Protein Evolution - Andrei Lupas
The Basic Building Blocks of Life
Proteins provide the chemical basis for all processes of life. We investigate their origin and the evolution of their folds and mechanisms of action by means of bioinformatics, biochemistry and sturctural biology.
Proteins are essential building blocks of all living cells. Indeed, life can be viewed as resulting substantially from the chemical activity of proteins. Because of their importance, it is hardly surprising that ancestors for most proteins observed today were already present at the time of the 'last common ancestor', a primordial organism from which all life on Earth is descended. How did the first proteins arise? How does their sequence of amino acids enable their chemical activity? These questions are at the centre of our scientific efforts at our Department of Protein Evolution.
Resources
Proteins are the most complex chemical structures found in nature. They have to fold into complicated three-dimensional structures in order to become active. This poses a particular challenge when it comes to explaining their origin from non-living matter.
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Departmental Research Groups
Group leader: Vikram Alva
Many proteins share detectable similarities in sequence and structure. Sequence-based comparison of modern proteins shows that they fall into only about ten thousand domain families
Group Leader: Yu-Chu Chang
We investigate the biophysical and biochemical properties of membrane proteins, focusing on their folding, stability, and function. We use a variety of techniques, including novel methods to study membrane protein stability and biochemical assays to characterize the function of bacterial proteins involved in virulence.
Group leader: Murray Coles
Our group concentrates on protein structure determination, with a special focus on proteins involved in transmembrane signaling.
Group leader: Stanisław Dunin-Horkawicz
We focus on the development and application of bioinformatics tools to study the function of protein-based systems from an evolutionary perspective. This approach allows us to describe present-day systems in the context of the evolutionary events that shaped them, to define their unique and conserved features, and to propose testable hypotheses.
Group leader: Marcus Hartmann
Our mission is to understand and manipulate macromolecular machines and systems.
Group leader: Birte Hernandez Alvarez
We study structure-function relationships in proteins from an evolutionary perspective.
Group Leader: Oliver Weichenrieder
‘Selfish’ RNA likely is at the origin of all life on earth and it persists today in the form of retrotransposons and RNA-based viruses. We study human LINE-1 and Alu RNAs and how these ‘molecular parasites’ copy their sequences into genomic DNA. We determine and interpret molecular structures combined with insight from biochemical approaches and cell-based assays.
Press releases & research news
Designing protein binders from scratch has long been a daunting challenge within the field of computational biology. Researchers have now developed an innovative, training-free pipeline that uses the fundamental principle of shape complementarity to design site-specific protein binders, which are then optimised to fit precisely onto chosen target sites. The researchers tested this on proteins linked to cancer, showing their ability to block tumour growth in animals. This discovery not only advances binder design but also enhances our understanding of protein folding and interactions at the molecular level.
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In a discovery that reframes our understanding of life’s fundamental organization, researchers have found that mechanical compression can induce the formation of tissue-like multicellular structures in archaea. This novel finding, focusing on the haloarchaeon
Haloferax volcanii, reveals a previously unknown pathway for the emergence of multicellularity within this domain of life, offering new insights into the evolutionary origins of multicellular complexity across all living organisms.
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A new family of protein-based antagonists has been created by researchers that efficiently block the granulocyte-colony stimulating factor receptor (G-CSFR), which is essential for the development of leukaemia and other inflammatory illnesses. This groundbreaking work paves the way for targeted therapies that could revolutionise treatment options for patients suffering from these conditions.
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The Damietta Toolkit is a web-based toolkit to accelerate and simplify protein design without needing powerful computers or extensive protein design expertise on the user’s end. The toolkit benefits its users with multiple design tools, fast analyses, easy interpretation, and downloadable results. Their framework, published in Nucleic Acids Research, offers a comprehensive resource for biological research community.
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Molecular structures and functions of the human LINE-1 Reverse Transcriptase (a.k.a. L1ORF2p) have now been unraveled in a massive international collaboration of groups from academia and industry, including the group of Oliver Weichenrieder from the Max Planck Institute for Biology in Tübingen. The results have been published in
Nature today.
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