Coarse-Grained Brownian Dynamics Simulations for Symmetric Diblock Copolymer Melts Based on the Soft Dumbbell Model

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus ; domestic chicken, Gallus gallus domesticus and human, Homo sapiens ) and an ectotherm (salt water crocodile, Crocodylus porosus ) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.

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Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes

Nucleic Acids Research ◽

10.1093/nar/gku694 ◽

2014 ◽

Vol 42 (15) ◽

pp. 9691-9699 ◽

Cited By ~ 11

Author(s):

Gi-Moon Nam ◽

Gaurav Arya

Keyword(s):

Brownian Dynamics ◽

Extreme Values ◽

Strong Dependence ◽

Critical Role ◽

Coarse Grained ◽

Naked Dna ◽

Coarse Grained Model ◽

Torsional Behavior ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

Abstract Torsionally stressed DNA plays a critical role in genome organization and regulation. While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization. Here we investigate the torsional behavior of nucleosome arrays by means of Brownian dynamics simulations of a coarse-grained model of chromatin. Our simulations reveal a strong dependence of the torsional response on the rotational phase angle Ψ0 between adjacent nucleosomes. Extreme values of Ψ0 lead to asymmetric, bell-shaped extension-rotation profiles with sharp maxima shifted toward positive or negative rotations, depending on the sign of Ψ0, and to fast, irregular propagation of DNA twist. In contrast, moderate Ψ0 yield more symmetric profiles with broad maxima and slow, uniform propagation of twist. The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where Ψ0 serves to modulate the energy landscape of nucleosomal states. Our results also explain the torsional resilience of chromatin, reconcile differences between experimentally measured extension-rotation profiles, and suggest a role of torsional stresses in regulating chromatin assembly and organization.

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