A method to optimize a conformational pathway through a space of well-chosen reduced variables is employed to advance our understanding of protein conformational equilibrium. The adaptively biased path optimization strategy utilizes unrestricted, enhanced sampling in the region of a path in the reduced-variable space to identify a broad path between two stable end-states. Application to the inactivation transition of the Src tyrosine kinase catalytic domain reveals new insight into this well studied conformational equilibrium. The mechanistic description gained from identifying the motions and structural features along the path includes details of the switched electrostatic network found to underpin the transition. The free energy barrier along the path results from rotation of a helix, αC, that is tightly correlated with motions in the activation loop (A-loop) as well as distal regions in the C-lobe. Path profiles of the reduced variables clearly demonstrate the strongly correlated motions. The exchange of electrostatic interactions among residues in the network is key to these interdependent motions. In addition, the increased resolution from an all-atom model in defining the path shows multiple components for the A-loop motion and that different parts of the A-loop contribute throughout the length of the path.
REFERENCES
1.
N.
Plattner
, S.
Doerr
, G.
De Fabritiis
, and F.
Noé
, “Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
,” Nat. Chem.
9
, 1005
(2017
).2.
B. E.
Husic
and V. S.
Pande
, “Markov state models: From an art to a science
,” J. Am. Chem. Soc.
140
, 2386
(2018
).3.
D. E.
Shaw
, P.
Maragakis
, K.
Lindorff-Larsen
, S.
Piana
, R. O.
Dror
, M. P.
Eastwood
, J. A.
Bank
, J. M.
Jumper
, J. K.
Salmon
, Y.
Shan
, and W.
Wriggers
, “Atomic-level characterization of the structural dynamics of proteins
,” Science
330
, 341
(2010
).4.
M. M.
Sultan
, R. A.
Denny
, R.
Unwalla
, F.
Lovering
, and V. S.
Pande
, “Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain
,” Sci. Rep.
7
, 15604
(2017
).5.
C.-M.
Suomivuori
, N. R.
Latorraca
, L. M.
Wingler
, S.
Eismann
, M. C.
King
, A. L. W.
Kleinhenz
, M. A.
Skiba
, D. P.
Staus
, A. C.
Kruse
, R. J.
Lefkowitz
, and R. O.
Dror
, “Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor
,” Science
367
, 881
(2020
).6.
L. T.
Chong
, A. S.
Saglam
, and D. M.
Zuckerman
, “Path-sampling strategies for simulating rare events in biomolecular systems
,” Curr. Opin. Struct. Biol.
43
, 88
(2017
).7.
D. K.
Wolfe
, J. R.
Persichetti
, A. K.
Sharma
, P. S.
Hudson
, H. L.
Woodcock
, and E. P.
O’Brien
, “Hierarchical Markov state model building to describe molecular processes
,” J. Chem. Theory Comput.
16
, 1816
(2020
).8.
A. C.
Pan
, T. M.
Weinreich
, Y.
Shan
, D. P.
Scarpazza
, and D. E.
Shaw
, “Assessing the accuracy of two enhanced sampling methods using EGFR kinase transition pathways: The influence of collective variable choice
,” J. Chem. Theory Comput.
10
, 2860
(2014
).9.
D.
Shukla
, Y. L.
Meng
, B.
Roux
, and V. S.
Pande
, “Activation pathway of Src kinase reveals intermediate states as targets for drug design
,” Nat. Commun.
5
, 3397
(2014
).10.
B. M.
Dickson
, H.
Huang
, and C. B.
Post
, “Unrestrained computation of free energy along a path
,” J. Phys. Chem. B
116
, 11046
(2012
).11.
D.
Branduardi
, F. L.
Gervasio
, and M.
Parrinello
, “From A to B in free energy space
,” J. Chem. Phys.
126
, 054103
(2007
).12.
M.
Chen
and W.
Yang
, “On-the-path random walk sampling for efficient optimization of minimum free-energy path
,” J. Comput. Chem.
30
, 1649
(2009
).13.
W.
E
, W.
Ren
, and E.
Vanden-Eijnden
, “Finite temperature string method for the study of rare events
,” J. Phys. Chem. B
109
, 6688
(2005
).14.
W.
Ren
, E.
Vanden-Eijnden
, P.
Maragakis
, and W.
E
, “Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide
,” J. Chem. Phys.
123
, 134109
(2005
).15.
R.
Elber
, “Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide
,” J. Chem. Phys.
93
, 4312
(1990
).16.
B. M.
Dickson
, “Approaching a parameter-free metadynamics
,” Phys. Rev. E
84
, 037701
(2011
).17.
