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* Residue conservation analysis
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PDB id:
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Motor protein
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Title:
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Crystal structure of myosin v motor without nucleotide soaked in 10 mm mgadp
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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. Other_details: soaked mgadp. Myosin light chain 1, slow-twitch muscle a isoform. Chain: b.
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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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3.00Å
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R-factor:
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0.252
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R-free:
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0.318
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Authors:
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P.-D.Coureux,H.L.Sweeney,A.Houdusse
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Key ref:
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P.D.Coureux
et al.
(2004).
Three myosin V structures delineate essential features of chemo-mechanical transduction.
EMBO J,
23,
4527-4537.
PubMed id:
DOI:
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Date:
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03-Sep-04
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Release date:
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22-Feb-05
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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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EMBO J
23:4527-4537
(2004)
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PubMed id:
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Three myosin V structures delineate essential features of chemo-mechanical transduction.
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P.D.Coureux,
H.L.Sweeney,
A.Houdusse.
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ABSTRACT
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The molecular motor, myosin, undergoes conformational changes in order to
convert chemical energy into force production. Based on kinetic and structural
considerations, we assert that three crystal forms of the myosin V motor
delineate the conformational changes that myosin motors undergo upon detachment
from actin. First, a motor domain structure demonstrates that nucleotide-free
myosin V adopts a specific state (rigor-like) that is not influenced by crystal
packing. A second structure reveals an actomyosin state that favors rapid
release of ADP, and differs from the rigor-like state by a P-loop rearrangement.
Comparison of these structures with a third structure, a 2.0 angstroms
resolution structure of the motor bound to an ATP analog, illuminates the
structural features that provide communication between the actin interface and
nucleotide-binding site. Paramount among these is a region we name the
transducer, which is composed of the seven-stranded beta-sheet and associated
loops and linkers. Reminiscent of the beta-sheet distortion of the F1-ATPase,
sequential distortion of this transducer region likely controls sequential
release of products from the nucleotide pocket during force generation.
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Selected figure(s)
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Figure 3.
Figure 3 Cleft closure. (A) The lower and upper 50 kDa
subdomains of myosin V MDE have been pulled apart exposing the
surface interactions allowing cleft closure. Note (in green on
the right) the U50 highly conserved linker that interacts with
the HW and HP helices (white on the left) of the L50 subdomain.
Switch II (orange) and the strut (pink) are two connectors
between the subdomains that help mediate the interactions
between these two surfaces and they are shown on both sides. In
particular, a hydrophobic residue of switch II (Y439, yellow
ball and stick) is a serine or alanine in all myosin II
isoforms. This difference may account in part for the difference
in the kinetics of cleft closure for the two molecules. (B) A
surface CPK representation of the residues involved in this
interface is presented in the same orientation as in A).
Depending on the conservation in the sequence of these residues
in the myosin superfamily, different colors are used (absolutely
conserved (green), conservative changes (pale green) and
nonconserved (purple)). A yellow star indicates how to
reposition the two surfaces to reconstruct the interface.
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Figure 6.
Figure 6 The transducer. The transducer is the central region of
the motor domain near the nucleotide-binding site that includes
the last three strands of the seven-stranded  -sheet
that undergo distortion between the rigor-like and post-rigor
states and the structural elements that accommodate this
distortion. Among these elements are the previously studied
loop, commonly referred to as loop 1 (residues 184 -191), and
the -bulge
(pale green) found at the end of the last two -strands.
Another of these elements is a linker that follows the HO helix,
which provides a pathway of communication to the actin
interface. We thus refer to this linker as the HO linker
(residues 424 -430); it leads to the fifth -strand
that is followed by switch II. Switch I and the P-loop are
connected via three parallel  -helices
that interact with the -sheet.
Loop 1 connects the ends of two of these helices (HF and HG).
When the -sheet
undergoes distortion, these helices rotate and translate
relative to each other.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2004,
23,
4527-4537)
copyright 2004.
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Figures were
selected
by the author.
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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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H.Schmidt,
E.S.Gleave,
and
A.P.Carter
(2012).
Insights into dynein motor domain function from a 3.3-Å crystal structure.
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Nat Struct Mol Biol,
19,
492.
