Molecular Dynamics Studies of the Phi29 Connector-DNA complex

by Rajendra Kumar
Doctoral thesis
Date of Examination:2014-07-18
Date of issue:2015-04-10
Advisor:Prof. Dr. Helmut Grubmüller
Referee:Prof. Dr. Helmut Grubmüller
Referee:Prof. Dr. Holger Stark
Referee:Prof. Dr. Wolfgang Fischle
Referee:Prof. Dr. Burkhard Morgenstern
Referee:Prof. Dr. Kai Tittmann
Referee:Prof. Dr. Ralf Ficner
Persistent Address: http://dx.doi.org/10.53846/goediss-5011

 

 

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Abstract

English

During replication of the Phi29 bacteriophage, a DNA packaging motor packages the viral DNA into the procapsid against a maximum pressure difference of ~60 atm, which is generated by the already packed DNA. Several models have been proposed to explain the DNA packaging mechanism and some of these models were ruled out by the experimental studies. Here, three remaining DNA packaging models, untwist-twist, one-way revolution, and push-roll models were studied to elucidate the role of the connector in the packaging process using all-atom explicit solvent molecular dynamics simulations. My simulations study with previous experimental data suggest that the connector does not actively push the viral DNA during the packaging process and therefore untwist-model is highly unlikely. Further, the available energy from ATP hydrolysis is too little to carry out the large-scale spring-like motions in the connector as proposed by this model. This study further suggest that the connector’s essential role is to minimize the DNA leakage as proposed in the one-way revolution model. The connector acts as a one-way valve by a check-valve mechanism, which is newly proposed in this study. During the packaging process, the viral DNA is packaged at a rate of ~2.5 base-pairs per step. As opposed to the one-way revolution model, this particular packaging step size appears to be independent of the connector’s structure on the basis of the current study. Recently, the motions of the DNA during the packaging process are controversially discussed in the one-way revolution and the push-roll models. My study suggests that the DNA revolution and rolling are implausible inside the connector because the gap between the DNA helix and the channel is not enough to carry out these motions. Furthermore, the current study neither supports nor opposes the proposed DNA rotation because the ATPase was not present in the MD simulations. Functional roles of the two motor components, the pRNA and the ATPase remain to be studied at atomic detail by assuming the crystal structure will be available. Understanding the coordination of the connector with the pRNA and the ATPase to transport the DNA is necessary to understand the mechanism of the DNA packaging process.
Keywords: Viral DNA packaging; Molecular Dynamics Simulations; Protein DNA interactions; DNA transport
 
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