R440, Astronomy-Mathematics Building, NTU
Speaker(s):
Luigi Catacuzzeno (University of Perugia)
Organizer(s):
Tai-Chia Lin (National Taiwan University)
Tzyy-Leng Horng (Feng Chia University)
This course is cancelled.
Schedule:
10:20-11:10 Lecture I
11:10-11:20 break
11:20-12:10 Lecture II
12:10-13:10 lunch
13:10-14:00 Lecture III
14:00-14:10 break
14:10-15:00 Free discussion
Title:
Understanding a Protein Three-dimensional Structure and Letting It Move with Molecular Dynamics
Abstract:
Nowadays the three dimensional structure of more and more proteins is becoming available at few Angstroms resolution. In the meantime, the growing computational power allows the prediction of atom dynamics for very large systems, such as a protein and the surrounding water. This scenario opens the possibility to apply physical laws in order to deeply understand the relationship existing between the chemical structure of a protein and its biological function. In this tutorial the basics of protein structure will first be reviewed. The chemical and physical properties of the twenty naturally occurring aminoacids will be presented, and how aminoacids assemble to form proteins having complex shapes will be discussed.
We will then describe how to use freely available software to read and visualize a 3D protein structure, and to perform on it simple molecular dynamics simulations, in order to understand its movement at the picosecond timesclales. At the end of the tutorial, the student will be able to look at the details of a protein three-dimensional structure, visualize and understand the relevant properties of the structure, such as the presence and location of electric charges on it, and finally to setup simple molecular dynamics simulations.
