I am a biochemist turned structural bioinformatician turned experimental synthetic biologist, or something like that. Through all these twists, my long-term research interests have been dealing with the interplay of protein dynamics, function and interactions. At present, I try to recombine modular domains into synthetic proteins and artificial protein "circuits". Such tightly controlled systems could become a perfect playground for untangling the complexities of molecular and cellular dynamics.
For my thesis, I examined different processes that put proteins on the edge of moving from one global state to another. For most of their time, proteins wiggle their atoms around some equilibrium average structure. But, when the action is on, at the moment of mechanical stress, binding, or [insert your process of interest] these benign structure fluctuations can, as I showed, turn into major forces. In a first example, our study of spectrin repeats described how structural flexibility in single repeats might eventually contribute to the elasticity of red blood cells. My research then focused on the interplay between structural dynamics and protein-protein recognition and, again, structural fluctuations turned out to be a major factor for the specificity and stability of protein-protein complexes. (Recent experimental studies are now beginning to corroborate our computational results).
I also dedicate some (sometimes perhaps too much) time on infrastructure projects:
- Biskit, a python platform for structural bioinformatics
- Open source biobrick management
- Serrano lab wiki
- Standardization in Synthetic Biology
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postdoc (2006-2010) |
|---|---|
| Protein Synthetic Biology | |
| ongoing... | |
| Poster | HFSP Fellows meeting, Tokyo, June 2009 |
| Abstract | Can synthetic proteins and sophisticated protein circuits be built from standard parts? Can we decompose dynamic protein networks into re-usable devices? What are the best strategies and methods for protein systems engineering? These are some of the questions that I have been working on since switching back to the wet lab bench. Despite all their complexity (see my previous projects below), I think that proteins are, in fact, a very good material for systems engineering. A focus on modular protein-protein interactions may be our best starting point for the manipulation of natural and the design of synthetic protein networks. In a proof-of-concept study, we have constructed 25 synthetic two-domain proteins from BioBrick-formatted standardized "parts", purified many of them and characterized different combinations of interaction input and output "devices" biophysically (using FRET and surface plasmon resonance). Our parts are (/will be) available for free re-use from the Registry of Standard Biological Parts and a growing list of protocols is maintained on OpenWetware. |
| Paper |
Grünberg R, Ferrar T, van der Sloot A, Constante M, Serrano L (2010)
Building Blocks for Protein Interaction Devices. Nucleic Acids Research in press.
Grünberg R, Serrano L (2010): Strategies for Protein Synthetic Biology. (review) Nucleic Acids Research in press. |
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postdoc (2007-2009) |
|---|---|
| (Voronoi-) Shelling of Protein Interfaces | |
| Collaboration with Frederic Cazals (INRIA Sophia-Antipolis), Benjamin Bouvier (CNRS Lyon) and Michael Nilges (Institut Pasteur) | |
| Abstract | Protein-protein interfaces are, traditionally, defined by different "ad-hoc" criteria such as atom contacts or changes in surface areas. However, these descriptions are rather arbitrary and complicate the systematic comparison of protein interface architectures. We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets (VSO) as a novel measure for an atom's depth inside the interface. VSO can predict the solvent exchange in different interface regions, that is, the occurence of "dry" or "wet" residues. In fact, the seemingly complex water dynamics at protein interfaces appears largely controlled by geometry. Also the sequence conservation and residue composition of interfaces is often "radially" structured. Voronoi Shelling Order thus reveals clear geometric patterns in protein interface composition, function and dynamics and facilitates the comparative analysis of protein-protein interactions. |
| Paper |
Bouvier B*, Grünberg R*, Nilges M, Cazals F (2009):
Shelling the Voronoi interface of protein-protein complexes
reveals patterns of residue conservation, dynamics, and composition.
Proteins 15;76(3):677-92.
