid binding stability.
  • Comparative analysis of the strengths and weaknesses of various prediction tools.
  • Discussion of integrated approaches for PNI analysis.

Main Results:

  • Identification and summary of current databases for evaluating PNI stability.
  • Evaluation of the capabilities and limitations of web tools for predicting PNI interaction energies.
  • Exploration of combined modeling strategies for PNI research.

Conclusions:

  • A comprehensive integration of dispersed data and tools is needed for a deeper understanding of PNI stability.
  • Web-based tools show promise in facilitating the discovery of PNI recognition mechanisms.
  • This review provides a consolidated overview to guide future research in protein-nucleic acid binding stability.