Max Planck Institute of Biophysics
Yearbook entries

Have you ever pulled a loop out of entangled cables, resulting in even more knots? A true safeguard in our body, the protein Smc5/6, can do this without creating an inextricable mess. It helps to store our meter-long DNA free of knots in the tiny nuclei of our cells and to maintain the integrity of our genes by forming DNA loops. If Smc5/6 makes a mistake, our genetic material can be damaged. Such defects can lead to rare hereditary diseases, developmental disorders or cancer. Understanding how Smc5/6 functions helps us to identify new target points for medical therapies.

As control units of our cells, nuclei contain and guard our genetic material. Pores in the nuclear membrane form the only gateway in and out of the nucleus, allowing important messenger molecules to pass but blocking dangerous invaders such as pathogens. They thus help the nucleus to communicate with the rest of the cell while protecting the genetic material. Such challenging task requires a complex biological structure that has kept many scientists occupied for over two decades; a jigsaw puzzle with missing pieces that we could now solve to near completion.

Single-particle electron cryo-microscopy (CryoEM) is ideal for determining the high-resolution structure membrane protein complexes that are too unstable or too dynamic for x-ray crystallography. Intact rotary ATPases have resisted crystallization for more than 40 years. However, central aspects of their mechanisms now have become clear thanks to the recent CryoEM based structures of intact, functional ATP synthases. The two best and most informative of these structures, the chloroplast ATP synthase and a mitochondrial ATP synthase dimer, have been shown by our department.

Flavin-based electron bifurcating (FBEB) enzyme complexes play a vital role in obligate anaerobic microorganisms for increasing the efficiency of their energy metabolism. They drive an endergonic reduction by an exergonic one via the same electron donor. The energy coupling is realized by a reduced flavin which transfers via energy splitting one strongly and one weakly reducing electron to two different substrates. How FBEB enzyme complexes are structurally constructed is outlined using the example of two acyl-CoA dehydrogenase/electron-transferring flavoproteins.

Living cells are coated and structured by lipid membranes. We addressed two important questions: how are membranes shaped into their often unusual forms, and how do cells monitor the membrane state? With molecular and coarse-grained simulations, we could show how the proteins Mga2 and Ire1 can sense the state of the endoplasmic reticulum. Also, new insights have been obtained about the fusion of vesicles, the formation of tubular structures in the endoplasmic reticulum, and the induction of autophagosomes aided by the Atg1 complex.

We determined the structure of a complete, dimeric F₁F_o-ATP synthase from mitochondria of the yeast Yarrowia lipolytica by a combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography. The structure resolves 58 of the 60 subunits in the dimer. Horizontal helices of subunit a in F_o wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Our data explain the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology.

Molecular oxygen appeared in the atmosphere about three billion years ago. Nature developed two membrane integrated enzymatic systems which reduce oxygen to water and use the energy of this reaction to produce biologically important energy carriers. These enzymes are the haem-copper terminal oxidases, e.g. cytochrome c oxidase, and the bd oxidases. The atomic structures of representative members of both enzyme families were determined. These evolutionary unrelated enzymes apparently use the same mechanisms to conserve energy and to prevent the formation of toxic reactive oxygen species.

Molecular simulations allow us to study the functional mechanisms of biomolecules. Thanks to their enormously detailed description, by resolving the motion of every atom, such simulations help to interpret complex experiments. Simulations also allow us to venture into areas which are difficult to access by experiments, such as the detailed characterization of enzymatic reaction mechanisms. Moreover, by “watching proteins at work”, new and fundamental processes can be discovered by using molecular simulations.

At fertilisation, we get one set of chromosomes from each parent and, in general, pass on either the paternal or the maternal allele of each gene with equal frequency to our children. This has been taught by Mendel. According to Richard Dawkins’ hypothesis, however, there are selfish genes which are not content with random selection and thus actively promote their increased transmission to the next generation. Evidence for this assumption comes from a mouse gene that is transmitted at a frequency of up to 99% from males to their offspring.

The solution of many medically important aspects depends on the prediction of the behaviour of complex networks, e.g. biological networks active within a tumor but also in other tissues of a patient under complex conditions, for example a particular therapy. So far, it is not possible to predict the success of a specific therapy for a specific patient. We are sequencing the genome of individual cancer patients as well as the genome and transcriptome of their tumor as a basis of a virtual-patient-model, used to predict effect and side effects of specific therapies on the individual patient.

