Carsten Baldauf
last updated:
November 30, 2015

Contact Info

Dr. Carsten Baldauf
Scientist/Group Leader Bio Group

Theory Department of the
Fritz Haber Institute
Faradayweg 4-6
D-14195 Berlin-Dahlem, Germany
Phone: +49 30 8413 4836
Fax: +49 30 8413 4701
Email: baldauf[at]fhi-berlin.mpg.de

Vorlesungen an der FU Berlin /
Teaching at FU Berlin

Die beiden Vorlesungsseiten sind Passwort-geschützt.
The two lecture-related websites are password protected.

Atombau und chemische Bindung (PCII) (LV 21302 a/b).
Vorlesungsmaterialien finden sie hier.

Bioorganic chemistry II (LV 21223 a/b).
Slides and seminar dates for the lecture BOCII can be found here.

Research Interests

Structure formation in natural and non-natural peptides. Comparably short sequences of amino acids, peptides, form periodic secondary structures, e.g., like helices and strands, and aperiodic secondary structures, e.g., loops and turns. These building blocks form the tertiary folds of functional proteins. Thus, understanding the principles of secondary structure formation gives insight into fundamental biochemical processes.
Non-natural oligomers, a.k.a. foldamers, can adopt defined structural motifs and studying their folding can broaden our general insight into structure formation. Furthermore, such alternative backbones can have interesting properties: (i) Resistance to physiological degradation. (ii) Novel types of folds. (iii) Increased chemical space for side chain functionalities.

Carbohydrate structure from first principles. Carbohydrates are a challenging class of biomolecules in many aspects of analytical chemistry, structural biology, and molecular simulation. We identify at least three major problems that we have to solve to be able to routinely predict structures of complex carbohydrates: (i) The structure space of complex carbohydrates does not only consist of rotating single bonds at the glycosidic linkage, but also of the many possible ring-pucker types and local H-bonding networks. (ii) Deprotonated species are of particular interest for analytical approaches. Here the search space explodes due to high chemical similarity of the hydroxy groups and due to dynamically interconverting protomers. (iii) A reliable level of (first principles) theory has to be identified to describe the relative energetics of the conformers. We are working toward an implementation of first-principles search techniques for complex carbohydrates in Fafoom and toward a conclusive assessment of the accuracy of first-principles methods in describing sugar structures.

The concept of landscapes in structural biology. The term fitness landscapes was first coined in the field of population genetics describing the different levels of fitness of individuals or sub-populations of a species with regards to an environmental condition. Similar descriptions can be employed to relate different folding states of a peptide or the binding modes of ligand-protein complexes. A first step towards the conformational energy landscape of a (bio)molecule is to find the minima on its potential-energy surface. We have developed Fafoom, a structure search tool that can be used with first-principles codes like FHI-aims.

Algorithms and energy functions for molecular docking. Molecular docking is a computational technique that aims at finding the native pose of a small-molecular ligand in the binding pocket of protein receptor. The resulting high-dimensional search problem can be solved by combining an energy function that describes the interaction with a global search approach, e.g., metaheuristics like genetic algorithms or particle-swarm optimizers. I am involved in the development of PARADOCKS, the parallel docking suite.

Protein mechanics of the von Willebrand factor. Von Willebrand factor (VWF) is a giant multimeric glycoprotein in human blood that plays a key role in primary hemostasis. Shear flow in blood induces a tumbling of VWF between a globular and an extended state. As a result, extensive mechanical force acts on the VWF monomers and the domains. This is the basis of VWF functional regulation; at a critical level of mechanical force, the opening of domain domain interfaces and the partial unfolding of individual domains results in distinct functional signals like the activation for blood clotting or for cleavage by a specific protease.


Further Information

Curriculum Vitae

Publications


Developed Software

Fafoom

PARADOCKS

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