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Juri Rappsilber

Co-workers:

Adam Belsom, Zhuo Angel Chen, Colin Combe, Lutz Fischer, Martin Graham, Georg Kustatscher, Christos Spanos, Juan Zou
Rappsilber Group

3D proteomics

Juri gives a brief overview of his research.

We aim at understanding how proteins fold, interact and associate in larger structures in their native environments. We interrogate proteins by two approaches that we developed in our lab.

1) We are one of the key labs driving the transition of cross-linking/mass spectrometry (CLMS) into a powerful and useful addition to the structural biology toolbox. These advances included developing algorithms, protocols and mass spectrometric methods (e.g. Giese et al. Mol Cell. Proteomics 2015). We thoroughly tested and then exploited these tools in numerous biological applications in our own lab and in collaboration with worldleading
scientists in their respective disciplines, including many of the labs collaborating on this application. These efforts included the first analysis of a large multi-protein complex using cross-linking/mass spectrometry (RNA Pol II-TFIIF) (Chen et al. EMBO J. 2010) and the efforts in conducting quantitative analyses (Fischer et al. J. Proteomics 2013), leading to insights into the maturation of the proteasome lid complex (Tomko et al. Cell 2015). As a next step we work on increasing the resolution of CLMS such that protein structure determination becomes feasible and have succeeded in obtaining the structure of human serum albumin in serum (Belsom et al. Mol. Cell. Proteomics 2016). We have provided data to CASP11 (11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction), being the first to ever provide experimental data to CASP,
to support modelling by data and work on gathering the cross-linking community to participate in CASP12 this year.

2) We propose a fundamentally new approach to analysing protein function. While trying to establish a definitive list of proteins that associate with mitotic chromosomes in vertebrates we realised shortcomings in standard concepts of organellar proteomics (that the composition of an organelle can be defined through biochemical purification). We developed a different approach, in collaboration with Bill Earnshaw’s lab, by analysing the composition of mitotic chromosome preps obtained in multiple different ways and integrating this by machine learning (Ohta, Bukowski-Wills et al. Cell 2010). We expanded this conceptually in several ways and proposed a view of interphase chromatin (Kustatscher et al. EMBO J. 2014) that helped reveal proteins involved in DNA replication and chromatin maturation (Alabert et al. Nat. Cell Biol. 2014). Our approach is large-scale data-driven and could complement annotation databases such as Gene Ontology with an urgently needed quantitative dimension. Building on physiological co-behaviour and machine learning could become a cornerstone in characterizing the proteome of biochemically intractable cellular structures and potentially reveal yet undisclosed functional relationships between proteins.

Selected publications:

Tomko RJ Jr, Taylor DW, Chen ZA, Wang HW, Rappsilber* J, Hochstrasser* M. A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly. Cell. 2015 Oct 8;163(2):432-44. [*shared senior authors]
Belsom A, Schneider M, Fischer L, Brock O, Rappsilber J. Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology. Mol Cell Proteomics. 2016 Mar;15(3):1105-16.
Giese SH, Fischer L, Rappsilber J. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides. Mol Cell Proteomics. 2016 Mar;15(3):1094-1104.


Quantitative Cross-linking/Mass Spectrometry Reveals Local Differences in LP2 and Lid Structures (A, B). A rigidbody rotation of the Rpn8-Rpn11 upon Rpn12 incorporation may account for the observed change in the Rpn8- Rpn11 cross-link network and constitutes the activating maturation step of the proteasome lid complex (C).