The Department elucidates the structure and function of membrane proteins as well as macromolecular protein complexes by using electron microscopy, x-ray crystallography, biochemical and biophysical methods. It consists of a group lead by director Werner Kühlbrandt and project groups operated by Janet Vonck and Özkan Yildiz. Thomas Meier and Daniel Rhinow run two independent research groups. Christine Ziegler, now appointed as professor at the University of Regensburg, is still associated with the Department. Here, we present current data and results from all over the Department’s research.

The scientific focus of the research group lies on the systematic analysis of the modulation of gene and protein expression. This process can be specifically influenced by the interaction of genes and natural products, which are e.g. derived from food. We analyse if and by which mechanisms natural products interfere with genes or gene products. The interdisciplinary approach comprises basic and applied research. The results can be useful for optimised application of natural products to improve various metabolic processes.

For more than 15 years, genome research has looked for clinically relevant genetic risk factors for common diseases, with meagre results. Now rare disorders come into focus of genome research worldwide. Scientists at the Department of Human Molecular Genetics have successfully dealt with rare genetic disorders for many years. Since the introduction of novel, affordable sequencing techniques it has become possible, in principle, to elucidate the molecular causes of all single gene disorders, with far-reaching consequences for diagnosis, prevention and therapy.

Isoprenoids are involved in vital processes of all organisms. Their biosynthesis proceeds via two C₅-building blocks, which are produced dependent on the organism either by the mevalonate- or the desoxyxylose (DOXP) pathway. The DOXP pathway is used by various human pathogens but not by man and therefore provides an attractive target for anti-infectious agents, e.g., against malaria and tuberculosis.

Late onset neurodegenerative disorders are progressive disorders, which usually strike during mid-age of affected individuals and with age result in profound neuronal degeneration. Even though these diseases are quite common worldwide, the mechanisms responsible for their pathogenesis are, in most cases, poorly understood, and effective preventative therapies for these devastating disorders are currently not at hand.

The new field of optogenetics describes mainly the use of the light-gated ion channel, Channelrhodopsin 2 (ChR2) and of the light-driven Cl-pump Halorhodopsin (NphR) for stimulation and silencing of neurons simply by light in cultured cells as well as in brains of living animals. In order to increase the possibilities of application we have focused our research to develop new and improved tools.

Give me five, high five, hello and good bye - all shown to others with one hand. Certainly everyone knows that this hand comprises five digits. But not everyone is born with exactly five digits. In humans, occasionally hereditary skeletal limb malformations do occur. One malformation, the so-called synpolydactyly, implies that patients are born with additional digits, and those are fused above all. This phenotype develops due to a mutation within the Hoxd13 gene, leading to a lack of retinoic acid and thereby causing uncontrolled cartilage production at wrong sites in the extremity.

Systematic protein interaction studies are an important part of functional genomics research. A powerful method to decipher protein-protein interaction networks is the yeast two-hybrid system that allows studying the possible interaction of billions of protein pairs. Resulting interactions are represented in protein networks which provide a framework for a systems understanding of the molecular biology of the cell and contribute to medical practice, facilitating identification of human disease genes and an improved interpretation of patient samples and records.

The research of the Department of Structural Biology focuses on understanding the structural basis of membrane transport and biological energy conversion at the highest possible level of detail. The main methods are crystallography of membrane protein crystals (2D and 3D), single-particle cryo-EM and electron cryo-tomography (cryo-ET) of biological membranes. With few exceptions, all membrane proteins for crystallography, as well as membranes or organelles for tomography are produced within the group.

The development of computational models for biological processes opens the possibility to predict new effects of virtual targeted perturbations that can in turn be validated by experimental observations. Such predictions are highly relevant for many practical applications, for example the development of new drugs. Through the last years, the Bioinformatics group has been developing different tools, methods, and databases that support the computational modeling of biological processes, such as the pathway integration database ConsensusPathDB and the modeling system PyBioS.

The huge amount of DNA sequence data derived from a multitude of species, which is at our disposal today, allows comparative studies of genome evolution. Such studies afford to trace back the evolution of genomic DNA sequences and to single out and study the processes that play an important role in changing and shaping the genomes of mammals. The interaction of these processes with other cellular operations is now being investigated and better understood.

