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Molecular Dynamics

Prof. Martin Zacharias

Research Field

The function of proteins and nucleic acids in living systems is strongly coupled to the molecular motion and dynamics of these biomolecules. Our group uses computer simulation methods to study the structure, function and dynamics of biomolecules. Our goal is to better understand structure formation processes and to elucidate the mechanism of ligand-receptor association in atomic detail. As the main computational technique we employ Molecular Dynamics simulations based on a classical force field to follow molecular motions including the surrounding solvent and ions. This allows us to extract thermodynamic and kinetic properties of the biomolecular system using methods of statistical mechanics. We also develop computational docking approaches to predict how proteins interact with other proteins or RNA and DNA molecules or how small drug-like compounds bind to biomolecular targets.

Address/Contact

Ernst-Otto-Fischer-Straße 8/I
85748 Garching b. München
+49 89 289 12393
Fax: +49 89 289 12444

Members of the Research Group

Professor

Office

Scientists

Students

Other Staff

Teaching

Course with Participations of Group Members

Titel und Modulzuordnung
ArtSWSDozent(en)Termine
Continuum Mechanics
eLearning-Kurs
Zuordnung zu Modulen:
VO 4 Reif, M. Zacharias, M. Mo, 14:00–16:00, PH HS2
Di, 08:00–10:00, PH HS2
Quantum Mechanics of Molecular Systems
eLearning-Kurs LV-Unterlagen
Zuordnung zu Modulen:
VO 2 Scherer, P. Do, 10:00–12:00, PH 2271
Seminar zu aktuellen Themen der molekularen Biophysik
Zuordnung zu Modulen:
PS 2 Zacharias, M. einzelne oder verschobene Termine
Exercise to Continuum Mechanics
eLearning-Kurs
Zuordnung zu Modulen:
UE 2 Burger, L. Kienlein, M. Mirzapour, F. Quoika, P. Sustay Martinez, C. … (insgesamt 6)
Leitung/Koordination: Zacharias, M.
Exercise to Quantum Mechanics of Molecular Systems
Zuordnung zu Modulen:
UE 2 Scherer, P.
FOPRA Experiment 74: Molecular Dynamics (AEP, BIO)
aktuelle Informationen
Zuordnung zu Modulen:
PR 1 Chen, S. Zschau, R.
Leitung/Koordination: Zacharias, M.
Praktikum Biophysik für Studenten der Biochemie
eLearning-Kurs LV-Unterlagen
Zuordnung zu Modulen:
PR 4 Bausch, A. Dietz, H. Lieleg, O. Rief, M. Simmel, F. … (insgesamt 7) Mi, 08:00–13:00, CPA EG.006A
Repetitorium zu Seminar zu aktuellen Themen der molekularen Biophysik
Zuordnung zu Modulen:
RE 2
Leitung/Koordination: Zacharias, M.

Offers for Theses in the Group

Computer simulation of the binding of peptides to RNA
RNA molecules are involved in many processes in cells. Typically, these processes involve the interaction with proteins and peptides. There are specific short peptide segments that often mediate the interaction between proteins and RNA. In the BSc thesis project the binding of short tripeptides with a central Arginine residue (often part of RNA binding peptides) and RNA will be studied using Molecular Dynamics simulations. Aim is to identify and characterize the preferred binding sites on the RNA molecules. It is hoped that it will allow the prediction of how and where larger proteins (that contain such short RNA binding motifs) bind to RNA molecules.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Martin Zacharias
Molecular simulation of amyloid structure folding
Natural proteins typically form stable globular structures. However, approximately 30% of natural proteins do not adopt a single stable structure but adopt a so called disordered state. Disordered proteins but also mutated globular proteins can aggregate to form regular amyloid structures. Such structures are involved in many diseases. In the BSc-project a computational methodologyto predict the amyloid structure of protein sequences will be developed and tested. The method is based on including information extracted from known amyloid structures to guide molecular dynamyics simulations.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Martin Zacharias
Studying amyloid flexibility using MD simulations
Amyloid structures can form by aggregation of misfolded protein molecules or peptides. These aggregates are involved in several diseases. The various amyloid structures differ in the conformational flexibility and stability. Very flexibile amyloid structures are more likely to disaggregate and can be recognized and eliminated by proteases and immune molecules. Aim of the BSc thesis is to investigate the conformational flexibility and dynamics of different amyloid structures using computer simulations and to understand the physical origin of the dynamics of amyloid structures.
suitable as
  • Master’s Thesis Biophysics
Supervisor: Martin Zacharias

Current and Finished Theses in the Group

The effect of mutations in the Translocator protein 18kDa (TSPO) on ligand binding studied with alchemical free-energy calculations
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
Computer Simulation of the Binding of Arginine-Rich Peptides to RNA
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
Studying amyloid deformability using MD simulations
Abschlussarbeit im Masterstudiengang Physik (Biophysik)
Themensteller(in): Martin Zacharias
Untersuchung der Ligandenbindung an die kleine Furche der DNA durch Moleküldynamiksimulationen
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
Stability of Collagen Fragments studied by Molecular Dynamics Simulations
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
Advanced sampling of protein-protein complexes
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
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