Our main aim is to develop and apply computer-aided methods to model, simulate and predict how biomolecules interact. The
focus is on the interactions of proteins. The methods make use of
three-dimensional macromolecular structures and combine approaches based
on physicochemical principles with those of chemo- and bio-informatics. Some Recent Stuff:
Structure, February 2012: Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex. Plants and bacteria assimilate sulfur into cysteine. Cysteine biosynthesis in plants is regulated by formation of the Cysteine Synthase complex (CSC), by Serine-Acetyl-Transferase (SAT) and O-Acetyl-Serine-(Thiol)-Lyase (OAS-TL) enzymes. In the CSC, one active site of the homodimeric OAS-TL is occupied by SAT. To understand the loss of OAS-TL activity in the plant CSC, we explored the flexibility of the second, unoccupied, active site of A. thaliana cytosolic and mitochondrial OAS-TLs. The results reveal two gates in the OAS-TL active site that show allosteric closure in the CSC, which can hinder substrate binding and its turnover to cysteine (see Feldman-Salit et al.).
Cover Picture, PLoS Comput. Biol., August 2011: The membrane-bound cytochrome P450 2C9 in action.
A
model of the full-length, membrane-bound human cytochrome P450 2C9, an
enzyme essential for drug metabolism in the human liver, derived using
an approach that combines coarse grained and atomic resolution molecular
simulations (see Cojocaru et al., 10.1371/journal.pcbi.1002152).
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Structure-based Drug Design
BioRN, LIGHTS, PPIMarker
COMBINE analysis
Systems Biology
SysmoLAB, Virtual liver
Sycamore
Bio- and Nanotechnology
PROSURF
Enzyme redesign
Simulation methods
Brownian dynamics simulation of diffusional association (SDA)
Random acceleration molecular dynamics simulation of ligand egress from proteins (RAMD)
Structural Bioinformatics
Protein Interaction Property Similarity Analysis (PIPSA)
Molecular visualization and analysis (MolSurfer, ProSAT, ProSAT2, DSMM)
page last modified: 22.03.2012,10:22
Project Manager
Prof. Dr. Rebecca Wade Email:
Phone: +49 (0)6221 - 533 - 247 Fax: +49 (0)6221 - 533 - 298 more >>
Structure, February 2012
