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From Biomolecular Structures to Thermodynamic Ensembles: Cellular Logistics Controlled by Disordered FG-Nucleoporins

Principal Investigator: Helmut Grubmüller, Theoretical and Computational Biophysics, Max-Planck-Institut für biophysikalische Chemie, Göttingen (Germany)
HPC Platform: SuperMUC of LRZ

The nucleus of all eukaryotic cells is separated from the cytoplasm by the nuclear envelope. The passage of large macromolecules across the nuclear envelope is a tightly regulated process; the maintenance of the integrity of this barrier is crucial to cellular viability. Perforating the nuclear envelope are nuclear pore complexes (NPCs) through which large molecules are transported into and out of the nucleus.

Transport must be highly selective: only specific molecules are allowed to enter and exit the nucleus. Ions and small molecules pass through the NPC via passive diffusion. However, larger cargo (like protein and RNA) must be bound to nuclear transport receptors in order to pass through the NPC. The selectivity of the nuclear pore complex is conferred by a class of proteins called FG-nucleoporins (FG-nups). The FG-nups are disordered in solution, which means that they populate many conformational states at equilibrium. Thus, their structure cannot be described as a single, well-defined structure like globular, folded proteins, but must instead be described as a structural ensemble (Figure 1).

Cellular Logistics Controlled by Disordered FG-NucleoporinsCopyright: Max Planck Institute for Biophysical Chemistry, Dept. Theoretical and Computational Biophysics, Göttingen

Figure 1: (a) 16 structures of globular proteins selected from the Protein Data Bank (PDB). The native state of globular proteins is a well-folded structure. (b) In contrast to the native state of globular proteins, the native state of a disordered protein consists of a collection of many possible structures (a “structural ensemble”). A collection of 16 randomly chosen structures from the ensemble of a disordered FG-nucleoporin is shown. One sequence forms a variety of secondary structures.

FG-nups are a prototypic example of the functional role of protein disorder in biological systems, and beyond their particular function are key model systems for disordered proteins. Intrinsically disordered proteins (IDPs) fulfill important biological roles including cell signalling and cell cycle regulation. Disordered proteins are highly abundant in all kingdoms of life: more than one-third of eukaryotic proteins and more than three-quarters of proteins linked to cancer are predicted to contain disordered regions.

Despite their importance as potential drug targets, disordered proteins are poorly understood relative to the wealth of structural information available for folded proteins. Disordered proteins are notoriously difficult to study using experimental approaches due to their tendency to aggregate. Moreover, and on a very fundamental level, their description poses formidable challenges. Disordered proteins and disordered regions of proteins have many energetically-accessible conformational states. Thus, even with hundreds of experimental observables, it is not possible to obtain an unambiguously-determined ensemble of conformations.

The structural characterization of disordered proteins is an inherently under-determined problem: a small number of restraints are insufficient to uniquely define the conformations of a system with thousands of degrees of freedom. Molecular simulations, with their empirical force fields, can offer the additional information required to obtain conformational ensembles for disordered states of proteins. However, these simulations must contend with a massive sampling problem, which was successfully achieved by a team of scientists of the Max Planck Institute for Biophysical Chemistry in Göttingen using the High Performance Computing (HPC) system of the Leibniz Supercomputing Centre, SuperMUC.

The central aim of this research project is to obtain an atomistic description of the aggregated state of the disordered FG-nups, which is necessary for a molecular-level understanding of the selectivity of the nuclear pore complex of eukaryotes. To achieve this, the scientists first obtained an ensemble description of monomeric FG-nups. One key finding in this step of the project was that the molecular mechanics force fields used in atomistic MD simulations lead to dramatically different structural ensembles. To address this issue, the researchers collaborated with experimental groups to compare their structural ensembles with experimental data.

The scientists have been able to identify a molecular mechanics force field that is in agreement with all available experimental results. This is a key finding, not only for this project, but for the wider community of researchers studying intrinsically disordered proteins. Prior to this work, it was not clear whether force fields, which were primarily developed for the study of globular proteins, could accurately represent disordered systems. Having overcome both the sampling problem and the force field problem, the scientists are now simulating aggregates of FG nucleoporins as well as nuclear transport receptors.

In ongoing work, the scientists are performing extensive simulations of aggregates towards identifying the important molecular interactions responsible for stabilizing aggregates of cohesive FG-nups, and the key structural differences that distinguish the two major classes of FG-nups, as well as the interactions leading to the specific transport of nuclear transport receptors through the nuclear pore complex.

Scientific Contact:

Prof. Dr. Helmut Grubmüller
Theoretical and Computational Biophysics
Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11, D-37077 Göttingen/Germany

November 2013