Physicalchemical profiling of organisms
Title: Physicalchemical profiling of organisms
SNIC Project: SNIC 2019/7-69
Project Type: SNIC Small Compute
Principal Investigator: Eloy Vallina Estrada <eloy.vallina@dbb.su.se>
Affiliation: Stockholms universitet
Duration: 2019-09-26 – 2020-10-01
Classification: 10203
Keywords:

Abstract

In contrast with dilute conditions typically imposed in biochemical experiments, macromolecular concentrations in the cellular interior are very high. In such a crowded cytosol, proteins engage in a vast and complex network of attracting and repelling interactions. Generally, in order to perform their functions, most proteins need to find a specific counterpart to which they will bind in a relatively long encounter. However, this search-for-partner involves sampling a huge space of possibilities, of which potentially very few are productive. Hence, proteins need to be able to spend as little time as possible on each encounter, so that they can explore a larger number of surfaces, while simultaneously making this interaction as intimate as possible, so that they do not miss their functional partners when they eventually cross paths. Since protein intracellular mobility plays a role in cellular fitness and the fate of any protein interaction is specific to the physicalchemical properties of the residues involved, fingerprints of evolutionary control are expected to be present in protein surfaces, constituting a fifth level of protein structure, often termed quinary structure. Moreover, organisms whose cytosols have adapted to life in different niches, can be expected to exhibit different patterns in terms of the particular physichalchemical properties of their proteomes that ensure the search is carried out successfully. In this project we intend to investigate trends in the physicalchemical properties of proteins, namely net-charge, hydrophobicity, etc., across all sequenced organisms in the databanks, in hope that we'll identify organising principles linking connecting these trends to the habitats in which different organisms thrive, in terms of temperature, pH and salt concentration.