This course will allow you to learn concepts about protein structure, in addition to the importance of proteins in a lipid environment for all those transmembrane proteins, you will do exercises to insert the protein into the membrane and run a dynamics of a system with these characteristics in addition to analyzing your results such as RMSD, Rg, RMSF, non-covalent protein interactions, conformational changes, etc.

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TEMARY

Unit I: Basic concepts about proteins and membranes (3 hours)

1. Biomolecules

   1. Importance of membranes as biomolecules

   2. Importance of proteins as biomolecules

   3. Properties and classification of amino acids

   4. Structural levels of proteins

   5. Structure and function relationship in proteins

1. Protein structural determination methods

   1. Structural determination methods

      1. X-ray crystallography 

      2. Nuclear magnetic resonance 

      3. Cryo-electro microscopy.

      4. Installation of VMD, NAMD and CARMA (asynchronous)

Unit II: Molecular Dynamics of transmembrane proteins (6 hours)

1. Application of molecular dynamics for the study of biomolecules

2.   Concepts on molecular dynamics

   1. Definition of molecular dynamics

   2. Methodology overview

   3. Force field and parameters

   4. Algorithms

   5. Periodic conditions

   6. Temperature and pressure controls

Unit III: Introduction to molecular dynamics programs

1. NAMD

2. Amber

3. Gromacs

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1. NAMD as a molecular dynamics package

   1. NAMD Overview

   2. Generation of the simulation system

      1. Analysis of the initial structure

      2. System load neutralization

      3. Solvation of the simulation system

      4. Establishment of the simulation routine

      5. Description of the phases of a simulation algorithm

      6. Generation of input files (inputs) for the simulation

      7. Run DM simulation with NAMD on your computers (continue asynchronous)

Unit IV: Analysis of molecular dynamics (6 hours)

1. Simulation analysis with Carma

2. Introduction to Carma

   1.   Description of an input file

   2. Calculation and analysis of root mean square deviation (RMSD)

   3. Calculation and analysis of radius of gyration (RG)

   4. Calculation and analysis of mean square fluctuation (RMSF)

   5. Structure grouping

   6. Calculation and analysis of principal components (PCA).

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