Protein Evolution

Andrei Lupas

Lupas portrait IMPRS 18
  • PhD in Molecular Biology at Princeton University, 1985-91
  • Postdoctoral training at the Gene Center of the University of Munich and at the MPI for Biochemistry, Martinsried, 1993-97
  • Senior Computational Biologist and Assistant Director of Bioinformatics at SmithKline Beecham Pharmaceuticals, 1997-2001
  • Director at the MPI since 2001

Research Interest

Proteins are essential components of all living cells. It is thus hardly surprising that precursors of most proteins observed today existed at the time of the last common ancestor of all life. How did they evolve? Randomly synthesized polypeptide chains form folded structures in less than one in a billion cases, so it seems impossible that proteins arose by chance. We have proposed that folded proteins evolved by fusion and accretion from an ancestral set of peptides active as cofactors of RNA-dependent replication and catalysis. Using bioinformatics, we have reconstructed this "vocabulary" of ancient peptides and are now exploring experimentally the processes by which it could have led to the emergence of folded proteins, using methods in biochemistry and structural biology (crystallography, NMR, cryo-EM).

We also study how changes in protein structure create new functionality, both by attempting to functionalize newly created proteins in vitro and by exploring structure-function relationships in natural proteins. In the latter, our particular focus is on signal transduction across membranes and cellular mechanisms for protein quality control. An essential aspect of our work is the development of new bioinformatic tools, which we deploy in our MPI Bioinformatics Toolkit (toolkit.tuebingen.mpg.de).

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Figure 1: A "vocabulary" of ancient peptides, reconstructed by sequence and structure comparisons of modern proteins. Peptides that interact with nucleic acids are highlighted yellow, with nucleotides blue, and with metals rose. Peptides that form folds by repetition are boxed.

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Figure 2: Model for the evolution of self-compartmentalizing proteases, exemplified by the proteasome. Extant protea- somes are shown at the bottom, the alpha subunits are outlined. An Anbu-type helical assembly is shown at the top.

Available PhD Projects

Project 1: Biochemistry and evolution of the proteasome system in prokaryotes (project leader Jörg Martin)

Project 2: Structure and mechanism of transmembrane signal transduction proteins (project leaders Andrei Lupas and Murray Coles)

Project 3: Origins and evolution of the cytoskeleton (project leader Felipe Merino)

Project 4: Mechanisms for the evolution of folded proteins from intrinsically unstructured precursor peptides (project leader Andrei Lupas)

Project 5: The relationship between sequence and structure in coiled-coil proteins (project leaders Andrei Lupas and Birte Hernandez Alvarez)

Project 6: New bioinformatic tools for protein sequence and structure analysis (project leader Vikram Alva)

Selected Reading

1) Alva V, Söding J, Lupas AN. (2015) A vocabulary of ancient peptides at the origin of folded proteins. eLife 4:e09410.

2) Fuchs ACD, Maldoner L, Wojtynek M, Hartmann MD, Martin J. (2018) Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system. Nature Commun. 9:2696.

3) Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. (2018) A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol. 430:2237-43.