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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...

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Related Experiment Video

Updated: Jul 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Hydrophobicity profiles for protein sequence analysis.

S R Krystek1, W J Metzler, J Novotny

  • 1Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey, USA.

Current Protocols in Protein Science
|April 23, 2008
PubMed
Summary

Hydrophobicity plots analyze protein surface features to understand protein folding. This method aids in generating testable hypotheses for experimental validation.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Hydrophobic interactions are fundamental to protein folding.
  • Various hydropathy scales quantify amino acid hydrophobicity.

Purpose of the Study:

  • To describe the application of hydrophobicity plots for analyzing protein surface features.
  • To provide guidance on using selected hydropathy scales for hypothesis generation.

Main Methods:

  • Utilizing hydropathy profiles to visualize amino acid hydrophobicity along a protein sequence.
  • Applying established hydropathy scales to generate surface feature hypotheses.

Main Results:

  • Demonstrated practical applications of hydrophobicity plots in addressing common biochemical problems.

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  • Highlighted the utility of specific scales for experimental design.

    • Conclusions:

    • Hydrophobicity plots are valuable tools for investigating protein surface characteristics.
    • This approach facilitates the formulation of experimentally verifiable hypotheses in protein science.