Marcus Fändrich strengthens protein biochemistry at Ulm University
After quite a long vacancy, the director’s post of the Institute for Pharmaceutical Biotechnology at the University of Ulm has finally been filled. Marcus Fändrich, 41, and his team moved into the laboratories and offices of the new life sciences building on the Oberer Eselsberg Ulm University campus in November 2012.
Prior to becoming the head of the Institute for Pharmaceutical Biotechnology, Fändrich carried out research at the Max Planck Research Unit for Enzymology of Protein Folding in Halle. In addition, he also led a research group at the Leibniz Institute for Age Research in Jena. Fändrich fills a gap in the Ulm Bioregion’s biopharmaceutical education activities as he will not only be teaching biochemistry undergraduate students, but also master’s students on the pharmaceutical biotechnology course that is run in cooperation with Biberach University of Applied Sciences.
From protein folding to the elucidation of amyloid fibril structures
At the start of his scientific career, Fändrich was specifically focussed on the basic mechanisms of protein folding and misfolding, but has since shifted his research interest to amyloid fibrils and the elucidation of their structure. In some diseases (so-called amyloidoses), rather than folding into their native, three-dimensional structures, several amino acid chains come together, twist and eventually form insoluble protein aggregates known as amyloid fibrils. Such amyloid fibrils are the hallmark of Alzheimer’s and Parkinson’s, amongst other neurodegenerative diseases. Systemic amyloidoses that affect several peripheral organs (e.g. the heart, liver or kidneys) and often have a fatal outcome have been known since the 17th century.
After completing his biology studies at Heidelberg University, Fändrich went to Great Britain to do a biochemistry master’s degree at the University of Cambridge. His master’s degree thesis addressed aspects of protein folding, and his subsequent doctoral thesis at the University of Oxford focussed on finding the causes that prevented some proteins from adopting their correct three-dimensional structure, instead forming insoluble amyloids and protein aggregates. He was highly fascinated by the basic research-oriented approach which he had chosen to elucidate one of the major principles of life. Only correctly folded proteins are able to carry out their various tasks in the body. Failure to fold correctly leads to the loss of a major prerequisite for life, resulting in disease and premature death.
A new phenomenon of many proteins
“The basic mechanisms of the ‘normal process’ of protein folding are relatively well understood, at least in relatively simple proteins,” says Fändrich, explaining that the entire process of a simple amino acid sequence folding into a three-dimensional structure follows specific pathways during which characteristic intermediates are formed. During his doctoral studies, Fändrich came across a phenomenon that was later confirmed by numerous research groups: he tested a number of protein chains that were known for their inability to form amyloids and expected to be completely unsuitable for such a process. Fändrich put myoglobin, a prime example of a protein whose structure was the first to be deciphered, to the test. The protein, which is found in the muscle tissue of vertebrates, had properties that made it rather unsuitable for forming amyloids: an alpha helical structure, rather than a beta-sheet structure which is typical for amyloid-forming proteins, it was soluble and had a globular structure. Despite all this, Fändrich was nevertheless able to show that myoglobin was able to form amyloid structures in the test tube (Fändrich et al. Nature 2001).
Weaknesses of proteins
In 2001, Fändrich went to work at the Institute for Molecular Biotechnology (now Leibniz Institute for Age Research) in Jena where he was able to show that the formation of amyloid fibrils was due to the fact that polypeptides were indeed able to form both normal and abnormal, disease-causing protein versions. In the meantime, several hundred proteins that are able to form amyloid fibrils have been found, which gives reason to assume that amyloid formation is a fundamental process of almost all proteins.
In 2002, Fändrich was one of the winners of the BMBF’s BioFuture Award, one of the most prestigious prizes in Germany for up-and-coming scientists. The funds enabled him to study the structure and composition of disease-associated amyloid fibrils for five years. With the new focus, Fändrich moved away from his initial research work and started focussing on the Aβ (amyloid-beta) peptide, which is regarded as the hallmark of Alzheimer’s.
Difficult to study: the structure of the Aβ peptide
Aβ is processed from the larger transmembrane amyloid precursor protein (APP) which often occurs in the brain. Everybody has certain amounts of Aβ in the body, which is normally no problem at all as the peptide is continuously being degraded. Although APP and its degradation products are formed throughout a person’s lifetime, little is yet known about their physiological function.
Fändrich has spent quite a few years on research into the composition of Aβ fibrils to be able to shed light on their function. The fact that little is known is down to the fact that amyloid fibrils have a high molecular weight, cannot be crystallised and have heterogeneous structures which makes them unsuitable for investigations using classical protein structure analysis techniques (X-ray crystallography and liquid-state NMR).
New methods had to be developed in order to obtain a better understanding of the Aβ structures. Solid-state NMR spectroscopy and cryo-electron microscopy are two methods used for this purpose. Fändrich usually applies the latter. Cryo-electron microscopy is used to study samples at cryogenic temperatures (achieved by freezing them in liquid ethane). The use of liquid ethane causes the water to freeze without forming ice crystals, thereby retaining the sample’s biological structure. “The sample is a freeze image of a protein in its native environment and can thus be studied under an electron microscope,” Fändrich explains. Images are taken from different angles and used to create a 3D reconstruction of the sample under investigation.
