Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights

Abstract

The binding of proteins to their respective specific sites on the DNA through facilitated diffusion serves as the initial step of various important biological processes. While this search process has been thoroughly investigated via in vitro studies, the cellular environment is complex and may interfere with the protein's search dynamics. The cytosol is heavily crowded, which can potentially modify the search by nonspecifically interacting with the protein that has been mostly overlooked. In this work, we probe the target search dynamics in the presence of explicit crowding agents that have an affinity toward the protein. We theoretically investigate the role of such protein−crowder associations in the target search process using a discrete-state stochastic framework that allows for the analytical description of dynamic properties. It is found that stronger nonspecific associations between the crowder and proteins can accelerate the facilitated diffusion of proteins in comparison with a purely inert, rather weakly interacting cellular environment. This effect depends on how strong these associations are, the spatial positions of the target with respect to the crowders, and the size of the crowded region. Our theoretical results are also tested with Monte Carlo computer simulations. Our predictions are in qualitative agreement with existing experimental observations and computational studies.

Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles

“…Motivated by the findings of the in vitro experiments by Riggs et al, it was proposed that the DBPs locate these target sites on the DNA via a facilitated diffusion mechanism which is comprised of 3D and 1D diffusion modes of the proteins. , With the help of a discrete state stochastic model analyzed using the first passage analysis, Kolomeisky and co-workers developed a minimal model to describe the target search process of a single DBP . In realistic situations, macromolecular bulk crowding occupies about 40% of the cellular matrix. , Using our theoretical results obtained via first passage analysis applied to a discrete-state model, supported by extensive Monte Carlo computer simulations, we were able to determine the conditions that facilitate or hamper the search process in a real cellular environment. − …”

“… 109 , 110 Using our theoretical results obtained via first passage analysis applied to a discrete-state model, supported by extensive Monte Carlo computer simulations, we were able to determine the conditions that facilitate or hamper the search process in a real cellular environment. 111 − 113 …”

Probing the modulation in facilitated diffusion guided by DNA–protein interactions in target search processes

“…In the current theoretical model, the quantified results on the modulation in the target search rates provide an easy handle to gain a deeper insight into the process. The study is found to be suitable to provide a convenient methodology to capture the modulation in the target search rate even in a complex situation such as, in the presence of blocking agents 28,30,39,57 or in a crowded and rearranging disordered media. A natural extension of this work will be the application of a similar theoretical framework to extract testable and quantified predictions to manipulate the target search technique in a more complicated scenario.…”

“…1) involving 1D motion along with a 3D diffusion has been theoretically conceptualized to explain the mechanism successfully. 5,[11][12][13][14]24,[28][29][30][51][52][53][54][55][56] The search strategy based on facilitated diffusion thus enables to capture the faster and more efficient target search method and hence seems to provide a reliable general technique for the target search process. Following the analytical model for the facilitated diffusion and expressing the 1D and 3D diffusion timescales with simple scaling arguments based on dimensional analysis, the target search time, t tst can be derived as, 12,[57][58][59][60][61]…”

“…Manipulating the target search process thus obviously provides a preliminary tool to control the overall dynamics of many fundamental life processes such as genetic regulations, protein synthesis, and many other biophysical events linked to the mechanistic details of these. Even though a large number of experimental and theoretical studies 3,8,[17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] have been performed to capture the microscopic details of this process, often, the target-searching process in vivo is found to be more complex. Also, the outcomes are largely guided by the modulation of the mechanistic details and the target searching process getting influenced by the specific nature of the cellular environment or media for a given condition of the concerned systems.…”