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* Residue conservation analysis
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PDB id:
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Atpase/myosin
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Title:
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Crystal structure of myosin v motor with essential light chain- nucleotide-free
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Structure:
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Myosin va. Chain: a. Fragment: motor domain, residues 1-792. Synonym: myosin 5a, dilute myosin heavy chain, non-muscle, myosin heavy chain p190, myosin-v. Engineered: yes. Myosin light chain 1, slow-twitch muscle a isoform. Chain: b. Fragment: residues 59-208.
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Source:
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Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Homo sapiens. Human. Organism_taxid: 9606.
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Biol. unit:
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Dimer (from PDB file)
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Resolution:
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2.05Å
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R-factor:
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0.222
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R-free:
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0.264
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Authors:
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P.-D.Coureux,A.L.Wells,J.Menetrey,C.M.Yengo,C.A.Morris,H.L.Sweeney, A.Houdusse
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Key ref:
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P.D.Coureux
et al.
(2003).
A structural state of the myosin V motor without bound nucleotide.
Nature,
425,
419-423.
PubMed id:
DOI:
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Date:
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21-Mar-03
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Release date:
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26-Sep-03
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PROCHECK
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Headers
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References
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DOI no:
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Nature
425:419-423
(2003)
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PubMed id:
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A structural state of the myosin V motor without bound nucleotide.
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P.D.Coureux,
A.L.Wells,
J.Ménétrey,
C.M.Yengo,
C.A.Morris,
H.L.Sweeney,
A.Houdusse.
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ABSTRACT
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The myosin superfamily of molecular motors use ATP hydrolysis and
actin-activated product release to produce directed movement and force. Although
this is generally thought to involve movement of a mechanical lever arm attached
to a motor core, the structural details of the rearrangement in myosin that
drive the lever arm motion on actin attachment are unknown. Motivated by kinetic
evidence that the processive unconventional myosin, myosin V, populates a unique
state in the absence of nucleotide and actin, we obtained a 2.0 A structure of a
myosin V fragment. Here we reveal a conformation of myosin without bound
nucleotide. The nucleotide-binding site has adopted new conformations of the
nucleotide-binding elements that reduce the affinity for the nucleotide. The
major cleft in the molecule has closed, and the lever arm has assumed a position
consistent with that in an actomyosin rigor complex. These changes have been
accomplished by relative movements of the subdomains of the molecule, and reveal
elements of the structural communication between the actin-binding interface and
nucleotide-binding site of myosin that underlie the mechanism of
chemo-mechanical transduction.
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Selected figure(s)
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Figure 2.
Figure 2: Nucleotide-binding site and distortion of the
beta- -sheet
at the interface of the N-terminal and upper 50-kDa subdomains.
a, Shown is an overlay of the  -sheet
(N-terminal subdomain superimposed) between myosin V in blue and
near rigor (Dictyostelium myosin II) in grey. Note that strands
5 -7, which belong to the upper 50-kDa subdomain are distorted
to allow the upper 50-kDa rotation that removes switch I from
the nucleotide-binding site. b, The positions of the
nucleotide-binding elements are shown for three myosin states.
The yellow asterisk in the myosin V structure marks the position
of the Mg2+ in the other structures. In the transition state,
switch II contributes to coordination of the  -phosphate
of the nucleotide, but it bends in myosin V in the opposite
direction and forms direct interactions (broken green lines)
with the fourth -strand
and the P loop of the N-terminal subdomain.
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Figure 3.
Figure 3: The actin -myosin interface. a, Myosin V as viewed
from the actin side of the interface reveals the positioning of
putative actin-binding elements. b, The same view of myosin V is
overlaid on the lower 50-kDa subdomains of Dictyostelium myosin
II structures. Note the conformational change in the strut and
the obvious rotation of the upper 50-kDa subdomain towards the
actin filament (represented by an arrow) in the myosin V
structure. c, The myosin V and transition state actin-binding
elements are docked on an actin filament, maintaining the
identical positioning of the lower 50-kDa subdomain in both
cases. In myosin V, the HCM loop has been repositioned in such a
way that it can directly contribute to actin binding.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2003,
425,
419-423)
copyright 2003.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.J.Jacobs,
D.Trivedi,
C.David,
and
C.M.Yengo
(2011).
Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle.
|
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J Mol Biol,
407,
716-730.
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|
|
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|
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S.Kühner,
and
S.Fischer
(2011).
Structural mechanism of the ATP-induced dissociation of rigor myosin from actin.
|
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Proc Natl Acad Sci U S A,
108,
7793-7798.
|
|
|
|
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|
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A.Málnási-Csizmadia,
and
M.Kovács
(2010).
Emerging complex pathways of the actomyosin powerstroke.
|
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Trends Biochem Sci,
35,
684-690.