H.
Huang
, R.
Zhao
, B. M.
Dickson
, R. D.
Skeel
, and C. B.
Post
, “αC helix as a switch in the conformational transition of Src/CDK-like kinase domains
,” J. Phys. Chem. B
116
, 4465
(2012
).18.
H.
Wu
and C. B.
Post
, “Protein conformational transitions from all-atom adaptively biased path optimization
,” J. Chem. Theory Comput.
14
, 5372
(2018
).19.
G.
Manning
, D. B.
Whyte
, R.
Martinez
, T.
Hunter
, and S.
Sudarsanam
, “The protein kinase complement of the human genome
,” Science
298
, 1912
(2002
).20.
J.
Schlessinger
, “Cell signaling by receptor tyrosine kinases
,” Cell
103
, 211
(2000
).21.
A. N.
Matthew
, J.
Zephyr
, D.
Nageswara Rao
, M.
Henes
, W.
Kamran
, K.
Kosovrasti
, A. K.
Hedger
, G. J.
Lockbaum
, J.
Timm
, A.
Ali
, N.
Kurt Yilmaz
, and C. A.
Schiffer
, “Avoiding drug resistance by substrate envelope-guided design: Toward potent and robust HCV NS3/4A protease inhibitors
,” mBio
11
, e00172
(2020
).22.
K. S.
Bhullar
, N. O.
Lagarón
, E. M.
McGowan
, I.
Parmar
, A.
Jha
, B. P.
Hubbard
, and H. P. V.
Rupasinghe
, “Kinase-targeted cancer therapies: Progress, challenges and future directions
,” Mol. Cancer
17
, 48
(2018
).23.
S.
Klaeger
, S.
Heinzlmeir
, M.
Wilhelm
, H.
Polzer
, B.
Vick
, P.-A.
Koenig
, M.
Reinecke
, B.
Ruprecht
, S.
Petzoldt
, C.
Meng
, J.
Zecha
, K.
Reiter
, H.
Qiao
, D.
Helm
, H.
Koch
, M.
Schoof
, G.
Canevari
, E.
Casale
, S. R.
Depaolini
, A.
Feuchtinger
, Z.
Wu
, T.
Schmidt
, L.
Rueckert
, W.
Becker
, J.
Huenges
, A.-K.
Garz
, B.-O.
Gohlke
, D. P.
Zolg
, G.
Kayser
, T.
Vooder
, R.
Preissner
, H.
Hahne
, N.
Tõnisson
, K.
Kramer
, K.
Götze
, F.
Bassermann
, J.
Schlegl
, H.-C.
Ehrlich
, S.
Aiche
, A.
Walch
, P. A.
Greif
, S.
Schneider
, E. R.
Felder
, J.
Ruland
, G.
Médard
, I.
Jeremias
, K.
Spiekermann
, and B.
Kuster
, “The target landscape of clinical kinase drugs
,” Science
358
, eaan4368
(2017
).24.
E.
Ozkirimli
, S. S.
Yadav
, W. T.
Miller
, and C. B.
Post
, “An electrostatic network and long-range regulation of Src kinases
,” Protein Sci.
17
, 1871
(2008
).25.
E.
Ozkirimli
and C. B.
Post
, “Src kinase activation: A switched electrostatic network
,” Protein Sci.
15
, 1051
(2006
).26.
Y.
Meng
, D.
Shukla
, V. S.
Pande
, and B.
Roux
, “Transition path theory analysis of c-Src kinase activation
,” Proc. Natl. Acad. Sci. U. S. A.
113
, 9193
(2016
).27.
Y.
Meng
, C.
Gao
, D. K.
Clawson
, S.
Atwell
, M.
Russell
, M.
Vieth
, and B.
Roux
, “Predicting the conformational variability of abl tyrosine kinase using molecular dynamics simulations and Markov state models
,” J. Chem. Theory Comput.
14
, 2721
(2018
).28.
M. M.
Sultan
, G.
Kiss
, and V. S.
Pande
, “Towards simple kinetic models of functional dynamics for a kinase subfamily
,” Nat. Chem.
10
, 903
(2018
).29.
E.
Pucheta-Martínez
, G.
Saladino
, M. A.
Morando
, J.
Martinez-Torrecuadrada
, M.
Lelli
, L.
Sutto
, N.
D’Amelio
, and F. L.
Gervasio
, “An allosteric cross-talk between the activation loop and the ATP binding site regulates the activation of Src kinase
,” Sci. Rep.
6
, 24235
(2016
).30.
