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Related links:
Streifzug durch die Energielandschaft der Proteine
Group description
The Computational Molecular Biophysics (CMB) group, formerly known as
Biocomputing, was established in October 1998.
The group performs modeling and simulation of biomolecular systems
at atomic detail.
It consists of several subgroups:
- A "physics" subgroup
examining basic questions such as the nature of internal motions
in proteins, and protein solvation.
- A "biochemistry" subgroup, led by
Dr. Stefan Fischer, interested in
enzyme reaction mechanisms, ligand binding, ion pumping, and
large-scale conformational changes in proteins.
- An "application" subgroup involved in
various projects such as fluoresence spectroscopy, AIDS vaccine design,
and membrane protein structure.
- In the period 2000-2003, a "bioenergetics"
subgroup concentrated on molecular electrostatics, protonation
states, and quantum chemistry; this group has moved
to the University of Bayreuth
in October 2003.
Research activity
The current projects involve research initiated and performed at
the CMB as well as in national and international collaborations
with industry and universities.
Physics
Keywords: protein vibrations and hydration; neutron and X-ray scattering;
protein glass transition; enzyme dynamics and activity.
| Hydration
- Exploration of the relationship between
the water structure around a globular protein and the electrostatic field
and topography of the protein surface.
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| Dynamics
- Correlation between the glass transition
observed in proteins and their function. Hydration water may play a decisive
role in activating functional motion in the protein core. The transition
temperature from glass to liquid state in internal protein motions and
the associated scattering are timescale dependant.
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Keywords: protein folding; enzyme reaction mechanism;
large-scale conformational pathways;
muscle contraction; ligand binding; proton and chloride pumping.
| Folding
- Investigation of the backbone torsional angle distribution on protein
folding, progress of a denaturation of a globular protein by molecular
dynamics simulations, and kinetics of salt-bridge formation.
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| Ligand binding
- Theoretical and experimental determination of the contribution of
vibrational entropy changes to ligand binding. Development of reliable
computational methods for accurate predictions.
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| Retinal proteins
- Molecular dynamics and Quantum mechanics studies on the mechanism of
proton transfer in bacteriorhodopsin and on chloride transport in
halorhodopsin. Free energy simulations of the configurational
equilibrium of the retinal chromophore.
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| Large-scale conformational changes
- Large conformational changes are investigated by determining the low-energy
pathways between two end-states. The method used can also be applied
to the study of translocation mechanisms of long sugar chains in the
maltoporin channel and proton or chloride pumping accross a membrane.
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Application
Keywords: force-field parameterization; protein and membrane
dynamics; peptide stability; drug-design.
| Applications include various studies such as:
peptide structure in a membrane environment, homology modelling of a
G-coupled receptor, fluorescence quenching applied to cancer biotechnology,
peptide simulations targetted at AIDS vaccine development.
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Bioenergetics
Keywords: proton uptake mechanism; protonation states; proton
transfer chains; channel hydration; membrane proteins; continuum
electrostatics.
| Computation of protonation states and redox
equilibria in proteins and study of the related electrostatic effects.
Coupling between electron transfer and conformational changes in the
photosynthetic reaction center. Studies of proton transfer mechanisms
using continuum electrostatics models.
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