A Minimal Kinetic Model for a Viral DNA Packaging Machine†

Biochemistry ◽  
2004 ◽  
Vol 43 (2) ◽  
pp. 289-299 ◽  
Author(s):  
Qin Yang ◽  
Carlos Enrique Catalano
Keyword(s):  
Kinetic Model ◽  
Dna Packaging ◽  
Viral Dna ◽  
Packaging Machine ◽  
Viral Dna Packaging

scholarly journals Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4

2014 ◽  
Vol 111 (42) ◽  
pp. 15096-15101 ◽  
Author(s):  
Reza Vafabakhsh ◽  
Kiran Kondabagil ◽  
Tyler Earnest ◽  
Kyung Suk Lee ◽  
Zhihong Zhang ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Bacteriophage T4 ◽  
Dna Packaging ◽  
Viral Dna ◽  
Packaging Machine ◽  
Viral Dna Packaging

Interaction of the adenoviral IVa2 protein with a truncated viral DNA packaging sequence

2009 ◽  
Vol 140 (1-3) ◽  
pp. 78-90 ◽  
Author(s):  
Teng-Chieh Yang ◽  
Qin Yang ◽  
Nasib Karl Maluf
Keyword(s):  
Dna Packaging ◽  
Viral Dna ◽  
Viral Dna Packaging ◽  
Packaging Sequence

scholarly journals Role for the Adenovirus IVa2 Protein in Packaging of Viral DNA

2001 ◽  
Vol 75 (21) ◽  
pp. 10446-10454 ◽  
Author(s):  
Wei Zhang ◽  
Jonathan A. Low ◽  
Joan B. Christensen ◽  
Michael J. Imperiale
Keyword(s):  
Gene Transfer ◽  
Direct Evidence ◽  
Helper Virus ◽  
Dna Packaging ◽  
Chimeric Virus ◽  
Viral Dna ◽  
293 Cells ◽  
Inverted Terminal Repeats ◽  
Viral Dna Packaging ◽  
Packaging Sequence

ABSTRACT Although it has been demonstrated that the adenovirus IVa2 protein binds to the packaging domains on the viral chromosome and interacts with the viral L1 52/55-kDa protein, which is required for viral DNA packaging, there has been no direct evidence demonstrating that the IVa2 protein is involved in DNA packaging. To understand in greater detail the DNA packaging mechanisms of adenovirus, we have asked whether DNA packaging is serotype or subgroup specific. We found that Ad7 (subgroup B), Ad12 (subgroup A), and Ad17 (subgroup D) cannot complement the defect of an Ad5 (subgroup C) mutant,pm8001, which does not package its DNA due to a mutation in the L1 52/55-kDa gene. This indicates that the DNA packaging systems of different serotypes cannot interact productively with Ad5 DNA. Based on this, a chimeric virus containing the Ad7 genome except for the inverted terminal repeats and packaging sequence from Ad5 was constructed. This chimeric virus replicates its DNA and synthesizes Ad7 proteins, but it cannot package its DNA in 293 cells or 293 cells expressing the Ad5 L1 52/55-kDa protein. However, this chimeric virus packages its DNA in 293 cells expressing the Ad5 IVa2 protein. These results indicate that the IVa2 protein plays a role in viral DNA packaging and that its function is serotype specific. Since this chimeric virus cannot package its own DNA, but produces all the components for packaging Ad7 DNA, it may be a more suitable helper virus for the growth of Ad7 gutted vectors for gene transfer.

Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine

2020 ◽  
Vol 63 (8) ◽  
pp. 1103-1129 ◽  
Author(s):  
Chenxi Liang ◽  
Tao Weitao ◽  
Lixia Zhou ◽  
Peixuan Guo
Keyword(s):  
Dna Packaging ◽  
Viral Dna ◽  
Viral Dna Packaging

scholarly journals A Mechanochemical Model of a Viral DNA Packaging Motor

2010 ◽  
Vol 98 (3) ◽  
pp. 656a
Author(s):  
Jin Yu ◽  
Jeffrey Moffitt ◽  
Craig Hetherington ◽  
Carlos Bustamante ◽  
George Oster
Keyword(s):  
Dna Packaging ◽  
Viral Dna ◽  
Dna Packaging Motor ◽  
Viral Dna Packaging ◽  
Mechanochemical Model ◽  
Viral Dna Packaging Motor

Mechanochemistry of a Viral DNA Packaging Motor

2010 ◽  
Vol 400 (2) ◽  
pp. 186-203 ◽  
Author(s):  
Jin Yu ◽  
Jeffrey Moffitt ◽  
Craig L. Hetherington ◽  
Carlos Bustamante ◽  
George Oster
Keyword(s):  
Dna Packaging ◽  
Viral Dna ◽  
Dna Packaging Motor ◽  
Viral Dna Packaging ◽  
Viral Dna Packaging Motor

scholarly journals Visualizing ATP hydrolysis in a viral DNA-packaging molecular motor

2014 ◽  
Vol 70 (a1) ◽  
pp. C1604-C1604
Author(s):  
Liang Tang ◽  
Haiyan Zhao ◽  
Theodore Christensen ◽  
Zihan Lin ◽  
Annie Lynn
Keyword(s):  
Chemical Reaction ◽  
Time Course ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Translational Motion ◽  
Alpha Helix ◽  
Dna Packaging ◽  
Side Chain ◽  
Viral Dna ◽  
Viral Dna Packaging

Many DNA viruses encode powerful molecular machines to package viral genome into preformed protein shells. These DNA-packaging motors contain an ATPase module that converts the chemical reaction of ATP hydrolysis to physical motion of DNA. We previously determined the structures of the DNA-packaging motor gp2 of Shigella phage Sf6 in the apo form and in complex with ADP and ATP-gamma-S (Zhao et al, 2013, PNAS, 110, 8075). Here we report the structure of gp2 in complex with its substrate ATP at 2.0 Angstrom resolution. To our knowledge, this is the first time to capture, at high resolution, a precatalytic state for ASCE-superfamily ATPases, which include a large group of nucleic acid helicases and translocases involved in a broad range of cellular and viral processes. The structure reveals the precise architecture of the ATP-bound state of the motor immediately prior to catalysis. Comparison with structures of the apo and ADP-complexed forms unveils motions of the Walker A motif coupled with ATP and Mg2+ binding and ATP hydrolysis. In the Walker B motif, residue E118 undergoes a side chain conformational switching coupled with the ATP hydrolysis, whereas residue E119 locks residue R51 side chain to a conformation that is readily reachable to residue E118 side chain. Residue E121 in the Walker B motif deprotonates a water molecule, which acts as a nucleophile to attack the gamma-phosphorous, leading to ATP hydrolysis. The alpha-helix (residue G182-R194) in the linker domain undergoes a translational motion against the ATPase domain triggered by ATP hydrolysis, serving as a mechanism for translating the energy from the chemical reaction into physical movement of DNA. We further observed the time course of ATP hydrolysis by gp2 by determining structures of gp2:ATP complexes captured at various incubation time. These structures have made it possible to delineate, at atomic detail, the complete cycle of ATP hydrolysis of this viral DNA-packaging molecular motor.

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