Technical University of Munich
Lehrstuhl für Molekulardynamik (Prof. Zacharias)
Ernst-Otto-Fischer-Str. 8
85748 Garching b. München
Molecular Dynamics Simulation of Biomolecules
My research group uses computer simulation methods to study the structure, function and dynamics of biomolecules and large biomolecular complexes. As the main computational technique we employ Molecular Dynamics simulations based on a force field to follow molecular motions including the surrounding solvent and ions. It allows us to better understand the molecular details of structure formation processes of proteins and nucleic acids and to extract thermodynamics properties. We apply these methods to study enzymes, amyloid structures and protein-protein interactions.
Our main research areas are:
Journal of Chemical Information and Modeling
Abstract: Protein-protein interactions (PPI) play a crucial role in nearly all cellular processes, and their dysregulation often leads to diseases. Stabilizing rather than inhibiting PPIs by small drug-like…
Computational and Structural Biotechnology Journal
Abstract: Cathepsins are papain-like proteolytic enzymes localized in lysosomes and the extracellular matrix, where they participate in diverse physiological and pathological processes. They are synthesized as…
Journal of chemical information and modeling
Abstract: Glycosaminoglycans (GAGs) are long, anionic polysaccharides abundant in the extracellular matrix and lysosomes, where their electrostatic interactions with proteins are essential for biological…
Nature Communications
Abstract: During eukaryotic DNA replication initiation, inactive MCM2–7 double-hexamers assembled at replication origins must be converted into two active CMG helicases, yet how this transition is coupled to…
Virchows Archiv
Abstract: Small cell lung carcinoma (SCLC) is classically defined by biallelic inactivation of RB1 and TP53. However, a small subset of tumors retains Rb expression and exhibits distinct molecular features.…
Proteins: Structure, Function and Bioinformatics
Abstract: The control and modulation of protein–protein interactions (PPIs) is of central importance for the majority of biological processes and most biomedical applications. Stabilization of PPIs, besides…
Journal of Molecular Biology
Abstract: Cellular metabolic systems but also the extracellular environment can generate reactive oxygen species that lead to oxidation of methionine (MET) and interfere with protein folding and protein–protein…
Bioinformatics
Abstract: Motivation The rational design of chemical compounds that bind to a desired protein target molecule is a major goal of drug discovery. Most current molecular docking but also fragment-based buildup or…
Chemical Science
Abstract: DNA mimic foldamers are helically folded aromatic oligoamides bearing negatively charged side chains that mimic the shape and charge distribution of double-stranded B-DNA. They have been shown to bind…
Computational Modeling of Biomolecular Interactions
Abstract: Great progress has been achieved in recent years to accurately model the structure of protein-protein, protein-peptide, and also protein-RNA complexes. Without doubt, recent artificial…
| Title | Dates | Duration | Type | Lecturer (assistant) |
|---|---|---|---|---|
| Continuum Mechanics |
|
4 | VO | |
| Exercise to Continuum Mechanics |
|
2 | UE | |
| FOPRA Experiment 74: Molecular Dynamics (AEP, BIO) |
|
1 | PR | |
| Lab course biophysics for students of biochemistry |
|
4 | PR | |
| Revision Course to Seminar on current topics in molecular biophysics |
|
2 | RE | |
| Seminar on current topics in molecular biophysics |
|
2 | PS |