Facilitated diffusion: Difference between revisions

Many physical and biochemical processes are regulated by [[diffusion]].<ref name="KleninMerlitz2006">{{cite journal|last1=Klenin|first1=Konstantin V.|last2=Merlitz|first2=Holger|last3=Langowski|first3=Jörg|last4=Wu|first4=Chen-Xu|title=Facilitated Diffusion of DNA-Binding Proteins|journal=Physical Review Letters|volume=96|issue=1|pages=018104|year=2006|issn=0031-9007|doi=10.1103/PhysRevLett.96.018104|pmid=16486524|arxiv=physics/0507056|bibcode=2006PhRvL..96a8104K|s2cid=8937433}}</ref> Facilitated diffusion is one form of diffusion and it is important in several metabolic processes. Facilitated diffusion is the main mechanism behind the binding of Transcription Factors (TFs) to designated target sites on the [[DNA]] molecule. The in vitro model, which is a very well known method of facilitated diffusion, that takes place outside of a living [[Cell (biology)|cell]], explains the 3-dimensional pattern of diffusion in the [[cytosol]] and the 1-dimensional diffusion along the DNA contour.<ref name="pmid23349772">{{cite journal | vauthors = Bauer M, Metzler R | title = In vivo facilitated diffusion model | journal = PLOS ONE | volume = 8 | issue = 1 | pages = e53956 | date = 2013 | pmid = 23349772 | pmc = 3548819 | doi = 10.1371/journal.pone.0053956| bibcode = 2013PLoSO...853956B | arxiv = 1301.5502 | doi-access = free }}</ref> After carrying out extensive research on processes occurring out of the cell, this mechanism was generally accepted but there was a need to verify that this mechanism could take place in vivo or inside of living cells. Bauer & Metzler (2013)<ref name="pmid23349772"/> therefore carried out an experiment using a bacterial genome in which they investigated the average time for TF – DNA binding to occur. After analyzing the process for the time it takes for TF's to diffuse across the contour and cytoplasm of the bacteria's DNA, it was concluded that in vitro and in vivo are similar in that the association and dissociation rates of TF's to and from the DNA are similar in both. Also, on the DNA contour, the motion is slower and target sites are easy to localize while in the [[cytoplasm]], the motion is faster but the TF's are not sensitive to their targets and so binding is restricted.

Single-molecule imaging is an imaging technique which provides an ideal resolution necessary for the study of the Transcription factor binding mechanism in living cells.<ref name="HammarLeroy2012">{{cite journal|last1=Hammar|first1=P.|last2=Leroy|first2=P.|last3=Mahmutovic|first3=A.|last4=Marklund|first4=E. G.|last5=Berg|first5=O. G.|last6=Elf|first6=J.|title=The lac Repressor Displays Facilitated Diffusion in Living Cells|journal=Science|volume=336|issue=6088|year=2012|pages=1595–1598|issn=0036-8075|doi=10.1126/science.1221648|pmid=22723426|bibcode=2012Sci...336.1595H|s2cid=21351861}}</ref> In [[prokaryotic]] [[bacteria]] cells such as ''E. coli'', facilitated diffusion is required in order for regulatory proteins to locate and bind to target sites on DNA base pairs.<ref name="KleninMerlitz2006"/><ref name="HammarLeroy2012"/><ref name="pmid25166711">{{cite journal | vauthors = Brackley CA, Cates ME, Marenduzzo D | title = Intracellular facilitated diffusion: searchers, crowders, and blockers | journal = Phys. Rev. Lett. | volume = 111 | issue = 10 | pages = 108101 | date = September 2013 | pmid = 25166711 | doi = 10.1103/PhysRevLett.111.108101 | arxiv = 1309.1010 | bibcode = 2013PhRvL.111j8101B | s2cid = 13220767 }}</ref> There are 2 main steps involved: the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain until it locates a target site, a process referred to as sliding.<ref name="KleninMerlitz2006"/> According to Brackley et al. (2013), during the process of protein sliding, the protein searches the entire length of the DNA chain using 3-D and 1-D diffusion patterns. During 3-D diffusion, the high incidence of Crowder proteins creates an osmotic pressure which brings searcher proteins (e.g. Lac Repressor) closer to the DNA to increase their attraction and enable them to bind, as well as [[steric effect]] which exclude the Crowder proteins from this region (Lac operator region). Blocker proteins participate in 1-D diffusion only i.e. bind to and diffuse along the DNA contour and not in the cytosol.

The in vivo model mentioned above clearly explains 3-D and 1-D diffusion along the DNA strand and the binding of proteins to target sites on the chain. Just like prokaryotic cells, in [[eukaryotes]], facilitated diffusion occurs in the [[nucleoplasm]] on [[chromatin]] filaments, accounted for by the switching dynamics of a protein when it is either bound to a chromatin thread or when freely diffusing in the nucleoplasm.<ref name="pmid21405302">{{cite journal | vauthors = Bénichou O, Chevalier C, Meyer B, Voituriez R | title = Facilitated diffusion of proteins on chromatin | journal = Phys. Rev. Lett. | volume = 106 | issue = 3 | pages = 038102 | date = January 2011 | pmid = 21405302 | doi = 10.1103/PhysRevLett.106.038102 | arxiv = 1006.4758 | bibcode = 2011PhRvL.106c8102B | s2cid = 15977456 }}</ref> In addition, given that the chromatin molecule is fragmented, its fractal properties need to be considered. After calculating the search time for a target protein, alternating between the 3-D and 1-D diffusion phases on the chromatin fractal structure, it was deduced that facilitated diffusion in eukaryotes precipitates the searching process and minimizes the searching time by increasing the DNA-protein affinity.<ref name="pmid21405302"/>