An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages.
A model is presented that treats the symmetry matching problem in structures made of two interacting coaxial helices of point charges. The charges are sources of a potential field that mediates a non-specific attractive interaction between the helices. The problem is represented in Fourier space, which affords the most generality. It is found that coaxial helices with optimally mated symmetries can lock into spatial resonance configurations that maximize their interaction. The resonances are represented as vectors in a discrete three-dimensional space. Two algebraic relations are given for the four symmetry parameters of two helices in resonance. One-start inner helices interacting with coaxial one-start or NR-start outer helices are considered. Applications are made to the filamentous bacteriophages Ff, Pf1, Xf, and Pf3. The interaction given by the linearized Poisson-Boltzmann equation is calculated in this formalism to allow comparison of the electrostatic free energy of interaction of different resonance structures. Experimental nucleotide/subunit ratios are accounted for, and models for the DNA-protein interfaces are presented, with particular emphasis on Pf1.
Marzec
C J
CJ
Public Health Research Institute, New York, New York 10016.
Day
L A
LA
D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000737:chemistry* / Q000235:genetics; D055592:Biophysical Phenomena; D001703:Biophysics; D002213:Capsid / Q000737:chemistry* / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry*; D004563:Electrochemistry; D017912:Inovirus / Q000737:chemistry / Q000235:genetics; D046911:Macromolecular Substances; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D013816:Thermodynamics
D004279:DNA, Viral; D046911:Macromolecular Substances