Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites

Physical Biology
Vahid RezaniaMichael Hendzel

Abstract

Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of non-relevant sequences on DNA molecules. Whether these transcription factors locate their target sites through a 1D or 3D pathway is still a matter of speculation. It has been suggested that the optimum search time is when the protein equally shares its search time between 1D and 3D diffusions. In this paper, we study the above problem using Monte Carlo simulations by considering a simple physical model. A 1D strip, representing a DNA, with a number of low affinity sites, corresponding to non-target sites, and high affinity sites, corresponding to target sites, is considered and later extended to a 2D strip. We study the 1D and 3D exploration pathways, and combinations thereof by considering three different types of molecules: a walker that randomly walks along the strip with no dissociation; a jumper that represents dissociation and then re-association of a TF with the strip at later time at a distant site; and a hopper that is similar to the jumper but it dissociates and then re-associates at a faste...Continue Reading

References

Jan 1, 1985·Annual Review of Biophysics and Biophysical Chemistry·O G Berg, P H von Hippel
Nov 14, 1970·Journal of Molecular Biology·A D RiggsM Cohn
Jul 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·W E JackP Modrich
Dec 2, 2000·The EMBO Journal·N P StanfordS E Halford
Dec 29, 2000·Nature·T MisteliD T Brown
Jul 18, 2002·European Biophysics Journal : EBJ·Stephen E Halford, Mark D Szczelkun
Sep 28, 2002·Nature·Helena Santos-RosaTony Kouzarides
Feb 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Cem ElbiDonald B DeFranco
Jun 5, 2004·Nucleic Acids Research·Stephen E Halford, John F Marko
Sep 14, 2004·Nature Genetics·Cameron S OsbornePeter Fraser
Oct 7, 2004·Biophysical Journal·Michael Slutsky, Leonid A Mirny
May 24, 2005·Biophysical Journal·Igor M SokolovMark C Williams
Jan 24, 2006·The Journal of Biological Chemistry·Kensal van Holde, Jordanka Zlatanova
Aug 1, 2006·Nature Genetics·Helen PickersgillBas van Steensel

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.