[Abstract] (* shared first co-authors) |
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PhD project (2001 - 2005) |
|---|---|
| The dynamics of protein-protein binding | |
| Institut Pasteur, Paris | |
| Talk | Protein flexibility and entropy on the edge of binding (International Biophysics Congress, August 2005, Montpellier) |
| Poster | Conference on "Modeling of Protein Interactions in Genomes", June 2003, Stony Brook, New York; June 2005, Kansas |
| Abstract |
The interplay between protein-protein binding and structural dynamics
is poorly understood. We selected a set of 17 protein-protein
complexes for which the three-dimensional structures of both free
components and the complex are available. Based on the analysis of
molecular dynamics simulations in explicit water for each of these 51
systems, we find: (1) most uncomplexed binding sites are more flexible
than the remaining surface; (2) as expected, they loose conformational
freedom upon complex formation; (3) however, in the majority of cases,
binding does not restrict the overall motion of proteins. We
calculated the change in conformational entropy from longer
simulations on 7 complexes (21 systems) using a new method based on
quasiharmonic analysis. Two small complexes and an antibody-antigen
system exhibited a significant loss whereas three larger complexes
showed increased or unchanged conformational entropy. Molecular fluctuations excert important influence both on the speed of recognition and the stability of protein complexes. Structure dynamics may be the missing link in our understanding of this fundamental process. This is the largest study so far on the influence of complex formation on protein flexibility and conformational entropy. |
| Paper |
Grünberg, R., M. Nilges, J. Leckner (2006):
Flexibility and entropy in protein-protein
binding. Structure 14(4), 683-93
[PDF] |
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PhD project (2001 - 2004) |
|---|---|
| A model of flexible protein-protein recognition | |
| Institut Pasteur, Paris | |
| Talk |
Complementarity of structure ensembles in protein-protein
binding
(CECAM workshop on "Flexible Macromolecular Docking", April 2004, Lyon) |
| Abstract |
Protein-protein association is often accompanied by changes in
receptor and ligand structure. This interplay between protein
flexibility and protein-protein recognition is currently the
largest obstacle to our understanding and also to the reliable
prediction of protein complexes. We performed two sets of
molecular dynamics simulations for the unbound receptor and
ligand structures of 17 protein complexes and applied
shape-driven rigid body docking to all combinations of
representative snapshots. The cross docking of structure
ensembles increased the chances to find near native
solutions. The free ensembles appeared to contain multiple
complementary conformations. These were in general not related
to the bound structure. We suggest that protein-protein
binding follows a three-step mechanism of diffusion, free
conformer selection and folding. This model combines
previously conflicting ideas and is in better agreement with
the current data on interaction forces, time scales, and
kinetics.
|
| Paper |
*Grünberg, R., *J. Leckner, M. Nilges (2004): Complementarity of
structure ensembles in protein-protein
binding. Structure 12, 2125-2136. [PubMed]
[pre-print] (with minor differences)
(* shared first co-authors)
Comment by M. Eisenstein in the same issue: Introducing a 4th dimension to protein-protein docking. [PDF] Quote of our model in a commentary by Boehr and Wright in Science: How do proteins interact? |
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PhD project (2002 - 2004) |
|---|---|
| CROW - A data integration platform for the semantic web | |
| Institut Pasteur, Paris | |
| Talk | Crowsing the semantic web (Journee bioinformatique, February 2004, Institut Pasteur) |
| Poster | Pacific Symposium on Biocomputing, January 2004, Hawaii |
| Abstract |
Crow (Computational Representation Of Whatever) is a
(alpha-stage) Java library for an anarchist approach
to data integration (i.e. link whatever you want
whenever you want to whereever you want). The library
is tailored (but not restricted) to the work with
semantic web documents. It allows the mining and
manipulation of distributed, heterogeneous,
chaotically cross-linked data. The design is
multi-threaded, event-based, and supports plugins and
third-party data types. It containes a simple Python
(Jython) interface for interactive
work.
The library is freely available under the GPL.
We currently use it to select targets for
protein-protein docking from sets of predicted protein interactions
and various other information.
SourceForge project... |
| Paper | I somehow never got to publish this...but the code is on sourceforge and well documented. If anybody wants to join me converting this into a Python library... send me an e-mail ;-) |
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PhD project (warm up) (06/2000 - 12/2001) |
|---|---|
| The dynamic topology of spectrin repeats | |
| EMBL, Heidelberg and Institut Pasteur, Paris | |
| Talk | Stretching a molecular shock absorber
(Congress des jeunes chercheurs, 18/06/2003, Institut Pasteur) |
| Poster | Gordon conference on "Protein folding dynamics", January 2002, Ventura, U.S. |
| Abstract |
Spectrin repeats are triple-helical domains found in many
proteins that are regularly subjected to mechanical stress. My collaborators
studied the behavior of a wild-type spectrin repeat and
two mutants with atomic force microscopy. I interpreted the results
of these single molecule experiments with steered molecular dynamics
simulations. The experiments indicated that spectrin repeats can form
stable unfolding intermediates when subjected to external forces. In
the simulations the unfolding proceeded via a variety of
pathways. Stable intermediates were associated to kinking of the
central helix close to a proline residue. A mutant stabilizing the
central helix showed no intermediates in experiments, in agreement
with the simulations. Simulations and experiments hence suggest a "hyphenation
point" within the domain and hint at the existence of force-resistant
intermediates with non-native topology. The simulations also explained the
broad variance of experimental unfolding lenghts. The combination of both
effects would allow for a smooth and elastic response to external forces
over a wide range of extensions. Spectrin molecules seem to be optimized for
elasticity on all scales of their molecular architecture.
