Effects of molecular crowding and confinement on the spatial organization of a biopolymer.
A chain molecule can be entropically collapsed in a crowded medium in a free or confined space. Here, we present a unified view of how molecular crowding collapses a flexible polymer in three distinct spaces: free, cylindrical, and (two-dimensional) slit-like. Despite their seeming disparities, a few general features characterize all these cases, even though the ϕc-dependence of chain compaction differs between the two cases: a > acand a < ac, where ϕcis the volume fraction of crowders, a is the monomer size, and acis the crowder size. For a > ac(applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio aϕc/ac, and "full" compaction occurs universally at aϕc/ac≈ 1; for ac> a (relevant for protein folding), it is controlled by ϕcalone and crowding has a modest effect on chain size in a cellular environment (ϕc≈ 0.3). Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independent of confinement.
Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada. byha@uwaterloo.ca.
Chanil
http://orcid.org/0000-0002-4609-0860
C
Jeon
Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 34141, Korea. yjung@kisti.re.kr.
Youngkyun
Y
Jung
Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada. byha@uwaterloo.ca and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea.
Bae-Yeun
BY
Ha