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PDB codes:
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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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N.Naber,
A.Larson,
S.Rice,
R.Cooke,
and
E.Pate
(2011).
Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.
|
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J Mol Biol,
408,
628-642.
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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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S.Masuda,
T.Tomohiro,
and
Y.Hatanaka
(2011).
Rapidly photoactivatable ATP probes for specific labeling of tropomyosin within the actomyosin protein complex.
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Bioorg Med Chem Lett,
21,
2252-2254.
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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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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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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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H.Shi,
and
G.Blobel
(2010).
UNC-45/CRO1/She4p (UCS) protein forms elongated dimer and joins two myosin heads near their actin binding region.
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Proc Natl Acad Sci U S A,
107,
21382-21387.
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PDB code:
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J.A.Spudich,
and
S.Sivaramakrishnan
(2010).
Myosin VI: an innovative motor that challenged the swinging lever arm hypothesis.
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Nat Rev Mol Cell Biol,
11,
128-137.
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J.C.Gebhardt,
Z.Okten,
and
M.Rief
(2010).
The lever arm effects a mechanical asymmetry of the myosin-V-actin bond.
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Biophys J,
98,
277-281.
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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.R.Sellers,
and
C.Veigel
(2010).
Direct observation of the myosin-Va power stroke and its reversal.
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Nat Struct Mol Biol,
17,
590-595.
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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.
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J Chem Phys,
133,
045103.
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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.
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Structure,
18,
471-481.
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|
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|
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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.
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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.
|
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J Mol Biol,
395,
815-833.
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Y.Oguchi,
S.V.Mikhailenko,
T.Ohki,
A.O.Olivares,
E.M.De La Cruz,
and
S.Ishiwata
(2010).
Robust processivity of myosin V under off-axis loads.
|
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Nat Chem Biol,
6,
300-305.
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|
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|
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Y.Togashi,
T.Yanagida,
and
A.S.Mikhailov
(2010).
Nonlinearity of mechanochemical motions in motor proteins.
|
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PLoS Comput Biol,
6,
e1000814.
|
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|
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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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|
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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.
|
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J Biol Chem,
284,
2138-2149.
|
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|
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H.Mahara,
K.Okada,
A.Nomura,
H.Miike,
and
T.Sakurai
(2009).
Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
80,
015306.
|
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|
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H.Onishi
(2009).
Yuji Tonomura: a pioneer in the field of energy transduction in muscle contraction.
|
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J Biochem,
146,
7.
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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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T.Komori,
S.Nishikawa,
T.Ariga,
A.H.Iwane,
and
T.Yanagida
(2009).
Simultaneous measurement of nucleotide occupancy and mechanical displacement in Myosin-v, a processive molecular motor.
|
| |
Biophys J,
96,
L4-L6.
|
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|
|
|
|
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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.
|
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Biophys J,
96,
2128-2137.
|
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|
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|
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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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|
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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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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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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.
|
| |
Cell Mol Life Sci,
65,
1378-1389.
|
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L.A.Amos
(2008).
Molecular motors: not quite like clockwork.
|
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Cell Mol Life Sci,
65,
509-515.
|
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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.H.Taft,
F.K.Hartmann,
A.Rump,
H.Keller,
I.Chizhov,
D.J.Manstein,
and
G.Tsiavaliaris
(2008).
Dictyostelium Myosin-5b is a conditional processive motor.
|
| |
J Biol Chem,
283,
26902-26910.
|
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|
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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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|
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R.Hertzano,
E.Shalit,
A.K.Rzadzinska,
A.A.Dror,
L.Song,
U.Ron,
J.T.Tan,
A.S.Shitrit,
H.Fuchs,
T.Hasson,
N.Ben-Tal,
H.L.Sweeney,
M.H.de Angelis,
K.P.Steel,
and
K.B.Avraham
(2008).
A Myo6 mutation destroys coordination between the myosin heads, revealing new functions of myosin VI in the stereocilia of mammalian inner ear hair cells.
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PLoS Genet,
4,
e1000207.
|
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S.A.Gabel,
and
R.E.London
(2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
|
| |
J Biol Inorg Chem,
13,
207-217.
|
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S.Watanabe,
N.Umeki,
R.Ikebe,
and
M.Ikebe
(2008).
