Molecular Modeling of Proteins and Biomolecules

Hydrophobic hydration of heme

2010-11-06T20:54:00.000-07:00

In this video the hydration of the heme in water is shows. The oxygens and hydrogens of the water are represented in red and gray color respectively. The surfaces represent the probability to find the atom and are related to the region of hight density. We found densities about four times the water density (at normal condition), its is consequent of the hydrophobic effect and accommodations not tetrahedral.

How to analyze the AutoDock results?

2009-08-10T15:26:00.000-07:00

In this video we show the analysis of the output of the AutoDock program.
Showing the secondary structure of the protein, the grid used in the rigid docking calculation and the two predominant conformations of the ligand in the binding site.
This work was developed by Teobaldo Cuya (PUC-Rio, Brazil.2009)

Molecular dynamics of the human serum albumin with two docked Protoporphyrins IX

2009-08-08T18:02:00.000-07:00

This is an interval of the trajectory of a molecular dynamic simulation of the human serum albumin with two docked Protoporphyrins IX. This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009)

Second binding site of the Protoporphyrin IX in HSA

2009-08-08T16:24:00.000-07:00

Using docking (AutoDock) and molecular dynamics (Gromacs ) in a simulation of 10 ns, we found the possible second binding site of this porphyrin. There are experimental information about the existence of this site, but their position in the protein is not determined. With this simulation we proposed this position (article in progress to be publicate). This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).

Parametrization necessary to model a molecule

2009-08-05T14:24:00.000-07:00

This video was made in the LMDM (Laboratorio de Modelagem e Dinamica Molecular) of the IBCCF (Instituto de Biofisica Carlos Chagas Filho da UFRJ.

Electrostatic Surface of the Human Serum Albumin

2009-08-04T13:52:00.000-07:00

We obtained the electrostatic surface using the PMV program with the aproximation Poisson-Boltzman. This surface was obtained at the end of 20 ns MD with the albumin docked with two protoporphyins IX (PPIX). As we can observed the second site of the of the PPIX molecule is localized in the central region. This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).

Firts principal component of the human serum albumin in a molecular dynamics of 100 ns.

2009-08-01T12:28:00.000-07:00

In order to make an analysis of relevant motions in the protein, we need to eliminated the no relevant motions (rotation + translation). With this filtered trajectory we make a diagonalization of the covariance matrix (matrix of the fluctuations), obtained the corresponding eigenvectors and eigenvalues. These relevant motions has biological importance in the bind and liberation of molecules.
The eigenvectors are the main motions and the corresponding eigenvalues are the amplitude of these motions. The first eigenvector has the more biggest contribution to total motion.
Here we show the first eigenvector of the human serum albumin in aqueous medium. This result was obtained from a molecular dynamics of 100 ns (using Gromacs). This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).