Home page of Aldo Jongejan

You probably had expected some kind of company behind a internet domain like "www.molmod.nl". However, it is just the home page of some geeky person having spend much of his time doing molecular modeling and computational chemistry. And when a webdomain with your first name is already occupied, you start looking at alternatives....

So, what can you expect here?

Well, some things about my past and present research and maybe in the future some more private things, I find interesting and might be of interest to other people as well.


My interest is in the fundamental understanding of biomolecular interactions and their effect on the function of proteins. During my Ph.D. research, although the title Computational Chemistry of PQQ and QH-ADH would suggest otherwise, I have combined both computational and wet chemistry experiments to elucidate the substrate binding properties and reaction mechanism of the enzyme QH-ADH. I have come to appreciate computational chemistry and molecular modelling as additional tools in unravelling protein structure-function relations.

Already before the completion of my thesis, I moved to the group of Prof. Leurs (section Medicinal Chemistry, VU Amsterdam) to investigate the ligand-receptor interactions of biogenic amine GPCRs. Homology models of these GPCRs have been derived from the crystal structure of rhodopsin and validated using MD simulation techniques (both in vacuum and in a lipid bilayer) and incorporation of both bioinformatics and experimental data. The electronic and conformational properties of the ligands have been investigated using advanced conformational search techniques and high-level quantum-mechanical methods. For this purpose, I have initiated extensive collaboration with the groups of Prof. Pardo (UAB, Barcelona, Spain) and Dr. Lloyd (Trinitity College, Dublin, Ireland).

Other research topics include docking of ligands into proteins (chemokine receptors, nicotinic acetylcholine receptors), calculation of ligand binding affinities, and calculation of reaction mechanisms. This integrative approach has been successful in unravelling the early steps of the activation mechanism of biogenic amine GPCRs and has led to publication in a prestigious journal, invited lectures and poster prizes.

Allthough there was enough exciting work to be done, it was decided that after 7.5 years of service it was time for me to move on. Since August 2007 I am teaching bioinformatics at the Hogeschool Leiden. Here I am part of an enthousiast team of experts providing the new generation of bioinformaticians with up-to-date knowledge of biology, chemistry and programming skills. We have established collaborations with many renowned institutes in the Netherlands. The first graduates of our education have obtained have performed outstanding work at these institutes resulting in publications in good journals.

Within the Hogeschool I have joined the readership Innovative Molecular Diagnostics headed by dr. Willem van Leeuwen (ERASMUS MC) to initiate collaborative projects between students of the Hogeschool, academia, medical centra and various companies. The aim is to establish a link with the field of activity and bring state-of-the-art knowledge to the students and teachers. Within this readership we have been succesful in high-throughput sequencing and assembly of a fungus, Madurella mycetomatis, responsible for devastating illnesses in Africa. Furthermore, a new project has started on the fast typing of bacteria responsible for sepsis using spectroscopic techniques. In this project, I supervise students in building a database and analysis tools using the obtained spectra. We collaborate with River Diagnostics, MicroDish and the ERASMUS MC.


Activation of a GPCR