Accessibility Tools

2024-09-13
Osiągnięcia

Hydrodynamic properties of intrinsically disordered proteins

J. Phys. Chem. Lett. 15, 5024 - 5033​ (2024)

(left) The diffusion of the intrinsically disordered protein (green) is slower than that of a protein with a globular structure (black), even though the green protein has a much lower molecular mass and a shorter chain, as shown by the autocorrelation curves measured by fluorescence correlation spectroscopy. (right) The coarse-grained globule-linker model allows rapid calculation of the hydrodynamic radii of intrinsically disordered proteins in agreement with experimentally measured results.
(left) The diffusion of the intrinsically disordered protein (green) is slower than that of a protein with a globular structure (black), even though the green protein has a much lower molecular mass and a shorter chain, as shown by the autocorrelation curves measured by fluorescence correlation spectroscopy. (right) The coarse-grained globule-linker model allows rapid calculation of the hydrodynamic radii of intrinsically disordered proteins in agreement with experimentally measured results.

Intrinsically disordered proteins (IDPs), essential for regulating critical cellular functions, have long posed research challenges due to their lack of fixed three-dimensional structure. They are now more accessible for study thanks to a new model that enables rapid and precise analysis of their hydrodynamic properties, marking a significant breakthrough in biophysical research. In recent years, the significance of intrinsically disordered proteins (IDPs) in cellular processes has become increasingly apparent. These proteins, often referred to as the "dark matter of molecular biology", play crucial roles in processes such as gene expression regulation and biomineralization. Unlike proteins with stable three-dimensional structures, IDPs lack a defined shape, which allows them to perform various functions in response to changing cellular conditions. However, this structural flexibility makes them challenging to study, particularly when it comes to predicting their hydrodynamic properties, which are necessary for understanding their biological roles. The hydrodynamic radius (Rh), which represents the radius of a hypothetical sphere moving in the solvent like the protein molecule, is the most critical parameter in describing a protein's movement in solution. For structured proteins, the hydrodynamic radius can be predicted with high accuracy based on their mass or chain length. However, this approach fails for disordered proteins, as traditional methods for estimating Rh either fall short or are computationally too complex to be practical, especially for long-chain IDPs. To address this challenge, a research team at the Environmental Laboratory of Biological Physics, led by Anna Niedźwiecka and in collaboration with Piotr Szymczak's theoretical group from the University of Warsaw, has developed a new model for disordered proteins specifically tailored for estimating Rh. This model employs accelerated conformational sampling through a self-avoiding random walk, accounts for hydrodynamic interactions between coarse-grained protein subunits, and quickly calculates the hydrodynamic radius based on minimal scattering approximation. This allows for accurate predictions of Rh based solely on the protein sequence, making it a new and effective tool for scientists. In a recent paper published in the Journal of Physical Chemistry Letters, the authors also presented results of testing on a range of new protein constructs that varied significantly in chain length and content of globular domains and disordered linkers. They measured their hydrodynamic radii using fluorescence correlation spectroscopy and demonstrated good agreement between their calculations and experimental results. This work provides the most comprehensive set of experimental data available for such studies. The new model not only provides Rh estimates within seconds but also achieves better accuracy than previous coarse-grained or phenomenological computational methods. The new method for predicting hydrodynamic properties based solely on protein sequence will impact both biophysical research and potential biomedical applications, where understanding the behavior of disordered proteins is crucial.

72

Publications

R. Waszkiewicz, A. Michaś, M.K. Białobrzewski, B.P. Klepka, M.K. Cieplak-Rotowska, Z. Staszałek, B. Cichocki, M. Lisicki, P. Szymczak, A. Niedzwiecka

Contact with IF PAN scientists

This email address is being protected from spambots. You need JavaScript enabled to view it.


See more

Fermi-Dirac Distribution Reformulated in Non-Hermitian Systems

Researchers have extended the traditional Fermi-Dirac distribution to non-Hermitian systems. This new formalism provides a general framework to compute quantum many-body observables in equilibrium systems coupled to dissipative environments.

Quantum thermodynamics with a single superconducting vortex

We control and monitor the state of the single superconducting vortex. Using our fastest thermometer in the nanoworld, we measured the thermal transient due to the vortex expulsion from the superconductor. An energy dissipated due to this expulsion is equivalent to the absorption of a single phot...

Pentagonal nanowires from topological crystalline insulators: a platform for intrinsic core-shell nanowires and higher-order band topology

We report on the first experimental realization of pentagonal nanowires within ionic compounds using Pb1-xSnxTe. The structures are potential candidates for realizing higher-order topology. The disclination and twin boundaries cause the states originating from the core region to generate a conduc...
Save
Cookies user preferences
We use cookies to ensure you to get the best experience on our website. If you decline the use of cookies, this website may not function as expected.
Accept all
Decline all
Read more
Essential
Essential cookies
These cookies are necessary for the correct operation of the website and therefore cannot be disabled on this level; the use of these cookies does not involve the processing of personal data. While you can disable them via your browser settings, doing so may prevent the website from working normally.
Accept
Analytical cookies
These cookies are particularly intended to enable the website administrator to monitor the website traffic statistics, as well as the sources of traffic. Such data is typically collected anonymously.
Google Analytics
Accept
Decline