A theoretical study of rotational diffusion models for rod-shaped viruses. The influence of motion on 31P nuclear magnetic resonance lineshapes and transversal relaxation.
Information about the interaction between nucleic acids and coat proteins in intact virus particles may be obtained by studying the restricted backbone dynamics of the incapsulated nucleic acids using 31P nuclear magnetic resonance (NMR) spectroscopy. In this article, simulations are carried out to investigate how reorientation of a rod-shaped virus particle as a whole and isolated nucleic acid motions within the virion influence the 31P NMR lineshape and transversal relaxation dominated by the phosphorus chemical shift anisotropy. Two opposite cases are considered on a theoretical level. First, isotropic rotational diffusion is used as a model for mobile nucleic acids that are loosely or partially bound to the protein coat. The effect of this type of diffusion on lineshape and transversal relaxation is calculated by solving the stochastic Liouville equation by an expansion in spherical functions. Next, uniaxial rotational diffusion is assumed to represent the mobility of phosphorus in a virion that rotates as a rigid rod about its length axis. This type of diffusion is approximated by an exchange process among discrete sites. As turns out from these simulations, the amplitude and the frequency of the motion can only be unequivocally determined from experimental data by a combined analysis of the lineshape and the transversal relaxation. In the fast motional region both the isotropic and the uniaxial diffusion model predict the same transversal relaxation as the Redfield theory. For very slow motion, transversal relaxation resembles the nonexponential relaxation as observed for water molecules undergoing translational diffusion in a magnetic field gradient. In this frequency region T2e is inversely proportional to the cube root of the diffusion coefficient. In addition to the isotropic and uniaxial diffusion models, a third model is presented, in which fast restricted nucleic acid backbone motions dominating the lineshape are superimposed on a slow rotation of the virion about its length axis, dominating transversal relaxation. In an accompanying article the models are applied to the 31P NMR results obtained for bacteriophage M13 and tobacco mosaic virus.
Magusin
P C
PC
Department of Molecular Physics, Agricultural University, Wageningen, The Netherlands.
Hemminga
M A
MA
D001435:Bacteriophages / Q000648:ultrastructure*; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry*; D004058:Diffusion; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008433:Mathematics; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D010758:Phosphorus; D012367:RNA, Viral / Q000737:chemistry*; D012984:Software
D004279:DNA, Viral; D012367:RNA, Viral; D010758:Phosphorus