Elementary Processes in Protein Folding

Initializing live version
Download to Desktop

Requires a Wolfram Notebook System

Interact on desktop, mobile and cloud with the free Wolfram Player or other Wolfram Language products.

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!


Contributed by: S. M. Blinder (January 2008)
Open content licensed under CC BY-NC-SA



Feedback (field required)
Email (field required) Name
Occupation Organization
Note: Your message & contact information may be shared with the author of any specific Demonstration for which you give feedback.