Structural, Functional, and Dynamical Responses of a Protein in a Restricted Environment Imposed by Macromolecular Crowding

Abstract

The intercellular environment is known to be very different from the environment where most of the elementary biological processes are studied in the laboratory. As a result, there was a considerable effort on cell mimicking either by confinement or by introducing macromolecular crowding. In the present study, dextran of varying sizes has been used to crowd the environment of a protein, human serum albumin (HSA), and its structure, dynamics, and activity were studied as a function of crowder concentration. By employing bulk and single molecular level spectroscopic measurements, we elucidate the overall structure and local microsecond dynamics of HSA. Further, we have attempted to correlate these structural changes with its activity.

Enzyme Stabilization by Virus-Like Particles

“…Prior studies and computation contain precedents for both phenomena, but thermodynamic factors are more often discussed. Macromolecular crowders like polyethylene glycol (PEG), dextran, protein, and DNA are believed to restrict the conformationally extended states of protein due to volume exclusion, , leading to entropy-driven stabilization of the folded state. − Entrapment in tight spaces may also simply bias the available thermodynamic population toward the more compact folded structure . On the other hand, intermolecular interactions between the protein and surrounding species, including surfaces or trapped water molecules, can be either stabilizing or destabilizing and thus may work in opposition to the excluded volume effect. , Thus, while the RNA concentration inside the Qβ capsid is quite high, perhaps enough to provide an excluded volume environment, it is likely not to be homogeneously distributed and thus is of uncertain relevance.…”

Reversible Ultra‐Slow Crystal Growth of Mixed Lead Bismuth Perovskite Nanocrystals: The Presence of Dynamic Capping

“…[27] The single component fitting suggests narrow distribution of NC sizes (see Figure 2g)a nd the calculated value of the radius of the NC is shown in Figure 2h. FCSi sav ery sensitive technique based on the temporalf luctuation of fluorescence intensity in av ery small observation volume and provides ad iffusion timescale of the emissive species.…”

“…Then using the Stokes–Einstein relationship, the size of the species can be calculated. The details of the experimental procedure, instrumentation and data fitting can be found in our previous publication as well as in the Section S2 of the Supporting Information . The single component fitting suggests narrow distribution of NC sizes (see Figure g) and the calculated value of the radius of the NC is shown in Figure h. It is to be noted that in this case the measured size of the NC is actually the size of the capped NC as the diffusion of the NC is accompanied by its capping agents.…”

Sucrose-Induced Stabilization of Domain-II and Overall Human Serum Albumin against Chemical and Thermal Denaturation

“…The role of sucrose in the stabilization of proteins has been explored experimentally by several groups including number of reports on HSA. − This is also to note that sucrose is the monomeric unit of the famous macromolecular crowder ficoll. Recently, our group is engaged in understanding the mechanism by which a crowder exerts its effect on a protein . We expect that the present study will be useful in elucidating the mechanism of crowder-induced changes of a protein.…”