Remote control of neural cells by light by means of the light-gated cation channel Channelrhodopsin2 (ChR2) and of the light-driven Cl^- pump Halorhodopsin (NphR) fulfils a long lasting desire of neurobiologists. With this method neurons in culture as well as in the brain of living animals can be activated or inactivated at different wavelengths of the exciting light in a non invasive, electrode free manner with high temporal and even more important with an up to now unknown spatial resolution. This new technique has set the basis for the fast developing field of optogenetics.

The central topic of the Bioinformatics / Structural Proteomics group is the analysis and prediction of protein structures via networks. Methods are developed to reconstruct the 3D structure from such networks with the aim to identify the determining contacts in these structure networks. This interdisciplinary work provides potential application in protein and drug design.

Mesoderm formation is an important process of embryonic development. It plays an essential role in trunk formation and organ development in mammals. It is controlled by several interacting signalling pathways, which also play an important role in tumour progression. Novel methods are utilized for deciphering the complex regulatory networks comprising thousands of gene products, which control mesoderm formation in the embryo and in tumours.

In the mouse, the sense of smell (olfaction) is mediated by more than 1200 odorant receptors (ORs), the largest gene family in the genome. These ORs are G-protein coupled receptors. Every olfactory sensory neuron (OSN) in the main olfactory epithelium is thought to express just one OR gene, from one allele. Axons of OSNs that express the same OR coalesce into the same structures in the olfactory bulb, termed glomeruli, where they form synapses with second-order neurons in the olfactory pathway.

Molecular approaches reveal components and mechanisms of cellular stress sensing and adaptation. In addition, mathematical modeling has proven to foster the understanding of some basic principles of signal transduction and signal processing as well as of sensitivity and robustness of information perception and cellular response. Main modeling principles are exemplified here for a model organism, the yeast Saccharomyces cerevisiae.

After the finalization of the human genome project, investigations into the transcriptome, proteome, and metabolome have been largely increased, since their concurrence determines the functionality of genes. In this context, recent mechanistic discoveries have induced a kind of “paradigm shift” regarding the mode of action of hormones and widened our understanding of these compounds in cell and gene regulation, particularly when involved in human diseases.

The atomic structures of a bacterial succinate:quinone oxidoreductase and of mechanistically interesting variants have been determined by X-ray crystallography. Together with complementary functional studies, these results have yielded unequivocal evidence for a novel type of essential transmembrane proton transfer driving transmembrane electron transfer in this protein complex.

1. Variants of the mitochondrial cytochrome bc₁ complex created by site-directed mutagenesis produce deleterious oxygen radicals, which are implied in aging processes and pathophysiological conditions. 2. The regulation of the cellular ion composition by sodium-proton-antiporters is essential. The first atomic structure of such a transporter was determined and a mechanistic model for regulation and transport developed.

The research group Development & Disease focuses on the molecular basis by which form and structure of the skeleton are regulated during vertebrate development. Our approach combines research on human genetic disorders with gene function analysis in vitro and in animal models. The studies are carried out in close collaboration with the Institute of Medical Genetics at the Charité, Berlin. Recent advances in the identification and functional analysis of human gene mutations have provided new insights into the biology and pathology of limb malformations and, in particular, in the mechanisms of joint formation. Genetic screens have identified a large number of novel genes that are currently investigated for their role in normal bone development, in disease, and during the regeneration of bone and cartilage.

Ribosomes translate the genetic DNA information into the amino-acid sequence of proteins and are one of the most complicated structures of the cell. High resolution methods such as X-ray analysis and cryo-electron microscopy as well as improved functional methods have led to a quantum leap in our understanding of the mechanisms of the ribosome by deducing functionality from structure.

In recent research the Department of Structural Biology at the Max Planck Institute of Biophysics addressed membrane transport proteins from thermophilic archaea, which are more robust than their eukaryotic counterparts yet often quite similar to them, and thus serve as good models for medically relevant systems. They determined the structure of a signaling protein that regulates nitrogen uptake in archaea and bacteria in three different states, which helped them to elucidate the regulatory mechanism. Furthermore they investigated pH- and ion-induced conformational changes that accompany activation and ion transport in sodium-proton exchange proteins, and in the outer membrane porin OmpG from E. coli.

