Basics of Protein Structure
From Proteopedia
Proteins perform many important functions in living organisms, including movement, immune responses, sensing the environment, energy acquisition, and catalyzing reactions. The protein shown to the right is insulin; when insulin isn't properly synthesized or recognized, diabetes occurs. Proteins are long chains of Amino Acids, and are synthesized by the ribosome, using messenger RNA as a template. There are 20 amino acids commonly found in proteins. contain an , a central carbon atom called the , and a . The 20 amino acids differ by what is attached to the central atom; is variable portion is referred to as the . The amino acid shown is alanine; its side chain is a methyl (-CH3) group. The atoms are displayed using the coloring convention Carbon, Hydrogen , Oxygen, Nitrogen: C, H, O, N. Proteins are sometimes compared to , where each amino acid residue is a bead. These long chains form complicated structures that allow them to perform their function. Even small alterations in any level of the structure can change how the protein does its job, and can lead to diseases. Levels of Protein StructureThere are four different levels of protein structure. The is the amino acid sequence. The amino acids are connected by an amide bond, made from the amino group (NH2) of one amino acid, and the carboxylic acid (C=O) from another amino acid. In the process of making the bond, a water molecule is removed. The amino acids are linked in a repeating pattern. The backbone of the protein is the repeating pattern, with the projecting out from the backbone. The end with the free -NH2 group is called the Amino or , while the end with a free carboxylic acid is called the . The sequence of amino acids is written and numbered from the N terminus (where protein synthesis begins) to the C terminus (where amino acids are added during protein synthesis), so for , the sequence would be Val-Asn-Gln, or VNQ, if one letter abbreviations are used for the amino acids. For more practice identifying peptide bonds between amino acids, please try Peptide tutorial 1 part 1 and Peptide tutorial 1 part 2. The second level of structure is called secondary structure, and is the shapes (conformations) formed by short sequences of amino acids. This level of structure is stabilized by along the backbone. Hydrogen bonds are attractions between an N, O or F and a hydrogen attached to an N, O or F (More about hydrogen bonds.) The two most common shapes are alpha helices and beta strands. These are favored simply because two atoms cannot occupy the same space (steric collisions). Protein Structure DataThe World Wide Protein Data Bank (WWPDB) is where all experimentally-determined published protein structures are made freely available. Each model has a unique accession code, called a PDB code. One model of human insulin, shown at right has the PDB code 3i40. Many examples are illustrated in the Atlas of Macromolecules. Looking for a model of a specific protein? See Is there an empirical model? After you find a PDB code of interest, see Introduction to molecular visualization. Further ReadingFor a more in depth discussion of protein structure, see Introduction to protein structure
| |||||||||||
