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Related Concept Videos

Protein Organization01:24

Protein Organization

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.
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

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Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens
08:49

Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens

Published on: June 6, 2020

PSC: protein surface classification.

Yan Yuan Tseng1, Wen-Hsiung Li

  • 1Department of Ecology and Evolution, University of Chicago 1101 East 57th Street, Chicago, IL 60637, USA. ytseng3@uchicago.edu

Nucleic Acids Research
|June 7, 2012
PubMed
Summary
This summary is machine-generated.

Protein classification is now based on functional surfaces, enabling the discovery of protein relationships and evolutionary changes. The Protein Surface Classification (PSC) database offers insights into protein function and evolution.

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Area of Science:

  • Biochemistry and Structural Biology
  • Bioinformatics and Computational Biology

Background:

  • Proteins function through local regions known as functional surfaces.
  • Understanding relationships between proteins is crucial for deciphering biological processes.
  • Existing classification methods may not fully capture functional similarities.

Purpose of the Study:

  • To develop a novel protein classification system based on functional surface structures.
  • To construct an expandable database (Protein Surface Classification - PSC) for exploring protein relationships.
  • To provide a tool for investigating functional divergence and evolutionary changes in proteins.

Main Methods:

  • Classification of proteins based on the structural attributes of their functional surfaces.
  • Inference of pairwise protein relationships using these structural attributes.
  • Development of a database (PSC) containing surface types, functional surfaces, and structural descriptors.
  • Normalization of geometric, physicochemical, and evolutionary features into surface profiles.

Main Results:

  • The Protein Surface Classification (PSC) database currently includes 1974 surface types and 25,857 functional surfaces from 24,170 bound structures.
  • A search tool allows users to find related surfaces with similar local structures and core functions.
  • Functional surfaces are characterized by normalized structural attributes forming a unique profile.
  • Data on binding ligands and residue changes in homologs are recorded for evolutionary analysis.

Conclusions:

  • Classification by functional surfaces provides a new perspective on protein relationships and may reflect functional similarities.
  • The PSC database serves as a valuable resource for exploring protein function, evolution, and divergence.
  • Analysis of residue substitutions in spatial patterns can illuminate the functional evolution of proteins.