With this method, Fändrich and Nikolaus Grigorieff, a German scientist who works in the USA and who has been working with Fändrich since his research stay in Cambridge, succeeded in elucidating the molecular architecture of amyloid fibrils associated with Alzheimer’s disease with a resolution of less than a nanometer, a hitherto unprecedented precision. Unexpectedly, the structure differed considerably from conventional structural models. “We believe that the basic unit of a fibril does not consist of a single U-shaped Aβ peptide. Instead, our investigations show that two juxtaposed Aβ peptide chains form the basic unit of a fibril and that mature fibrils consist of stacks of such units,” Fändrich says (Sachse, Fändrich, Grigorieff, PNAS 2008).
Complex process of fibril formation
Although the mechanism of fibril formation is not yet known in detail, Fändrich and other researchers around the world have now collected a vast amount of knowledge: the formation of amyloid fibrils is the result of a complex, multistep reaction of aggregation, which leads to the temporary stabilisation of a number of intermediates of different conformation. Different groups of amyloid intermediates have been identified, including non-fibrillar aggregates known as oligomers, as well as protofibrils and spherical aggregates. Each of these groups represents a number of different states and comprises numerous subgroups.
The assembly process leads to mature amyloid fibrils; they are straight and have a fairly uniform structure that is visible under the transmission electron microscope. Mature fibrils have a β-sheet structure that is characteristic of all amyloid filaments, whatever the appearance of their original polypeptide chains. Mature amyloid fibrils can be several micrometres long and ten to twenty nanometres thick. They are thus thicker than protofibrils which are usually less than ten nanometres thick (Fändrich, Cell. Mol. Life Sci. 2007; Meinhardt et al., J. Mol. Biol. 2009).
Aβ intermediates can already damage nerve cells
Meanwhile, there is increasing evidence that in the case of Alzheimer’s, Aβ oligomers damage the neural networks and synaptic plasticity at a fairly early stage, with the end point being reached with the death of the nerve cells (Fändrich, J. Mol. Biol., 2012). Using synthetic Aβ oligomers Fändrich and colleagues from the Leibniz Institutes for Age Research (Jena) and Neurobiology (Magdeburg) have recently come up with evidence that even low-molecular, loosely aggregated oligomers are able to damage the contact sites of neurons (synapses) (Haupt et al., Angewandte Chemie 2012).
It is not yet known whether one or several factors trigger the pathogenesis of Alzheimer’s; and the factors’ exact structures are not yet known either. However, the assumption that amyloid fibrils are the major culprit of amlyoid-associated neurodegenerative diseases seems to be obsolete (Fändrich, J. Mol. Biol., 2012).
In vivo results are still lacking
Despite all the knowledge that has been built up over recent years, fibril expert Marcus Fändrich remains cautious and points out that “almost everything that has been investigated with biochemical and structural imaging techniques is fibrils and aggregates that formed in vitro”. He therefore regards the discussions among experts about the possibility that major areas of body structures can be reconstructed in the test tube as “not entirely unjustified”. Although imaging methods have been developed that are able to demonstrate the presence of amyloid in living patients, Fändrich still finds it difficult to say whether this is really the case as long as details about the structures remain unknown.
Help for biomedical research groups
Fändrich will continue investigating the structures of amyloid fibrils in Ulm. He now plans to purchase a cryo-electron microscope in order to investigate the structure of many proteins other than those of amyloid fibrils. He hopes that these investigations will benefit biomedical research groups at Ulm University who do not have access to high-resolution protein structure investigation techniques. With the appointment of Marcus Fändrich, Ulm University now has a specialist in protein biochemistry, which basically links the university’s traditional biomedical research with the fields of chemistry and physics.
Fändrich M: Oligomeric Intermediates in Amyloid Formation: Structure Determination and Mechanisms of Toxicity, J. Mol. Biol., 2012, 421, p. 427-440; DOI: 10.1016/jmb.2012.01.006).
Haupt C, Leppert J, Rönnicke et al.: Structural Basis of β-Amyloid-Dependant Synaptic Dysfunctions, Angewandte Chemie, 51/7, 13.2.2012, p. 1576-1579 (DOI: 10.1002/ange.201105638)
Fändrich M, Schmidt M, Grigorieff N: Recent progress in understanding Alzheimer’s β-amyloid structures, Trends In Biochemical Sciences, 2011, 36(6), p. 338-345 (DOI: 10.1016/j.tibs.2011.02.002)
Meinhardt J, Sachse C, Hortchansky P, Grigorieff N, Fändrich M: Aβ (1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils, J. Mol. Biol., 2009, 386, p. 869-877 (DOI: 101016/jmb.2008.11.005).
Meinhardt J., Fändrich M: Struktur von Amyloidfibrillen, Der Pathologe, 2009, 30, p. 175-181 (DOI: 10.1007/s00292-009-1127-2).
Sachse C, Fändrich M, Grigorieff N: Paired β-sheet structure of an Aβ(1-40) amyloid fibril revealed by electron microscopy, PNAS, 2008, 105 (21), p. 7462-7466 (DOI: 10.1073/pnas.0712290105)
Fändrich M: On the structural definition of amyloid fibrils and other polypeptide aggregats, Cellular and Molecular Life Sciences. 2007 (64), p. 2066-2078 (DOI: 10.1007/s00018-007-7110-2)
Fändrich M, Fletcher M A, Dobson C M: Amyloid fibrils from muscle myoglobin, Nature 2001, 410, p. 165-166 (DOI:10.1038/35065514.)