Protein Entrapment in Polymeric Mesh: Diffusion in Crowded Environment with Fast Process on Short Scales

Abstract

The natural environment of proteins is a crowded environment as in cells, extracellular fluids, or during processing. Semidilute polymer solutions have been a source of rich structural and dynamical properties and mimic a crowded environment, but a proper understanding of protein dynamics in the crowded environment is far lagging. Such a study not only realizes protein's natural environment in a crowded solution in the cell or during processing but also manifests the underlying protein−polymer interaction. By dispersing model globular proteins like α-lactalbumin (La) and hemoglobin (Hb), in aqueous solution of poly(ethylene oxide) (PEO) we mimic a crowded environment and use state-of-the-art neutron spin echo (NSE) and small-angle neutron scattering (SANS) techniques to observe the corresponding protein dynamics in semidilute polymer solution. NSE can access the fast diffusion process (D fast ) prior to the slow diffusion process on long times and length scales (D γ ). The protein dynamics in a crowded environment can be described analogous to the diffusion in a periodic potential. The fast dynamics corresponds to diffusion inside a trap built by the polymer mesh while the slower process is the long time diffusion on macroscopic length scales also observed by other techniques. We observe the onset of fractional diffusion for higher concentrated polymer solutions.

Jscatter, a program for evaluation and analysis of experimental data

“…Diffusion in a harmonic potential for 1,2 and 3 dimensions is implemented[58]. diffusionPeriodicPotential describes fractal diffusion with a fast in trap diffusion and a long time diffusion in periodic potentials[59].…”

Protein-Driven Mechanism of Multiorgan Damage in COVID-19

“…Once inside the new organ, the exosomes, or other EVs, can liberate the perturbed human protein (or their complexes with a viral protein). The perturbed BRD4 protein finds itself in a crowded cellular environment in which it navigates in a subdiffusive way [ [66] , [67] , [68] ]. This subdiffusive displacement of the perturbed BRD4 proteins is illustrated in Step 4 and it allows to encounter NSD2, which is a vulnerable protein.…”

“…Protein-protein interaction occurs after the encounter of the two proteins in the intracellular environment. For such encounter to take place the proteins need to navigate in a very crowded media which is know to produce subdiffusive dynamics [ [66] , [67] , [68] ]. In this scenario, the mean square displacement 〈 x 2 ( t )〉 of a protein scales as a power-law with the time t of diffusion, such that where 0< κ <1 is the anomalous diffusion exponent.…”

“…In this scenario, the mean square displacement 〈 x 2 ( t )〉 of a protein scales as a power-law with the time t of diffusion, such that where 0< κ <1 is the anomalous diffusion exponent. Experiments conducted by Gupta et al [ 66 ] using state-of-the-art neutron spectroscopy at a resolution of up to 10 −9 s has shown that the motion of (globular) proteins in a crowded media is well-described by the fractional Fokker-Planck equation (FFPE) with a periodic potential. Here we consider the case in which there is no external force in the FFPE, which reduces it to the fractional diffusion equation (FDE).…”

Protein‐inorganic calcium‐phosphate supraparticles as a robust platform for enzyme co‐immobilization

“…Enzymes may be encapsulated, which can increase biocatalyst lifetime by mitigating unfolding events. Encapsulation methods are often broadly applicable to many enzymes (Espanol, Casals, Lamtahri, Valderas, & Ginebra, 2012; Fujita et al, 2012; Gupta et al, 2016; Nguyen, Qiao, & Olvera de la Cruz, 2018). However, encapsulation can inhibit enzyme motion or diffusion of substrate, product or cofactors, leading to a decrease in catalytic efficiency (Fu & Kao, 2010; Macha et al, 2019; Shakya & Nandakumar, 2018).…”