Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins’ shape, height, contact angle with the bilayer, as well as the local membrane curvature. Although interaction energies are not pairwise additive, for sufficiently low protein density, thermodynamic propertie...

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most e...

Thermal shift assays (TSAs) have been extensively used to study thermodynamics of proteins and provide an efficient means assess protein-ligand binding or protein-protein interaction. However, existing TSAs limitations such as time consuming, labor intensive, low sensitivity. Here we introduce a novel acousto thermal assay (ATSA), the first ultrasound enabled TSA, for real-time analysis protein...

Despite significant efforts and promising progress, the understanding of membrane protein folding lags behind that of soluble proteins. Insights into the energetics of membrane protein folding have been gained from biophysical studies in membrane-mimicking environments (primarily detergent micelles). However, the development of techniques for studying the thermodynamics of folding in phospholip...

PDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbi...

The two classes of membrane transport, namely, secondary active and passive are understood as different reaction pathways in the same protein structure, described by 16-state model this paper. To quantify thermodynamic difference between transport we extend second law information thermodynamics autonomous demon four-state composed subsystems to four representing transport. We reduce 16 states 4...

Glucose/galactose binding protein (GGBP) functions in two different larger systems of proteins used by enteric bacteria for molecular recognition and signaling. Here we report on the thermodynamics of conformational equilibrium distributions of GGBP. Three fluorescence components appear at zero glucose concentration and systematically transition to three components at high glucose concentration...

DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout")...