Postdoc and PhD positions

Saskia M. van der Vies vdvies at chem.vu.nl
Thu Jul 6 07:24:40 EST 2000


4 POST-DOCTORAL FELLOWSHIPS AND  4 Ph.D. STUDENTSHIPS

The Vrije Universiteit (VU) has recently embarked on a university-wide
initiative to develop research and education in areas related to
Beta-Complexity. The goal of this initiative is to develop new
interdisciplinary research and education programmes aimed at studying the
complexity of biological systems and will include the areas of Biology,
(Bio) Chemistry and (Bio) Physics. As part of the VU initiative, a new
Centre of Complex Molecules (CCM) will be established in which the areas of
Biochemistry, Molecular Toxicology, Applied Spectroscopy and Computational
Chemistry are brought together. The multidisciplinary programme entitled
"Chemistry of Complex Molecules" is aimed at studying the underlying
mechanism of protein folding and enzymatic catalysed biotransformation with
a focus on the dynamic behaviour of proteins. The programme involves both
theoretical as well as experimental approaches including molecular dynamics
(MD and QM/MM), computational modelling, fast laser fluorescence and Raman
spectroscopy (FRET, TRRS and T-jump) and protein structure/function
analysis.

The Vrije Universiteit (VU) is a medium size, modern and actively growing
university with 15 000 students and more than 2000 scientific staff
members. The university is situated in the lively and cosmopolitan area of
Amsterdam with easy access to all parts of The Netherlands and Europe. The
Faculty of Sciences supports a variety of research programmes in
(Bio)-Physics, (Bio and Pharmaco)-Chemistry, Mathematics and
(Bio)-Informatics. Undergraduate programmes in Physics, Informatics,
Mathematics, Artificial Intelligence in Physics, Informatics, Mathematics,
Artificial Intelligence, Pharmaceutical Sciences, Chemistry and Medical
Life Sciences and more than thirty specialised graduate programmes are
available. For general information please visit <www.few.nl> and
<www.chem.vu.nl>.


We are looking to recruit 4 Ph.D. Students and 4 Post-Doctoral Fellows

Post-Doctoral position in Biochemistry  (4 years)
Prof. S. M. van der Vies, Prof. C. Gooijer and Dr. H. van Heerikhuizen
The project focuses on the molecular mechanism by which the molecular
chaperones GroEL/Gp31 facilitate the folding of the bacteriophage T4 capsid
protein.  In particular it concerns a study of the dynamic interactions of
the three proteins using FRET spectroscopy as well as classical molecular
biochemical methods. Successful candidates should have a PhD in
Biochemistry or Molecular Biology, practical experience with all major
molecular genetic and biochemical techniques. Knowledge of spectroscopy is
a distinct advantage.

Post-Doctoral position in Molecular Dynamics  (2 years)
Prof. N. P.E. Vermeulen, Prof. S. M. van der Vies and Dr. A. M. ter Laak
The project focuses on structural and conformational dynamics of GroEl/Gp31
molecular chaperone system and Cytochromes P450 using 'classical' molecular
dynamics (MD) simulations like AMBER and/or GROMOS MD as well as less
CPU-intensive methods such as the novel CONCOORD method (or 'Essential
Dynamics'). Coordinates obtained from homology models and/or (partial)
X-ray crystal structures will be starting points for the MD calculations.
Predicted conformational changes will be experimentally validated by FRET-
and T-jump and time-resolved Resonance Raman Spectroscopy. Successful
candidates should have a PhD in computational (medicinal) chemistry or
protein chemistry.

Post-Doctoral position in Spectroscopy (2 years)
Prof. C. Gooijer, Prof. S.M. van der Vies and Dr. G. van der Zwan
The project involves the development of fast triggering techniques to study
protein (re)-folding and protein-ligand interactions on time scales shorter
than 1 microsecond. A tuneable picosecond pulsed laser system with high
repetition rate and a fast gatable CCD camera will be used to monitor
time-resolved fluorescence and Raman scattering. Successful candidates
should have a PhD in biochemistry or physical chemistry. Practical
experience in the field of time resolved laser spectroscopy and an interest
in (bio)-physical systems is a distinct advantage.

