Group Bojan Zagrovic

Laboratory of Molecular Biophysics

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The Question

Nucleic acids and proteins are the key building blocks of life, yet many essential aspects of their relationship remain enigmatic. The aim of our research is to decipher the fundamental rules behind the interactions between nucleic acids and proteins in crowded environments, understand the impact these interactions have had in shaping life’s evolutionary history and study their role in present-day systems. The central hypothesis behind our research is that direct interactions between nucleic acids and proteins have contributed to the establishment of the universal genetic code and that, in turn, the code can be seen as a Rosetta stone for understanding RNA-protein interactions in general. A corollary of this hypothesis, which we are particularly interested in, is that mRNA coding sequences may be complementary to and bind in co-aligned fashion to their cognate proteins, especially if unstructured.

The Approach

We use and develop different techniques of computational biology, including molecular dynamics simulations, free energy and entropy calculations and structural bioinformatics methods, in close conjunction with experiment. Moreover, we develop novel methods of what could best be described as physicochemical bioinformatics, an approach to representing, analyzing and comparing biological sequences as physicochemical objects, which they invariably are. By combining rigorous, atomistic description of individual biomolecules with the richness of modern-day proteomic and genomic datasets, we strive to discover new fundamental principles behind the organization of biological matter and explain essential biological phenomena from a quantitative, physicochemical perspective.

Bojan Zagrovic

Bojan Zagrovic obtained an undergraduate degree in biochemistry from Harvard University and a PhD in biophysics from Stanford University, working with Vijay S. Pande. He was an EMBO postdoc with Wilfred F. van Gunsteren at ETH Zurich and a group leader and scientific director at Mediterranean Institute for Life Sciences in native Croatia. He joined Max Perutz Labs and University of Vienna in 2010.

Campus Vienna Biocenter 5
1030 Vienna
Room: 1.601

+43-1-4277-52271

Spotlights

Complementary binding between mRNAs and their cognate proteins

We have shown that the nucleotide-density profiles of mRNA coding sequences closely match the nucleotide-affinity profiles of their cognate proteins, suggesting that mRNAs and the proteins that they encode may, in general, be physicochemically complementary to each other and bind in a co-aligned fashion, especially if unstructured.

A server for analyzing sequence properties

We have recently developed VOLPES, a server for visualizing and comparing sequence profiles of different physicochemical properties of proteins and nucleic acids. VOLPES supports over 600 amino-acid and nucleotide property scales and enables multi-scale detection of patterns that may be inaccessible to standard methods of primary sequence analysis.

Conformational entropy suite

We have developed a parallel computational suite for the determination of conformational entropy change in biomolecular interactions from molecular dynamics simulation trajectories and have used it to demonstrate that intramolecular couplings provide a surprisingly constant contribution to the overall conformational entropy change in compact proteins.

Averaging in structural biology

We have used molecular dynamics simulations to study the issues of conformational averaging in structural biology experiments and have shown that crystallographic B-factors significantly underestimate the level of structural heterogeneity in protein crystals.

Team

Marlene Adlhart
Diploma/Master Student
+43-1-4277-52272
Room: 1.114

Santiago Alonso Gil
PostDoc
+43-1-4277-52272
Room: 1.114

Benjamin Bernrieder
Diploma/Master Student
+43-1-4277-52272
Room: 1.612

Felix Fischer
Diploma/Master Student
+43-1-4277-52272
Room: 1.114

Anna Gfrerer
Diploma/Master Student
+43-1-4277-74320
Room: 1.612

Thomas Kapral
PhD Student
+43-1-4277-52272
Room: 1.114

Fran Miocic-Stosic
PhD Student
+43-1-4277-52272
Room: 1.114

Melitta Münster
Technician
+43-1-4277-52275
Room: 1.321

Anton Polyansky
Staff Scientist
+43-1-4277-52271
Room: 1.612

Bojan Zagrovic
Group Leader
+43-1-4277-52271
Room: 1.601

Selected Publications

RNA-protein interactions in an unstructured context.

2018 FEBS Lett;592(17):2901-2916.
PMID: 29851074

Zagrovic, Bojan; Bartonek, Lukas; Polyansky, Anton A

Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides.

2019 NUCLEIC ACIDS RES;47(21):11077-11089.
PMID: 31612955

Polyansky, Anton A; Kreuter, Mathias; Sutherland, John D; Zagrovic, Bojan

Frameshifting preserves key physicochemical properties of proteins.

2020 P NATL ACAD SCI USA;117(11):5907-5912.
PMID: 32127487

Bartonek, Lukas; Braun, Daniel; Zagrovic, Bojan

Collaborations & Funding

ERC Proof of Concept Grant 2018

European Research Council: Short, weakly interacting RNAligands for the development of high-concentration monoclonal antibody therapeutics

FWF Stand-alone Project 2018

Austrian Science Fund: RNA-protein interactions in an unstructured context, 2018

FWF Stand-alone Project 2017

Austrian Science Fund: 2’ vs. 3’ aminoacylation in biological translation

Doctoral Program "Integrative Structural Biology"

2016-2019: The Group Zagrovic participates in the special Doctoral Program "Integrative Structural Biology" reviewed and funded by the Austrian Science Fund FWF.

ERC Starting Grant 2011

Awardee of a "Starting Independent Researcher Grant" from the European Research Council ERC

START Prize 2010, Austrian Science Fund (FWF)

Project title: “Specific and global aspects of protein interactions”

Previous Group: Weitzer

Molecular aspects of cardiomyogenesis

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