Abstract
The hypothesis is presented that bacteriophage DNA packaging motors have a cycle comprised of bind/release thermal ratcheting with release-associated DNA pushing via ATP-dependent protein folding. The proposed protein folding occurs in crystallographically observed peptide segments that project into an axial channel of a protein 12-mer (connector) that serves, together with a coaxial ATPase multimer, as the entry portal. The proposed cycle begins when reverse thermal motion causes the connector’s peptide segments to signal the ATPase multimer to bind both ATP and the DNA molecule, thereby producing a dwell phase recently demonstrated by single-molecule procedures. The connector-associated peptide segments activate by transfer of energy from ATP during the dwell. The proposed function of connector/ATPase symmetry mismatches is to reduce thermal noise-induced signaling errors. After a dwell, ATP is cleaved and the DNA molecule released. The activated peptide segments push the released DNA molecule, thereby producing a burst phase recently shown to consist of four mini-bursts. The constraint of four mini-bursts is met by proposing that each mini-burst occurs via pushing by three of the 12 subunits of the connector. If all four mini-bursts occur, the cycle repeats. If the mini-bursts are not completed, a second cycle is superimposed on the first cycle. The existence of the second cycle is based on data recently obtained with bacteriophage T3. When both cycles stall, energy is diverted to expose the DNA molecule to maturation cleavage.
Highlights
Analysis of bacteriophage DNA packaging motors is performed to understand basic principles of energy transduction and associated signaling in multimolecular assemblies
The activated peptide segments push the released DNA molecule, thereby producing a burst phase recently shown to consist of four mini-bursts
The existence of the second cycle is based on data recently obtained with bacteriophage T3
Summary
Analysis of bacteriophage DNA packaging motors is performed to understand basic principles of energy transduction and associated signaling in multimolecular assemblies. A sudden decrease in resistance to in vitro bacteriophage packaging has been observed at 90% packaging by single-molecule nanometry [31] This decrease is possibly caused by shell hyper-expansion, capsid rupture is the explanation proposed by the authors. Assuming that the HK97 covalent cross-links are produced before packaging is completed, these crosslinks could have evolved to stabilize a hyper-expanded capsid at the end of DNA packaging In this case, any change in cross-linked shell size would occur by refolding of each of the subunits, possibly via a rubber-like (and, by analogy, exothermic) stretching. Some aspects should be applicable to energy transducing systems of other types, including systems in which protein folding is assisted by chaperonins
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