Transcription factors play a central role for the regulation of genes. The Department of Computational Biology at the MPI for Molecular Genetics utilizes a panel of mathematical methods to analyze function and interaction of transcription factors in order to achieve new insights into gene regulation.

Thanks to the sequencing of the human genome, we have access to detailed and extensive information about the complexity of biological processes. The comparison of the human genome with the chimpanzee genome leeds to a better understanding of molecular processes. This will set up a basis for the advancement of new medical diagnostics and treatments.

Phototaxis and photophobic responses of the green alga Chlamydomonas reinhardtii are mediated by microbial rhodopsins with the chromophore retinal. Sequence comparison with other microbial rhodopsins from archaea as the light-driven proton pump bacteriorhodopsin and the light-driven chloride pump halorhodopsin showed an overall homology of 15 to 20 % of those two algae chromoproteins. It is equally important that the N-terminal half approximately 300 of 712 and 737 amino acids, respectively, comprises seven hypothetical transmembrane helices as it is typical for rhodopsin-like proteins. Morover, several of the amino acids are conserved, which define the retinal binding site as well as the H⁺ -transporting pathway in bacteriorhodopsin. Recently, we demonstrated that two of these retinal-binding proteins from the eyespot of the alga, which we named channelrhodopsin-1 and -2 (ChR1 and ChR2), showed channel activity, directly activated by light when expressed in oocytes from Xenopus laevis or HEK 293 cells. ChR1 is selective for protons, whereas ChR2 is also conductive for monovalent and divalent cations. For both proteins the N-terminal hydrophobic half is sufficient to enable light-gated channel activity, demonstrating that the seven transmembrane helix motif represents a new class of ion channels.

Mental retardation is the biggest unsolved problem of Medical Genetics and a major burden for Health Care. Most severe forms of mental retardation are due to chromosome aberrations and gene defects, but so far, only a small proportion of these defects is known. For the mapping and identification of the relevant genetic factors we employ four different complementary strategies: i. investigation of patients with balanced chromosome rearrangements; ii. development and application of methods for high-resolution detection of unbalanced changes in the DNA; iii. systematic search for mutations in families with X-linked mental retardation; and iv. mapping of autosomal recessive gene defects by identifying homozygous genome segments in children of consanguineous parents. During recent years we have already identified numerous molecular causes of cognitive disorders. The characterization of these genes promises major progress for the diagnosis and prevention of mental retardation as well as new insights into normal and disturbed brain development and function.

The development of the body anlage with its organs is controlled by a multitude of complex regulatory mechanisms which follow a strict order. On top of these processes is the formation of mesenchyme, an event with similarities to metastasis formation of tumors. Novel methods are utilized to unravel regulatory networks controlling mesenchyme formation and tissue differentiation.

The one-carbon (C₁) carrier tetrahydromethanopterin (H₄MPT), that non-covalently binds as cofactor to proteins, became more and more important in the last years, as it was discovered in several phylogenetically distinct microorganisms where it plays a pronounced role in the C₁ metabolism. Interestingly, its structure is highly similar to that of tetrahydrofolate (H₄F), the most universal C₁ carrier in biochemistry, but most likely H₄MPT and H₄F were separately developed within a convergent evolutionary process. The mode how H₄MPT binds to enzymes was recently established on a structural level for two systems that will be introduced.

The Department of Structural Biology at the Max Planck Institute of Biophysics focuses on the structure and molecular mechanisms of membrane transport proteins. The structures of membrane proteins purified from natural sources or expressed in suitable host organisms are determined by electron microscopy or x-ray crystallography. The 2.5Å x-ray structure of the plant light-harvesting complex LHC-II reveals the mechanism of photoprotection and a likely pathway for dissipating excess solar energy. A three-dimensional map of a neuronal ion channel, determined by single-particle electron microscopy, shows the position of the alpha and beta subunits in the functional assembly. The 8Å map of the bacterial protein translocase SecYEG in the membrane shows how the structure adapts to the early steps of protein translocation. Structural studies of the protein translocase from outer and inner membranes of mitochondria reveal a twin pore. Two-dimensional crystals of various secondary transporters show different arrangements of membrane-spanning helices, indicative of different transport mechanisms.