Exploring the molecular grammar of IDP assembly and condensation at ultra-high throughput

Descripción del proyecto

Revelación de los misterios de las proteínas intrínsecamente desordenadas

Las proteínas intrínsecamente desordenadas (PID) carecen de una estructura tridimensional estable y bien definida, y adoptan múltiples conformaciones, a menudo con un alto grado de flexibilidad. Las PID también desempeñan una serie de funciones biológicas importantes, como la señalización, la transcripción y la división celular. A pesar de su importancia, las PID se han considerado durante mucho tiempo un misterio en el campo de la ciencia de las proteínas. El objetivo del proyecto EMMA, financiado por el Consejo Europeo de Investigación, es desvelar este misterio. Mediante el uso de biofísica experimental avanzada, algoritmos de aprendizaje automático y simulaciones moleculares, el equipo de EMMA busca una comprensión cuantitativa de cómo la estructura y las interacciones de las PID están definidas por su secuencia de aminoácidos. Creará una novedosa estrategia experimental que permitirá estudiar simultáneamente el comportamiento de millones de secuencias de aminoácidos.

Objetivo

The last years have seen unprecedented breakthroughs in protein structural biology, with the resolution revolution in cryo-electron microscopy and the release of AlphaFold. The combination of advanced experimental structural biology, machine learning algorithms and molecular simulations has put the fully quantitative description of how the structure and interactions of folded proteins are defined by their amino acid sequence within close reach.
This leaves us with a final frontier in protein science, namely to achieve a similar level of understanding for intrinsically disordered proteins (IDPs). The energy landscapes of IDPs often comprise a multitude of nearly isoenergetic states, that include assembled forms, such as amyloid fibrils and liquid condensate droplets.
Much effort has been spent in order to achieve an understanding of the molecular grammar of IDP assembly and condensation, i.e. how amino acid sequence defines both kinetics and thermodynamics of these processes. Current state of the art is to evaluate a few dozens of sequence perturbations quantitatively in vitro.
In EMMA, I propose to develop a fundamentally new approach that will ultimately allow to improve on current methods by more than 8 orders of magnitude. This ground-breaking improvement will be achieved by exploiting the power of mRNA display, in which the biophysical behavior of each individual sequence within large libraries of protein-mRNA constructs can be evaluated in a “one pot” reaction. We will combine quantitative screening of the energetics of liquid condensate droplet formation of up to 10^10 sequences by mRNA display with a multiparametric biophysical toolbox that allows the key thermodynamic and kinetic parameters of binding and assembly to be evaluated for thousands of selected sequence variants.
EMMA will transform our ability to probe the mechanisms and interrelationships of the interactions and assembly processes that define IDP function and disease-related malfunction.