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Related Concept Videos

Protein Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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-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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Related Experiment Video

Updated: Jun 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

High-resolution mapping of protein sequence-function relationships.

Douglas M Fowler1, Carlos L Araya, Sarel J Fleishman

  • 1Department of Genome Sciences, University of Washington, Seattle, WA, USA.

Nature Methods
|August 17, 2010
PubMed
Summary
This summary is machine-generated.

This study developed a high-throughput method to map protein sequence variations and their functional effects. It reveals detailed mutational preferences in a human WW domain, offering insights into protein function and sequence relationships.

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Last Updated: Jun 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Protein engineering
  • Molecular biology
  • Genomics

Background:

  • Understanding protein function is crucial for many biological processes.
  • Sequence variations can significantly alter protein activity and interactions.
  • Previous methods lacked the scale to comprehensively analyze sequence-function relationships.

Purpose of the Study:

  • To develop and apply a large-scale approach for investigating the functional consequences of protein sequence variation.
  • To create a high-resolution map of mutational preferences in a human WW domain.
  • To provide a general method for linking protein sequence to function.

Main Methods:

  • Employing phage display to generate and select hundreds of thousands of protein variants.
  • Utilizing moderate selection for protein activity and high-throughput DNA sequencing.
  • Quantifying the performance of over 600,000 variants of a human WW domain for peptide ligand binding.

Main Results:

  • Generated a high-resolution map of mutational preferences across the WW domain.
  • Demonstrated unique mutational features at each amino acid position.
  • Quantified the performance of >600,000 protein variants after selection rounds.

Conclusions:

  • The developed approach provides a general method for understanding protein sequence-function relationships.
  • This strategy can be applied to various in vitro and in vivo protein assays.
  • Detailed mutational mapping offers insights beyond representative mutations.