Evidence for a Partially Stalled γ Rotor in F1-ATPase from Hydrogen–Deuterium Exchange Experiments and Molecular Dynamics Simulations

2018 ◽  
Vol 140 (44) ◽  
pp. 14860-14869 ◽  
Author(s):  
Angela Murcia Rios ◽  
Siavash Vahidi ◽  
Stanley D. Dunn ◽  
Lars Konermann
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
F1 Atpase ◽  
Hydrogen Deuterium ◽  
Dynamics Simulations

scholarly journals Conservation of the conformational dynamics and ligand binding within M49 enzyme family

RSC Advances ◽  
2018 ◽  
Vol 8 (24) ◽  
pp. 13310-13322 ◽  
Author(s):  
Saša Kazazić ◽  
Zrinka Karačić ◽  
Igor Sabljić ◽  
Dejan Agić ◽  
Marko Tomin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Ligand Binding ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Dipeptidyl Peptidase ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Enzyme Family ◽  
Hydrogen Deuterium

The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family).

Molecular Dynamics Simulations of Yeast F1-ATPase before and after 16° Rotation of the γ Subunit

2013 ◽  
Vol 117 (12) ◽  
pp. 3298-3307 ◽  
Author(s):  
Yuko Ito ◽  
Takashi Yoshidome ◽  
Nobuyuki Matubayasi ◽  
Masahiro Kinoshita ◽  
Mitsunori Ikeguchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
F1 Atpase ◽  
Γ Subunit ◽  
Before And After ◽  
Dynamics Simulations

scholarly journals Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90

2015 ◽  
Vol 112 (25) ◽  
pp. E3189-E3198 ◽  
Author(s):  
Edgar E. Boczek ◽  
Lasse G. Reefschläger ◽  
Marco Dehling ◽  
Tobias J. Struller ◽  
Elisabeth Häusler ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Activity ◽  
Molecular Chaperone ◽  
Src Kinase ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Client Proteins ◽  
Dynamics Simulations

Hsp90 is a molecular chaperone involved in the activation of numerous client proteins, including many kinases. The most stringent kinase client is the oncogenic kinase v-Src. To elucidate how Hsp90 chaperones kinases, we reconstituted v-Src kinase chaperoning in vitro and show that its activation is ATP-dependent, with the cochaperone Cdc37 increasing the efficiency. Consistent with in vivo results, we find that Hsp90 does not influence the almost identical c-Src kinase. To explain these findings, we designed Src kinase chimeras that gradually transform c-Src into v-Src and show that their Hsp90 dependence correlates with compactness and folding cooperativity. Molecular dynamics simulations and hydrogen/deuterium exchange of Hsp90-dependent Src kinase variants further reveal increased transitions between inactive and active states and exposure of specific kinase regions. Thus, Hsp90 shifts an ensemble of conformations of v-Src toward high activity states that would otherwise be metastable and poorly populated.

Hydrogen/Deuterium Exchange and Molecular Dynamics Analysis of Amyloid Fibrils Formed by a D69K Charge-Pair Mutant of Human Apolipoprotein C-II

Biochemistry ◽  
2015 ◽  
Vol 54 (31) ◽  
pp. 4805-4814 ◽  
Author(s):  
Yu Mao ◽  
Courtney O. Zlatic ◽  
Michael D. W. Griffin ◽  
Geoffrey J. Howlett ◽  
Nevena Todorova ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amyloid Fibrils ◽  
Deuterium Exchange ◽  
Dynamics Analysis ◽  
Hydrogen Deuterium Exchange ◽  
Human Apolipoprotein ◽  
Apolipoprotein C ◽  
Hydrogen Deuterium

scholarly journals Conformational Change of F1-ATPase ε Subunit upon ATP Binding Studied by Molecular Dynamics Simulations and Small-angle X-ray Scattering

2009 ◽  
Vol 96 (3) ◽  
pp. 299a
Author(s):  
Tomotaka Oroguchi ◽  
Yasuyuki Kato-Yamada ◽  
Hiroshi Hashimoto ◽  
Satoru Unzai ◽  
Mamoru Sato ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Change ◽  
Small Angle ◽  
Atp Binding ◽  
X Ray ◽  
F1 Atpase ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering
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