Study of Triptofan cage folding using Molecular dynamics simulation

Proteins are the most important group of bilogical molecules which usderstanding the relation between their structure and functions is the subject of many theoretcial and experimental studies. By using the computer simulations we can obtain useful information about the microscopic beghaviour of these materails. One of the most important properties of proteins is their folding and unfolding in different medias. Tryptona cage (TC5B) is a simple protein with 20 amino acids which is a suitable candidate for studying the protein folding. The native structure of TC5B, includes different elements of secondary structure, α helix from residue of 2 to 9 and 10 3 helix from residue of 11 to 15 and cage-like structure ( hydrophobic core) around the residue of Trp6, witch have been formed from the N terminal of polypeptide.