Literature DB >> 31444739

Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.

Sujit Basak1, Sombuddha Sengupta2, Krishnananda Chattopadhyay2.   

Abstract

In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.

Keywords:  Anomalous diffusion; Biological functions; Conformational equilibria; Gene expression; Macromolecular crowding; Protein stability; Protein–protein interaction

Year:  2019        PMID: 31444739      PMCID: PMC6957588          DOI: 10.1007/s12551-019-00580-9

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  154 in total

1.  Brownian motion in biological membranes.

Authors:  P G Saffman; M Delbrück
Journal:  Proc Natl Acad Sci U S A       Date:  1975-08       Impact factor: 11.205

2.  Fluorescence correlation spectroscopy simulations of photophysical phenomena and molecular interactions: a molecular dynamics/monte carlo approach.

Authors:  James A Dix; Erik F Y Hom; A S Verkman
Journal:  J Phys Chem B       Date:  2006-02-02       Impact factor: 2.991

3.  The shape of protein crowders is a major determinant of protein diffusion.

Authors:  Jessica Balbo; Paolo Mereghetti; Dirk-Peter Herten; Rebecca C Wade
Journal:  Biophys J       Date:  2013-04-02       Impact factor: 4.033

4.  Continuous-time random-walk model for anomalous diffusion in expanding media.

Authors:  F Le Vot; E Abad; S B Yuste
Journal:  Phys Rev E       Date:  2017-09-12       Impact factor: 2.529

5.  Anomalous diffusion due to obstacles: a Monte Carlo study.

Authors:  M J Saxton
Journal:  Biophys J       Date:  1994-02       Impact factor: 4.033

6.  Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

Authors:  Sean R McGuffee; Adrian H Elcock
Journal:  PLoS Comput Biol       Date:  2010-03-05       Impact factor: 4.475

7.  Superdiffusion dominates intracellular particle motion in the supercrowded cytoplasm of pathogenic Acanthamoeba castellanii.

Authors:  Julia F Reverey; Jae-Hyung Jeon; Han Bao; Matthias Leippe; Ralf Metzler; Christine Selhuber-Unkel
Journal:  Sci Rep       Date:  2015-06-30       Impact factor: 4.379

8.  Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.

Authors:  Michael Feig; Isseki Yu; Po-Hung Wang; Grzegorz Nawrocki; Yuji Sugita
Journal:  J Phys Chem B       Date:  2017-07-12       Impact factor: 2.991

9.  The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.

Authors:  Khanh Dao Duc; Yun S Song
Journal:  PLoS Genet       Date:  2018-01-16       Impact factor: 5.917

Review 10.  Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

Authors:  Matthieu Chavent; Anna L Duncan; Mark Sp Sansom
Journal:  Curr Opin Struct Biol       Date:  2016-06-21       Impact factor: 7.786

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  2 in total

1.  2019-A year in Biophysical Reviews.

Authors:  Damien Hall
Journal:  Biophys Rev       Date:  2019-11-18

2.  Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2.

Authors:  Ernesto Estrada
Journal:  Chaos       Date:  2020-08       Impact factor: 3.642

  2 in total

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