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PDBsum entry 1vri
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Virus/viral protein
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PDB id
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1vri
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References listed in PDB file
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Key reference
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Title
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Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by prna of phi29 DNA-Packaging motor.
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Authors
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Y.Y.Guo,
F.Blocker,
F.Xiao,
P.Guo.
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Ref.
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J Nanosci Nanotechnol, 2005,
5,
856-863.
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PubMed id
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Abstract
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The bottom-up assembly of patterned arrays is an exciting and important area in
current nanotechnology. Arrays can be engineered to serve as components in chips
for a virtually inexhaustible list of applications ranging from disease
diagnosis to ultrahigh-density data storage. In attempting to achieve this goal,
a number of methods to facilitate array design and production have been
developed. Cloning and expression of the gene coding for the connector of the
bacterial virus phi29 DNA-packaging motor, overproduction of the gene products,
and the in vitro construction of large-scale carpet-like arrays composed of
connector are described in this report. The stability of the arrays under
various conditions, including varied pH, temperature and ionic strength, was
tested. The addition of packaging RNA (pRNA) into the array caused a dramatic
shift in array structure, and resulted in the conversion of tetragonal arrays
into larger decagonal structures comprised of both protein and RNA. RNase
digestion confirmed that the conformational shift was caused by pRNA, and that
RNA was present in the decagons. As has been demonstrated in biomotors,
conformational shift of motor components can generate force for motor motion.
The conformational shift reported here can be utilized as a potential
force-generating mechanism for the construction of nanomachines.
Three-dimensional computer models of the constructed arrays were also produced
using a variety of connector building blocks with or without the N- or
C-terminal sequence, which is absent from the current published crystal
structures. Both the connector array and the decagon are ideal candidates to be
used as templates to build patterned suprastructures in nanotechnology.
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Secondary reference #1
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Title
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Detailed architecture of a DNA translocating machine: the high-Resolution structure of the bacteriophage phi29 connector particle.
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Authors
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A.Guasch,
J.Pous,
B.Ibarra,
F.X.Gomis-Rüth,
J.M.Valpuesta,
N.Sousa,
J.L.Carrascosa,
M.Coll.
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Ref.
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J Mol Biol, 2002,
315,
663-676.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. (a) Atom-sphere model of the p10 connector
particle. Colour coding of the side-chains: green for Asn/Gln,
red for Asp/Glu, grey for hydrophobic residues, and dark blue
for Lys/Arg. The model was generated with GRASP.[63] (b)
Molecular surface coloured according to electrostatic potential
(red for negative, blue for positive) belonging to six vicinal
protein monomers generated with GRASP. [63] The position of the
two interior lysine rings (made up by Lys209 and Lys200 of each
monomer, respectively) is indicated. (c) Ribbon plot showing a
longitudinal cut of the connector particle. Note that the
colours of the distal domains are different from the central and
SH3-like domains since they belong to different monomers. A
dsB-DNA molecule is shown traversing the central channel. The
side-chains of Lys200 and Lys209 are indicated. (d) View along
the connector axis with the modelled DNA. The side-chains of
Lys200 and Lys209 are displayed as a balls and sticks.
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Figure 6.
Figure 6. The spinning connector model. (a) Schematic
arrangement of a portal vertex in projection view from the viral
prohead. A1 to A6 represent the ATPase (p16), S1 to S12
represent the connector subunits, and P1, 2, 3, etc. represent
the DNA phosphates of a DNA chain. For clarity, the model is
restricted to the description of one single DNA chain and one
lysine ring. The starting position (I) aligns a Lys (blue star)
of subunit S1 with the phosphate P1. Firing of the p16 ATPase
(A1) rotates the connector 12° clockwise while the DNA moves
linearly along the connector axis by 2 bp. A transient
interaction among the corresponding Lys from S2 and the
phosphates P2 (II) occurs at 6° rotation. The final stage
(III) is characterized by the interaction of Lys S3 and the
phosphate P3, which is accomplished after a further clockwise
rotation of the connector by 6°. This movement positions the
next p16 ATPase (A2) in an equivalent position with respect to
the DNA, to that of A1 in step I. (b) Schematic representation
of a side view of the model, corresponding to the same steps as
in (a). The lysine residues are depicted as blue spheres
labelled K1, K2,.... In step I there is a strong interaction
between lysine K1 and phosphate P1 (continuous line), while the
interaction of lysine K2 with phosphate P2 is still weak because
P2 is on a lower plane than the ring of lysine residues (broken
line). In step II the 6° rotation of the connector places
lysine K2 in an optimal position to interact with phosphate P2,
provided there is a longitudinal displacement of the DNA by 1
bp. In step III there has been a further 6° rotation of the
connector and another 1-bp displacement of the DNA, implying
that lysine K3 is now aligned with phosphate P3. The movement of
two base-pairs of DNA from I to III is, thus, correlated with a
rotation of the connector by 12°.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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