Post-Doctoral position in Computational Chemistry (2 years)
Prof. K. Lammertsma , Prof. N.P.E. Vermeulen and Dr. A. W. Ehlers
The project involves modelling of the Cytochrome P450 catalytic cycle.
Multi-layered Quantum Mechanics (QM), Molecular Mechanics (MM) and
Molecular Dynamics (MD) will be used in order to model structural,
electronic, and spectroscopic properties of the metallo porphyrin core of
cytochrome P450. Emphasis will be on establishing sensitivities between the
ab initio, semi-empirical, and molecular mechanics layers using ADF, G98,
PM3, and MM. Successful candidates should have a PhD in computational
chemistry with experience in ab initio methods.


Ph.D. Positions (4 years)

Project 1
Expression and dynamics analysis of human Cytochrome P450s
Prof. S. M. van der Vies , Prof. N.P.E. Vermeulen and Dr. J.N.M. Commandeur
In this project selected human Cytochrome P450 isozymes will be purified
from overexpressing E. coli cells. Moreover, site-specifically mutated and
fluorescently labelled cytochrome P450 isozymes will be generated and
characterised enzyme kinetically and structurally. Conformations and
dynamics of the purified cytochromes P450 will be determined using a
combination of several techniques such as
fluorescence-resonance-energy-transfer (FRET) spectroscopy, T-jump- and
time-resolved Resonance Raman Spectroscopy.
Background of applicants: molecular biology, protein biochemistry, drug
metabolism.

Project 2
Computational Modelling of the Cytochrome P450 catalytic cycle
Prof. K. Lammertsma , Prof. N.P.E. Vermeulen and Dr. A. W. Ehlers
The project involves optimisation of Fe-porphyrin geometries with different
electronic states, H-bonding sites, and O2 and substrate interactions using
QM/MM methods.  The dependence of the role of the transition metal on the
heme and enzyme conformation is an important facet in studying P450's
catalytic role. Interactions with the molecular dynamics studies of this
programme are important.
Background of applicants: computational chemistry

Project 3
Fast folding events
Prof. C. Gooijer, Prof. S.M. van der Vies and Dr. G. van der Zwan
The project concerns a study of fast dynamic conformational changes of the
capsid protein bacteriophage T4 using time--resolved fluorescence (FRET)
spectroscopy, in combination with fast triggering techniques. The capsid
protein will be tagged with various fluorescence dyes  (in vivo and in
vitro labelling) in order to monitor FRET changes in the protein with the
aim to characterise the folding pathway. Practical experience in the field
of protein spectroscopy and/or labelling techniques will be a distinct
advantage
Background of applicant: (Bio) Chemistry, (Bio) Physics

Project 4
Time-resolved resonance Raman Spectroscopy of complex molecules
Prof. C. Gooijer, Prof. N.P.E. Vermeulen and Dr. G. van der Zwan
The aim of this project is to study the electron transfer dynamics of
cytochrome P450. Changes in the oxidation state of the central Fe atom are
reflected in the vibrational fingerprint of the heme, and of separate
fluorescent labels built in the protein. This will be used in combination
with modelling techniques to obtain information about the electronic
structure of the heme, and to monitor local changes upon alteration of the
oxidation state. Practical experience in the field of protein spectroscopy
will be a distinct advantage.
Background of applicants: (Bio) Chemistry, (Bio) Physics

Please contact Professor Saskia M. van der Vies for detailed information,
email: vdvies at chem.vu.nl or telephone +31 (0)20 4447548 or the secretary,
Mrs. L. de Wit email: FAR at chem.vu.nl or telephone +31 (0)20 4447600.
Postdoctoral candidates are expected to work independently, to have good
supervisory and communication skills and to have published in high impact
molecular/biochemical/biophysical/computational journals. The period of
employment will be for the indicated time period and includes a salary of
Dfl 5205 - 6581 per month. Ph.D. students are expected to participate in
the teaching of undergraduates. The period of employment will be 4 years,
including an incrementing salary starting at Dfl 2398 (first year) to Dfl
4077 (final year) per month.
Interested candidates should state clearly what position they are applying
for and send a curriculum vitae, a summary of research experience and the
names of two references to:  Ms. R. Pereira, Head of personnel department,
Faculty of Sciences, de Boelelaan 1081a, 1081 HV Amsterdam, The
Netherlands, or alternatively by email to mpereira at few.vu.nl

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Dr. Saskia M. van der Vies
Professor of  Biochemistry
Head of Department of Biochemistry and Molecular Biology
Faculty of Science
Vrije Universiteit
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

Phone:	+ 31 20 4447548 (office)
	+ 31 20 4447555 (secretary)
FAX:	+ 31 20 4447553
email:	vdvies at chem.vu.nl
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