|
| Paper | *Altmann S.M., R. *Grünberg, P.F. Lenne, J. Ylänne, A. Raae, K. Herbert, M. Saraste, M. Nilges, J.K. Hörber (2002): Pathways and intermediates in forced unfolding of spectrin repeats. Structure 10, 1085-1096. [PubMed] (* shared first co-authors) |
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Diploma Project (03/99 - 10/99) |
|---|---|
| Rational Design of Trypsin Variants for Peptide Synthesis | |
| University of Leipzig, under the guidance of Dr. Frank Bordusa | |
| Talk | Hacking Trypsin (given on June 25st 1999 in Leipzig) |
| Abstract |
Based on their catalytic mechanism it is possible to employ serine proteases like
trypsin for enzymatic peptide bond formation. Especially, substrate mimetics -
a new class of artificial substrates, allow for efficient ligations of amino acid
derivatives and peptides, as Bordusa et al. demonstrated in recent years.
However, if product or starting material contain specific cleavage sites recognised
by the protease, this ligation is counteracted by the (natural) proteolytic reaction.
A promising approach to overcome this problem is the direct manipulation of the enzyme's natural specifity. I prepared and isolated two variants of rat-trypsin with altered S1-binding pocket (D189A and D189A/S190A). The proteins were examined by HPLC-based acyl-transfer experiments revealing promising catalytic properties as well as an impaired specifity towards natural trypsin and chymotrypsin substrates. Parallely, I employed the program AutoDock to simulate the binding of several substrates to the altered enzymes in silico. With these docking studies I could elucidate, in part unexpected, experimental results on a structural basis. |
| Paper | Grünberg, R., I. Domgall, R. Günther, H.-J. Hofmann, and F. Bordusa (2000): Peptide Bond Formation Mediated by Substrate Mimetics: Structure-guided Optimisation of Trypsin for Synthesis. Eur J Biochem 267(24), 7024-30. |
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4th-year-project (02/98 - 06/98) |
|---|---|
| Analysing the adc promoter in Clostridium beijerinckii with the gusA reporter gene |
|
| University of Wales, Aberystwyth, under the guidance of Dr. Adriana Ravagnani and Prof. Michael Young | |
| Talk | A reporter gene for Chlostridium (given in April 1998 in Aberystwyth) |
| Abstract | I introduced ß-D-glucuronidase (gusA) of Escherichia
coli as reporter gene in Clostridium beijerinckii, so far lacking a
versatile reporter system, by constructing
the promoter probe vector pRGus. This vector was
employed to evaluate the significance of three putative "OA box" sequence motifs within
the promoter of the acetoacetate decarboxylase gene (adc) in vivo.
I fused the adc promoter, as well as a variant with destroyed OA boxes,
to the gusA gene in pRGus and introduced them into C. beijerinckii
by electroporation. Preliminary tests revealed a high ß-D-glucuronidase (GUS) activity in transformants containing the wild type adc promoter compared with no detectable GUS activity in case of the construct with destroyed OA boxes. Since OA boxes are recognition sequences for the Spo0A transcription factor, these findings indicate that the expression of the adc gene is directly regulated by Spo0A. Acetoacetate decarboxylase is involved in the metabolic conversion of starches (and various other substrates) into commercially significant solvents like acetone and butanol. The gusA reporter gene will facilitate further investigation into the trancsiptional regulation of this pathway. |
| Paper | Ravagnani, A., K. C. B. Jennert, E. Steiner, R. Grünberg, J. R. Jefferies, S. R. Wilkinson, D. I. Young, E. C. Tidswell, D. P. Brown, P. Youngman, J. G. Morris & M. Young. (2000): Spo0A directly controls the switch from acid to solvent production in solvent-forming clostridia. Molecular Microbiology 37(5), 1172-85. |
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