Elementary Processes in Protein Folding

Biologically active -amino acids are compounds with the general formula , where represents one of about 20 possible side groups (or residues). An amide linkage is formed by the reaction of the carboxyl group of one molecule with the amide group of another. Proteins are built up of chains of amino acids connected by amide (or peptide) linkages, with the general structure . Chains can vary in length from about 100 to several thousand amino acid units.
The linear sequence of amino acids, identified by the side groups , , ..., determines the primary structure of the protein. The amide C-N bond is relatively rigid (attributed to its partial double-bond character) and creates a planar unit incorporating six connected atoms. However, the adjacent C-C and N-C bonds can undergo torsional motions, characterized by the angles ψ and , one set for each amino acid unit. Although possible torsional motions might be restricted by steric and electrostatic effects, an immense number of conformations remain possible for every protein. In order to fulfill its biological function, a protein must attain a very specific three-dimensional secondary and tertiary structure. The "protein folding problem", a very active area of current research, explores the details of how the final configuration is achieved.
This Demonstration presents a simplified schematic representation of the possible motions of a protein chain. Two amino-acid units, with side groups and , are shown. The green cylinders represent the continuation of the protein chain in each direction. The torsional angles and can be independently varied between 0° and 360°. The immense number of possibilities, for just two of the hundreds or thousands of configuration variables, is soon apparent.
Remarkably, a linear sequence of amino acids will biologically self-assemble in a matter of milliseconds!



  • [Snapshot]
  • [Snapshot]
  • [Snapshot]
    • Share:

Embed Interactive Demonstration New!

Just copy and paste this snippet of JavaScript code into your website or blog to put the live Demonstration on your site. More details »

Files require Wolfram CDF Player or Mathematica.

Mathematica »
The #1 tool for creating Demonstrations
and anything technical.
Wolfram|Alpha »
Explore anything with the first
computational knowledge engine.
MathWorld »
The web's most extensive
mathematics resource.
Course Assistant Apps »
An app for every course—
right in the palm of your hand.
Wolfram Blog »
Read our views on math,
science, and technology.
Computable Document Format »
The format that makes Demonstrations
(and any information) easy to share and
interact with.
STEM Initiative »
Programs & resources for
educators, schools & students.
Computerbasedmath.org »
Join the initiative for modernizing
math education.
Step-by-Step Solutions »
Walk through homework problems one step at a time, with hints to help along the way.
Wolfram Problem Generator »
Unlimited random practice problems and answers with built-in step-by-step solutions. Practice online or make a printable study sheet.
Wolfram Language »
Knowledge-based programming for everyone.
Powered by Wolfram Mathematica © 2018 Wolfram Demonstrations Project & Contributors  |  Terms of Use  |  Privacy Policy  |  RSS Give us your feedback
Note: To run this Demonstration you need Mathematica 7+ or the free Mathematica Player 7EX
Download or upgrade to Mathematica Player 7EX
I already have Mathematica Player or Mathematica 7+