Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online





Learning Goals/Objectives for Chapter 2C:  After class and this reading, students will be able to

  • describe the differences between primary, secondary, supersecondary, tertiary, quaternary and domain protein structure
  • explain the basis of CD measurements for secondary structure
  • describe the similarities between torsion angles and an energy vs torsion angle plot for the rotation of the C2-C3 torison angle with phi/psi angles of peptide bonds and the 2D plots off allowed conformations around a given amino acid in a protein (Ramachandran plot).
  • (from reading give explanation for observed propensities of amino acids for different secondary structure)

C4.  Common Motifs in Proteins

Super-Secondary Structure - Given the number of possible combinations of 1o, 2o, and 3o structures, one might guess that the 3D structure of each protein is quite distinctive. This is true. However, it has been found that similar substructures are found in proteins. For instance, common secondary structures are often grouped together to form a motifs called super-secondary structure (SSS). See some examples below:

Figure:   helix-loop-helix (image made with VMD)


Figure:  EF Hand


Jmol:   Updated helix-loop-helix of the lambda Repressor Jmol14 (Java) |  JSMol  (HTML5)

Jmol: Updated  helix-loop-helix (EF hand) from calmodulin   Jmol14 (Java) |  JSMol  (HTML5)

Figure:  beta-hairpin, or beta-beta (image made with VMD)


  Jmol: Updated  beta-hairpin from bovine pancreatic trypsin inhibitor   Jmol14 (Java) |  JSMol  (HTML5)     

Figure:   Greek Key Motiff

Jmol:  Greek Key

Figure: beta-alpha-beta (image made with VMD with H atoms added by Molprobity

 Jmol: Updated  beta-helix-beta motif from triose phosphate isomerase   Jmol14 (Java) |  JSMol  (HTML5)

Domains -

Domains are the fundamental unit of 3o structure. It can be considered a chain or part of a chain that can independently fold into a stable tertiary structure. Domains are units of structure but can also be units of function. Some proteins can be cleaved at a single peptide bonds to form two fragments. Often, these can fold independently of each other, and sometimes each unit retains an activity that was present in the uncleaved protein. Sometimes binding sites on the proteins are found in the interface between the structural domains. Many proteins seem to share functional and structure domains, suggesting that the DNA of each shared domain might have arisen from duplication of a primordial gene with a particular structure and function.

Evolution has led towards increasing complexity which has required proteins of new structure and function.  Increased and different functionalities in proteins have been obtained with additions of domains to base protein.  Chothia (2003) has defined domain in an evolutionary and genetic sense as "an evolutionary unit whose coding sequence can be duplicated and/or undergo recombination".  Proteins range from small with a single domain (typically from 100-250 amino acids) to large with many domains.  From recent analyzes of genomes, new protein functionalities appear to arise from addition or exchange of other domains which, according to Chothia, result from

Structural analyses show that about half of all protein coding sequences in genomes are homologous to other known protein structures.  There appears to be about 750 different families of domains (i.e small proteins derived from a common ancestor) in vertebrates, each with about 50 homologous structures.  About 430 of these domain families are found in all the genomes that have been solved.   


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Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.