Impacts of Usher syndrome type IB mutations on human myosin VIIa motor function.
|
| |
Biochemistry,
47,
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|
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X.D.Li,
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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|
|
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|
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Y.Takagi,
Y.Yang,
I.Fujiwara,
D.Jacobs,
R.E.Cheney,
J.R.Sellers,
and
M.Kovács
(2008).
Human myosin Vc is a low duty ratio, nonprocessive molecular motor.
|
| |
J Biol Chem,
283,
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|
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B.Kintses,
M.Gyimesi,
D.S.Pearson,
M.A.Geeves,
W.Zeng,
C.R.Bagshaw,
and
A.Málnási-Csizmadia
(2007).
Reversible movement of switch 1 loop of myosin determines actin interaction.
|
| |
EMBO J,
26,
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|
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B.Morriswood,
G.Ryzhakov,
C.Puri,
S.D.Arden,
R.Roberts,
C.Dendrou,
J.Kendrick-Jones,
and
F.Buss
(2007).
T6BP and NDP52 are myosin VI binding partners with potential roles in cytokine signalling and cell adhesion.
|
| |
J Cell Sci,
120,
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|
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C.Cohen,
and
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(2007).
Seeing and knowing in structural biology.
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282,
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H.Onishi,
and
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Proc Natl Acad Sci U S A,
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and
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Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.
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PLoS Comput Biol,
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H.Yu,
L.Ma,
Y.Yang,
and
Q.Cui
(2007).
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.
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PLoS Comput Biol,
3,
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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,
77-88.
|
|
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PDB code:
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|
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|
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J.R.Sellers,
and
P.J.Knight
(2007).
Folding and regulation in myosins II and V.
|
| |
J Muscle Res Cell Motil,
28,
363-370.
|
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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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K.Shiroguchi,
and
K.Kinosita
(2007).
Myosin V walks by lever action and Brownian motion.
|
| |
Science,
316,
1208-1212.
|
|
|
|
|
|
|
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,
e1123.
|
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|
|
|
|
|
S.Tang,
J.C.Liao,
A.R.Dunn,
R.B.Altman,
J.A.Spudich,
and
J.P.Schmidt
(2007).
Predicting allosteric communication in myosin via a pathway of conserved residues.
|
| |
J Mol Biol,
373,
1361-1373.
|
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|
|
|
|
|
Y.Sun,
H.W.Schroeder,
J.F.Beausang,
K.Homma,
M.Ikebe,
and
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Rigor-like structures from muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor.
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PDB codes:
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B.Geislinger,
and
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Brownian molecular motors driven by rotation-translation coupling.
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Flexible light-chain and helical structure of F-actin explain the movement and step size of myosin-VI.
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Biophys J,
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Proc Natl Acad Sci U S A,
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J.Liu,
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(2006).
Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography.
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Nature,
442,
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PDB code:
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J.R.Sellers,
and
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(2006).
Walking with myosin V.
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The cargo-binding domain regulates structure and activity of myosin 5.
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Nature,
442,
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M.Sun,
J.L.Oakes,
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Dynamics of the upper 50-kDa domain of myosin V examined with fluorescence resonance energy transfer.
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J Biol Chem,
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N.R.Guydosh,
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Backsteps induced by nucleotide analogs suggest the front head of kinesin is gated by strain.
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Proc Natl Acad Sci U S A,
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The actin-binding cleft: functional characterisation of myosin II with a strut mutation.
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Adaptability of myosin V studied by simultaneous detection of position and orientation.
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The globular tail domain of myosin Va functions as an inhibitor of the myosin Va motor.
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PDB codes:
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J.S.Allingham,
R.Smith,
and
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The structural basis of blebbistatin inhibition and specificity for myosin II.
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PDB code:
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Magnesium regulates ADP dissociation from myosin V.
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Crystal structure of the GTPase domain of rat dynamin 1.
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Proc Natl Acad Sci U S A,
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PDB code:
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|
H.L.Sweeney,
and
A.Houdusse
(2004).
The motor mechanism of myosin V: insights for muscle contraction.
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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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