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|
|
|
|
|
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B.Takács,
N.Billington,
M.Gyimesi,
B.Kintses,
A.Málnási-Csizmadia,
P.J.Knight,
and
M.Kovács
(2010).
Myosin complexed with ADP and blebbistatin reversibly adopts a conformation resembling the start point of the working stroke.
|
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Proc Natl Acad Sci U S A,
107,
6799-6804.
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|
|
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|
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C.V.Sindelar,
and
K.H.Downing
(2010).
An atomic-level mechanism for activation of the kinesin molecular motors.
|
| |
Proc Natl Acad Sci U S A,
107,
4111-4116.
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E.Prochniewicz,
H.F.Chin,
A.Henn,
D.E.Hannemann,
A.O.Olivares,
D.D.Thomas,
and
E.M.De La Cruz
(2010).
Myosin isoform determines the conformational dynamics and cooperativity of actin filaments in the strongly bound actomyosin complex.
|
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J Mol Biol,
396,
501-509.
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G.Purushotham,
K.Madhumohan,
M.Anwaruddin,
H.Nagarajaram,
V.Hariram,
C.Narasimhan,
and
M.D.Bashyam
(2010).
The MYH7 p.R787H mutation causes hypertrophic cardiomyopathy in two unrelated families.
|
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Exp Clin Cardiol,
15,
e1-e4.
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|
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|
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H.L.Sweeney,
and
A.Houdusse
(2010).
Structural and functional insights into the Myosin motor mechanism.
|
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Annu Rev Biophys,
39,
539-557.
|
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|
|
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|
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I.Ben Rebeh,
M.Morinière,
L.Ayadi,
Z.Benzina,
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J.Feki,
H.Ayadi,
A.Ghorbel,
F.Baklouti,
and
S.Masmoudi
(2010).
Reinforcement of a minor alternative splicing event in MYO7A due to a missense mutation results in a mild form of retinopathy and deafness.
|
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Mol Vis,
16,
1898-1906.
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J.J.Frye,
V.A.Klenchin,
C.R.Bagshaw,
and
I.Rayment
(2010).
Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236.
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Biochemistry,
49,
4897-4907.
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PDB codes:
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J.T.Granados-Riveron,
T.K.Ghosh,
M.Pope,
F.Bu'Lock,
C.Thornborough,
J.Eason,
E.P.Kirk,
D.Fatkin,
M.P.Feneley,
R.P.Harvey,
J.A.Armour,
and
J.David Brook
(2010).
Alpha-cardiac myosin heavy chain (MYH6) mutations affecting myofibril formation are associated with congenital heart defects.
|
| |
Hum Mol Genet,
19,
4007-4016.
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K.Amano,
T.Yoshidome,
M.Iwaki,
M.Suzuki,
and
M.Kinoshita
(2010).
Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models.
|
| |
J Chem Phys,
133,
045103.
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M.Cecchini,
Y.Alexeev,
and
M.Karplus
(2010).
Pi release from myosin: a simulation analysis of possible pathways.
|
| |
Structure,
18,
458-470.
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|
|
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|
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M.Lorenz,
and
K.C.Holmes
(2010).
The actin-myosin interface.
|
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Proc Natl Acad Sci U S A,
107,
12529-12534.
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R.Tehver,
and
D.Thirumalai
(2010).
Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture.
|
| |
Structure,
18,
471-481.
|
|
|
|
|
|
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S.Wu,
J.Liu,
M.C.Reedy,
R.T.Tregear,
H.Winkler,
C.Franzini-Armstrong,
H.Sasaki,
C.Lucaveche,
Y.E.Goldman,
M.K.Reedy,
and
K.A.Taylor
(2010).
Electron tomography of cryofixed, isometrically contracting insect flight muscle reveals novel actin-myosin interactions.
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PLoS One,
5,
0.
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PDB codes:
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T.P.Burghardt,
K.L.Neff,
E.D.Wieben,
and
K.Ajtai
(2010).
Myosin individualized: single nucleotide polymorphisms in energy transduction.
|
| |
BMC Genomics,
11,
172.
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|
|
|
|
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V.Ovchinnikov,
B.L.Trout,
and
M.Karplus
(2010).
Mechanical coupling in myosin V: a simulation study.
|
| |
J Mol Biol,
395,
815-833.
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|
|
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W.Wriggers
(2010).
Using Situs for the integration of multi-resolution structures.
|
| |
Biophys Rev,
2,
21-27.
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|
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Y.Togashi,
T.Yanagida,
and
A.S.Mikhailov
(2010).
Nonlinearity of mechanochemical motions in motor proteins.
|
| |
PLoS Comput Biol,
6,
e1000814.
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D.Parker,
Z.Bryant,
and
S.L.Delp
(2009).
Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.
|
| |
Cell Mol Bioeng,
2,
366-374.
|
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E.Forgacs,
T.Sakamoto,
S.Cartwright,
B.Belknap,
M.Kovács,
J.Tóth,
M.R.Webb,
J.R.Sellers,
and
H.D.White
(2009).
Switch 1 mutation S217A converts myosin V into a low duty ratio motor.
|
| |
J Biol Chem,
284,
2138-2149.
|
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|
|
|
|
|
K.Ajtai,
M.F.Halstead,
M.Nyitrai,
A.R.Penheiter,
Y.Zheng,
and
T.P.Burghardt
(2009).
The myosin C-loop is an allosteric actin contact sensor in actomyosin.
|
| |
Biochemistry,
48,
5263-5275.
|
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|
|
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|
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K.Teilum,
J.G.Olsen,
and
B.B.Kragelund
(2009).
Functional aspects of protein flexibility.
|
| |
Cell Mol Life Sci,
66,
2231-2247.
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P.Pierobon,
S.Achouri,
S.Courty,
A.R.Dunn,
J.A.Spudich,
M.Dahan,
and
G.Cappello
(2009).
Velocity, processivity, and individual steps of single myosin V molecules in live cells.
|
| |
Biophys J,
96,
4268-4275.
|
|
|
|
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|
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R.Fedorov,
M.Böhl,
G.Tsiavaliaris,
F.K.Hartmann,
M.H.Taft,
P.Baruch,
B.Brenner,
R.Martin,
H.J.Knölker,
H.O.Gutzeit,
and
D.J.Manstein
(2009).
The mechanism of pentabromopseudilin inhibition of myosin motor activity.
|
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Nat Struct Mol Biol,
16,
80-88.
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PDB codes:
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W.Zheng,
and
D.Thirumalai
(2009).
Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II.
|
| |
Biophys J,
96,
2128-2137.
|
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Y.L.Wong,
K.A.Dietrich,
N.Naber,
R.Cooke,
and
S.E.Rice
(2009).
The Kinesin-1 tail conformationally restricts the nucleotide pocket.
|
| |
Biophys J,
96,
2799-2807.
|
|
|
|
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Y.Sugimoto,
O.Sato,
S.Watanabe,
R.Ikebe,
M.Ikebe,
and
K.Wakabayashi
(2009).
Reverse conformational changes of the light chain-binding domain of myosin V and VI processive motor heads during and after hydrolysis of ATP by small-angle X-ray solution scattering.
|
| |
J Mol Biol,
392,
420-435.
|
|
|
|
|
|
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A.Cammarato,
C.M.Dambacher,
A.F.Knowles,
W.A.Kronert,
R.Bodmer,
K.Ocorr,
and
S.I.Bernstein
(2008).
Myosin transducer mutations differentially affect motor function, myofibril structure, and the performance of skeletal and cardiac muscles.
|
| |
Mol Biol Cell,
19,
553-562.
|
|
|
|
|
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A.Vilfan
(2008).
Myosin V passing over Arp2/3 junctions: branching ratio calculated from the elastic lever arm model.
|
| |
Biophys J,
94,
3405-3412.
|
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|
|
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|
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B.Kintses,
Z.Yang,
and
A.Málnási-Csizmadia
(2008).
Experimental investigation of the seesaw mechanism of the relay region that moves the Myosin lever arm.
|
| |
J Biol Chem,
283,
34121-34128.
|
|
|
|
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J.C.Klein,
A.R.Burr,
B.Svensson,
D.J.Kennedy,
J.Allingham,
M.A.Titus,
I.Rayment,
and
D.D.Thomas
(2008).
Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR.
|
| |
Proc Natl Acad Sci U S A,
105,
12867-12872.
|
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|
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|
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J.Ménétrey,
P.Llinas,
J.Cicolari,
G.Squires,
X.Liu,
A.Li,
H.L.Sweeney,
and
A.Houdusse
(2008).
The post-rigor structure of myosin VI and implications for the recovery stroke.
|
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EMBO J,
27,
244-252.
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PDB codes:
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K.M.Trybus
(2008).
Myosin V from head to tail.
|
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Cell Mol Life Sci,
65,
1378-1389.
|
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|
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|
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M.Cecchini,
A.Houdusse,
and
M.Karplus
(2008).
Allosteric communication in myosin V: from small conformational changes to large directed movements.
|
| |
PLoS Comput Biol,
4,
e1000129.
|
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M.Gyimesi,
B.Kintses,
A.Bodor,
A.Perczel,
S.Fischer,
C.R.Bagshaw,
and
A.Málnási-Csizmadia
(2008).
The mechanism of the reverse recovery step, phosphate release, and actin activation of Dictyostelium myosin II.
|
| |
J Biol Chem,
283,
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M.Sun,
M.B.Rose,
S.K.Ananthanarayanan,
D.J.Jacobs,
and
C.M.Yengo
(2008).
Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle.
|
| |
Proc Natl Acad Sci U S A,
105,
8631-8636.
|
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R.E.DeVille,
and
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(2008).
Regular gaits and optimal velocities for motor proteins.
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Biophys J,
95,
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and
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IQ motif selectivity in human IQGAP1: binding of myosin essential light chain and S100B.
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| |
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318,
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H.S.Jung,
Q.Wang,
R.Ikebe,
R.Craig,
and
M.Ikebe
(2008).
The globular tail domain puts on the brake to stop the ATPase cycle of myosin Va.
|
| |
Proc Natl Acad Sci U S A,
105,
1140-1145.
|
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A.C.Dosé,
S.Ananthanarayanan,
J.E.Moore,
B.Burnside,
and
C.M.Yengo
(2007).
Kinetic mechanism of human myosin IIIA.
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J Biol Chem,
282,
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A.R.Hodges,
E.B.Krementsova,
and
K.M.Trybus
(2007).
Engineering the processive run length of Myosin V.
|
| |
J Biol Chem,
282,
27192-27197.
|
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B.Kintses,
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W.Zeng,
C.R.Bagshaw,
and
A.Málnási-Csizmadia
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Reversible movement of switch 1 loop of myosin determines actin interaction.
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C.Cohen,
and
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282,
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C.R.Bagshaw
(2007).
Myosin mechanochemistry.
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H.Park,
A.Li,
L.Q.Chen,
A.Houdusse,
P.R.Selvin,
and
H.L.Sweeney
(2007).
The unique insert at the end of the myosin VI motor is the sole determinant of directionality.
|
| |
Proc Natl Acad Sci U S A,
104,
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|
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H.Yu,
L.Ma,
Y.Yang,
and
Q.Cui
(2007).
Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.
|
| |
PLoS Comput Biol,
3,
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H.Yu,
L.Ma,
Y.Yang,
and
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(2007).
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.
|
| |
PLoS Comput Biol,
3,
e23.
|
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J.Bosch,
S.Turley,
C.M.Roach,
T.M.Daly,
L.W.Bergman,
and
W.G.Hol
(2007).
The closed MTIP-myosin A-tail complex from the malaria parasite invasion machinery.
|
| |
J Mol Biol,
372,
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|
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PDB code:
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J.S.Davis,
and
N.D.Epstein
(2007).
Mechanism of tension generation in muscle: an analysis of the forward and reverse rate constants.
|
| |
Biophys J,
92,
2865-2874.
|
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K.M.Trybus,
M.I.Gushchin,
H.Lui,
L.Hazelwood,
E.B.Krementsova,
N.Volkmann,
and
D.Hanein
(2007).
Effect of calcium on calmodulin bound to the IQ motifs of myosin V.
|
| |
J Biol Chem,
282,
23316-23325.
|
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|
|
|
|
|
N.Naber,
T.J.Purcell,
E.Pate,
and
R.Cooke
(2007).
Dynamics of the nucleotide pocket of myosin measured by spin-labeled nucleotides.
|
| |
Biophys J,
92,
172-184.
|
|
|
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|
N.Volkmann,
H.Lui,
L.Hazelwood,
K.M.Trybus,
S.Lowey,
and
D.Hanein
(2007).
The R403Q Myosin Mutation Implicated in Familial Hypertrophic Cardiomyopathy Causes Disorder at the Actomyosin Interface.
|
| |
PLoS ONE,
2,
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|
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S.Tang,
J.C.Liao,
A.R.Dunn,
R.B.Altman,
J.A.Spudich,
and
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The globular tail domain of myosin Va functions as an inhibitor of the myosin Va motor.
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The structure of the myosin VI motor reveals the mechanism of directionality reversal.
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Nature,
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PDB codes:
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J.Tóth,
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Myosin V from Drosophila reveals diversity of motor mechanisms within the myosin V family.
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Proc Natl Acad Sci U S A,
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PDB codes:
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N.Volkmann,
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L.Hazelwood,
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Mol Cell,
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Proc Natl Acad Sci U S A,
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Magnesium regulates ADP dissociation from myosin V.
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J Biol Chem,
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Initiation of the power stroke in muscle: insights from the phosphate analog AlF4.
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Proc Natl Acad Sci U S A,
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Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.
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Biological, biochemical, and kinetic effects of mutations of the cardiomyopathy loop of Dictyostelium myosin II: importance of ALA400.
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J Biol Chem,
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Proc Natl Acad Sci U S A,
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PDB codes:
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H.L.Sweeney,
and
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The motor mechanism of myosin V: insights for muscle contraction.
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PDB code:
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PDB codes:
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The sliding filament model: 1972-2004.
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A model of myosin V processivity.
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Dynamics of actomyosin interactions in relation to the cross-bridge cycle.
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Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide.
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Nature,
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Structure,
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PDB code:
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|
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|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
 |
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