Computer simulations of DNA packing inside bacteriophages: Elasticity, electrostatics and entropy

DOI10.1080/17486700802168205MaRDI QIDQ1001564zbMATH OpenOpenAlexFDO

Authors Davide Marenduzzo

Publication date 18 February 2009

Published in Computational \& Mathematical Methods in Medicine (Search for Journal in Brave)

Full work available at URL https://eudml.org/doc/223642

Mathematics Subject Classification ID

Statistical mechanics of polymers (82D60) Protein sequences, DNA sequences (92D20)

Review text

Summary: There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packaging inside the phi29 phage, modelled either as a capped sphero-cylinder or as a sphere with the same internal volume. These simulations include electrostatics and a realistic genome length, and contribute to seriously questioning the inverse spool model, which arises from a purely continuum mechanics view of the problem, and is still commonly adopted to describe the shape of the packaged genome.

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(10)

• DNA knotting in spooling like conformations in bacteriophages
• Conformational changes in the connector protein complex of the bacteriophage \(\varphi 29\) DNA packaging motor
• A director-field model of DNA packaging in viral capsids.
• Force steps during viral DNA packaging?
• Three-dimensional director-field predictions of viral DNA packing arrangements
• Compressed wormlike chain moving out of confined space: a model of DNA ejection from bacteriophage
• A Model for Viral Genome Packing
• A headful of T4 coliphage DNA: dynamical modelling
• Statics and dynamics of condensed DNA within phages and globules
• Modelling DNA as a flexible thick polymer: DNA elasticity and packaging thermodynamics

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