C.-C.
Tsai
, Z.
Yue
, and J.
Shen
, “How electrostatic coupling enables conformational plasticity in a tyrosine kinase
,” J. Am. Chem. Soc.
141
, 15092
(2019
).31.
Y.
Meng
and B.
Roux
, “Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop
,” J. Mol. Biol.
426
, 423
(2014
).32.
W.
Xu
, A.
Doshi
, M.
Lei
, M. J.
Eck
, and S. C.
Harrison
, “Crystal structures of c-Src reveal features of its autoinhibitory mechanism
,” Mol. Cell
3
, 629
(1999
).33.
S. W.
Cowan-Jacob
, G.
Fendrich
, P. W.
Manley
, W.
Jahnke
, D.
Fabbro
, J.
Liebetanz
, and T.
Meyer
, “The crystal structure of a c-Src complex in an active conformation suggests possible steps in c-Src activation
,” Structure
13
, 861
(2005
).34.
S. S.
Taylor
and A. P.
Kornev
, “Protein kinases: Evolution of dynamic regulatory proteins
,” Trends Biochem. Sci.
36
, 65
(2011
).35.
D.
Liu
, Y.
Yuan
, R.
Xu
, and D.
Cowburn
, “Domain interactions of C-terminal Src Kinase determined through NMR spectroscopy with segmental isotope labeling
,” Protein Cell
8
, 67
(2017
).36.
M.
Tong
, J. G.
Pelton
, M. L.
Gill
, W.
Zhang
, F.
Picart
, and M. A.
Seeliger
, “Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites
,” Nat. Commun.
8
, 2160
(2017
).37.
M. K.
Joshi
, R. A.
Burton
, H.
Wu
, A. M.
Lipchik
, B. P.
Craddock
, H.
Mo
, L. L.
Parker
, W. T.
Miller
, and C. B.
Post
, “Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics
,” Protein Sci.
29
, 350
(2020
).38.
W.
Gan
, S.
Yang
, and B.
Roux
, “Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories
,” Biophys. J.
97
, L8
(2009
).39.
M.
LaFevre-Bernt
, F.
Sicheri
, A.
Pico
, M.
Porter
, J.
Kuriyan
, and W. T.
Miller
, “Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue
,” J. Biol. Chem.
273
, 32129
(1998
).40.
S.
Gonfloni
, A.
Weijland
, J.
Kretzschmar
, and G.
Superti-Furga
, “Crosstalk between the catalytic and regulatory domains allows bidirectional regulation of Src
,” Nat. Struct. Biol.
7
, 281
(2000
).41.
S.
Gonfloni
, F.
Frischknecht
, M.
Way
, and G.
Superti-Furga
, “Leucine 255 of Src couples intramolecular interactions to inhibition of catalysis
,” Nat. Struct. Biol.
6
, 760
(1999
).42.
S.
Gonfloni
, J. C.
Williams
, K.
Hattula
, A.
Weijland
, R. K.
Wierenga
, and G.
Superti-Furga
, “The role of the linker between the SH2 domain and catalytic domain in the regulation and function of Src
,” Embo J.
16
, 7261
(1997
).43.
Y.
Meng
and B.
Roux
, “Computational study of the W260A activating mutant of Src tyrosine kinase
,” Protein Sci.
25
, 219
(2016
).44.
M.
Fajer
, Y.
Meng
, and B.
Roux
, “The activation of c-Src tyrosine kinase: Conformational transition pathway and free energy landscape
,” J. Phys. Chem. B
121
, 3352
(2017
).45.
E.
Milanetti
, A. G.
Trandafir
, J.
Alba
, D.
Raimondo
, and M.
D’Abramo
, “Efficient and accurate modeling of conformational transitions in proteins: The case of c-Src kinase
,” J. Phys. Chem. B
122
, 8853
(2018
).46.
A.
Berteotti
, A.
Cavalli
, D.
Branduardi
, F. L.
Gervasio
, M.
Recanatini
, and M.
Parrinello
, “Protein conformational transitions: The closure mechanism of a kinase explored by atomistic simulations
,” J. Am. Chem. Soc.
131
, 244
(2009
).47.
G.
La Sala
, L.
Riccardi
, R.
Gaspari
, A.
Cavalli
, O.
Hantschel
, and M.
De Vivo
, “HRD motif as the central hub of the signaling network for activation loop autophosphorylation in Abl kinase
,” J. Chem. Theory Comput.
12
, 5563
(2016
).© 2020 Author(s).
2020
Author(s)
You do not currently have access to this content.
