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Park, H.,Im, W.,Seok, C. Biophysical Society ; Published for the Biophysica 2011 Biophysical journal Vol.100 No.12
Transmembrane signaling of chemotaxis receptors has long been studied, but how the conformational change induced by ligand binding is transmitted across the bilayer membrane is still elusive at the molecular level. To tackle this problem, we carried out a total of 600-ns comparative molecular dynamics simulations (including model-building simulations) of the chemotaxis aspartate receptor Tar (a part of the periplasmic domain/transmembrane domain/HAMP domain) in explicit lipid bilayers. These simulations reveal valuable insights into the mechanistic picture of Tar transmembrane signaling. The piston-like movement of a transmembrane helix induced by ligand binding on the periplasmic side is transformed into a combination of both longitudinal and transversal movements of the helix on the cytoplasmic side as a result of different protein-lipid interactions in the ligand-off and ligand-on states of the receptor. This conformational change alters the dynamics and conformation of the HAMP domain, which is presumably a mechanism to deliver the signal from the transmembrane domain to the cytoplasmic domain. The current results are consistent with the previously suggested dynamic bundle model in which the HAMP dynamics change is a key to the signaling. The simulations provide further insights into the conformational changes relevant to the HAMP dynamics changes in atomic detail.
Physical Origin of the Contact Frequency in Chromosome Conformation Capture Data
Hahn, S.,Kim, D. Biophysical Society ; Published for the Biophysica 2013 Biophysical journal Vol.105 No.8
Physical proximity between each pair of genomic loci in a nucleus is measured as a form of contact frequency in chromosome conformation capture-based methods. Complexity of chromosome structure in interphase can be characterized by measuring a statistical property of physical distance between genomic loci according to genomic separation along single chromatids. To find a relationship between the physical distance and the contact frequency, we propose a polymer model derived from the Langevin equation. The model is derived by considering a structure of a chromosome as a trajectory of a particle, where each consecutive segment in the chromosome corresponds to a transient position in the trajectory over time. Using chromosome conformation capture data, we demonstrate the functional relationship between the two quantities. The physical distances derived from the mean contact frequencies by the model show a good correlation with those from experimental data. From the model, we present that the mean contact frequency curve can be divided into three components that arise from different physical origins and show that the contact frequency is proportional to the contact surface area, not to the volume of segments suggested by the fractal globule model. The model explains both a decaying pattern of the contact frequency and the biphasic relationship between the physical distance and the genomic length.
Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function
Ando, D.,Zandi, R.,Kim, Y.,Colvin, M.,Rexach, M.,Gopinathan, A. Biophysical Society ; Published for the Biophysica 2014 Biophysical journal Vol.106 No.9
The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.