Investigating the Effects of Molecular Crowding on Protein Structure using Atomic Force Microscopy

Abstract

To explore the structure-dynamics-function relationship in proteins, most studies are usually conducted in simple salt-buffer solutions, however, the interior of a cell is densely crowded. The concentration of macromolecular crowders such as proteins, nucleic acids, ribosomes, and lipids ranges between 100 and 450 g/L inside a cell. The crowded intracellular environment, entirely different from the dilute conditions used in in vitro studies, can cause crowding and confinement effects. Previous studies have shown molecular crowding can significantly influence protein stability and can induce changes in protein dynamics and function. In order to investigate the effects of these macromolecular crowders on protein structure, we employ the use of Atomic Force Microscopy or AFM. AFM uses a nanoscopic probe to tap the surface of a sample to create a topographical representation of it. By analyzing the topography of the samples of our protein of interest in the presence of different macromolecular crowders, we hope to conclude how the chemical and structural nature of macromolecular crowders affect the protein structure.