Basic Principles of Protein Structure, Structural Levels, Protein Databases and Other Internet Resources

Short introduction
Protein structures contain four levels of complexity. Each level has its own characteristics, and all levels are related to each other and depend on each other, together creating an extremely complex network of interactions between hundreds and thousands of atoms packed according to certain rules into an entity we call a tertiary protein structure. The first level of a protein structure is built up by the 20 amino acid residues, arranged in a protein sequence, which essentially determines how the polypeptide chain will be folded, how the secondary structure elements will be arranged in space and create protein motifs, how they interact with each other, etc. The simplest folded unit of a protein structure is a domain. Some proteins contain one single domain while others may have several domains. Protein domains are classified into protein folds, basic structural units. However, domains with the same fold may or may not be related evolutionary, even though their tertiary structures are similar. These folds are classified in protein structure classification databases, which I will discuss in this part of this course. Specific issues will also include protein secondary structure, Ramachandran angles the Ramachandran plot, protein motifs, protein fold and fold classification. There is also a tutorial on the use of the major protein structure-related databases and the information that can be retrieved from these databases.
In the introduction I will discuss the basic ideas, the 4 levels of protein structure, the types of amino acid residues and the different roles they play in the protein tertiary structure:
Introduction
Amino acids

Secondary structure, torsion angles and the Ramachanran plot
Here I discuss the next level of protein structure, the secondary structure, their characteristic features and the forces that stabilize them. I will also discuss one of the main charateristics of the local environment of amino acids in a protein structure, the torsion angles, also called Ramachandran angles, and the Ramachandran plot with its charachteristic features and their relation the secondary structure elements of proteins:
Helices & sheets
Torsion Angles and the Ramachandran plot

Protein motifs, folds and domains
In this section I will discuss the next level of complexity in a protein structure, the secondary structure motifs, the typical ways by which secondary structure elements can be arranges in space. These arrangements are found in all protein families. However, I should note here that the presence of similar motifs in different protein families is not necessarily a result of evolutionary relationships. I will also discuss protein fold and the basic folding unit in proteins, protein domains.
Protein motifs
Protein Folds
Protein Domains

Protein databases, overview of protein databank files
Here I will give an introduction to the major protein structure databases and the way I usually use them. The number of databases presented here is not large, but from teaching experience I find that it is better to keep this number limited in the beginning to give the students the opportunity to get acquainted with the major ideas and resources. You may always find other resources on the Internet, when you know what you are looking for:
Protein Databases
Protein DataBank Files