Genome Analysis (B070)
Im Neuenheimer Feld 580
|Synthetic Biology and Systems
Biology have become key research areas in the quest for understanding
cells. What is missing is an experimental system in which the knowledge
system-wide analyses could be artificially reproduced and studied. Our
to create a mirror-image synthetic biology: that is, to mimic, entirely
independent of nature, a biological system and to re-create it from
Starting from enantiomeric L-nucleotides and
D-amino acids, we intend to use chemical synthesis to establish a
mirror-image biological system. Several basic DNA-DNA, DNA-protein and
protein-protein interactions as well as the functions of few enzymes
copied from nature into a totally synthetic artificial system based on
and D-proteins. This will require a few D-form enzymes and L-DNA
co-factors that would form a basic enantiomeric system. In addition,
binder molecules, such as nanobodies and DARPins, and transcription
the DNA-binding domains thereof, are generated and studied in
their natural partners. We actively pursue the production of molecules,
exhibit superior performance, by also modulating parameters such as
and aggregation behaviour. This is complemented by modelling so as to
define and predict structural feature that are critical for molecules'
activity. Next to the establishment of components
for artificial biology, there are immediate practical utilities that
at within this project, such as the protection of therapeutic binders
degradation as they will not be substrates of natural proteases,
oral application, for example.
In the long run, the objective is to
set up a self-replicating system, eventually including D-protein
While this is still some way off, it would offer a major advance in
Molecules produced in such a system could overcome several of the limitations that are currently still
of a fully synthetic mirror-image biological system (MirrorBio)
The basic motivation behind the project is the ambition
biological processes to an extent that will permit their re-creation.
ability would be documented best, if functioning molecular systems
established that are entirely independent of any natural compounds but
generated by initially only chemical
processes for the production of synthetic biomolecules and their
into artificial molecular systems. Also, artificial experimental
complement current Systems Biology,
evaluating biological models experimentally. Similar to what is ongoing
insight into cellular functioning will be gained by an iterative
information resulting from experimental and theoretical analyses.
this may lead to an archetypical model of a cell.
The project is performed as an EraSynBio consortium with partners from
three other institutions:
- Philip E.
Dawson, The Scripps Research Institute, USA
Plückthun, University of Zürich, Switzerland
Taipale, University of Helsinki, Finland
Hauser et al. (2006) Nucleic Acids Res. 34, 5101-5111.
Olea et al. (2015) Chem. Biol. 22, 1437-1441.
Weidmann et al. (2016) Org. Lett. 18, 164-167.
sequence and stability information for directing nanobody stability
Variable domains of camelid
heavy-chain antibodies, commonly named nanobodies, have high
potential. In view of their broad range of applications in research,
diagnostics and therapy, engineering their stability is of particular
Towards these ends, we analyzed the sequences and thermostabilities of
purified nanobody binders. From this data, potentially stabilizing
variations were identified and studied experimentally. Some improved
stability of nanobodies by up to 6.1°C, with an average of
2.3°C across eight
modified nanobodies. The stabilizing mechanism involves an improvement
conformational stability and aggregation behavior, explaining the
effect on individual molecules. Other potentially stabilizing
actually led to thermal destabilization of the proteins. The reasons
contradiction between prediction and experiment were investigated. The
illustrate the potential and limitations of engineering nanobody
thermostability from a medium-throughput data set and indicate
a species-specificity of nanobody architecture.
Kunz et al. (2015) BBA-Gen. Subjects 1861, 2196-2205.
Figure legend: Mechanism of
nanobody stabilisation by N-terminal
mutations (Q1E and Q5V). (A) The thermodynamic stability of nanobody
its N-terminally mutated variant was measured in guanidinium chloride
equilibrium unfolding experiments. Unfolded protein was measured by
tryptophan fluorescence. Red lines represent fitted curves. (B)
of thermostabilisation by single and double mutations in nanobody NbD4,
measured by differential scanning fluorimetry in triplicate.
mutations Q5V (0.9 °C) and Q1E (2.3 °C) match the stabilisation
in the double
mutant (3.1 °C). (C, D) Tryptophan fluorescence ratio (350 nm/330
melting nanobody NbD1 and its N-terminally mutated variant; in panel C,
concentration of 32.7 μM was used; in panel D, concentration was
13.1 μM. Aggregation is indicated by a reduced amplitude of the
transitions in the fluorescence traces and can be quantified by
values of both concentration sets. Heating rate: 0.5 °C/min.
Revised CHARMM force field parameters for iron-containing co-factors of
Photosystem II is a complex
protein–cofactor machinery that splits water molecules into molecular
protons, and electrons. All-atom molecular dynamics simulations have
potential to contribute to our general understanding of how photosystem
To perform reliable all-atom simulations, we need accurate force field
parameters for the cofactor molecules. We present here CHARMM bonded
non-bonded parameters for the iron-containing cofactors of photosystem
include a six-coordinated heme moiety coordinated by two histidine
a non-heme iron complex coordinated by bicarbonate and four histidines.
force field parameters presented here give water interaction energies
geometries in good agreement with the quantum mechanical target data.
Adam et al. (2018) J. Comput. Chem. 39, 7-20.
Figure legend: Cover image of the Journal of Computational Chemistry,
volume 39, issue 1, on 5 January 2018. It presents artwork that is
based on the results reported in the above mentioned publication.
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