Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter

2016-trek2

Matthew P. Harrigan; Keri A. McKiernan; Veerabahu Shanmugasundaram; Rajiah Aldrin Denny; Vijay S. Pande

2017-04-04 (online) – 2017-12-01 (print)

Scientific Reports (Sci. Rep.). 7, 1, doi:10.1038/s41598-017-00256-y

Instantaneous ion configurations in the K+ion channel selectivity filter revealed by 2D IR spectroscopy

2016-kratochvil-soft-knock

Huong T. Kratochvil; Joshua K. Carr; Kimberly Matulef; Alvin W. Annen; Hui Li; Michał Maj; Jared Ostmeyer; Arnaldo L. Serrano; H. Raghuraman; Sean D. Moran; J. L. Skinner; Eduardo Perozo; Benoît Roux; Francis I. Valiyaveetil; Martin T. Zanni

2016-09-01 (online) – 2016-09-02 (print)

Science (Science). 353, 6303, 1040-1044. doi:10.1126/science.aag1447

Polymodal activation of the TREK-2 K2P channel produces structurally distinct open states

mcclenaghan2016polymodal

Conor McClenaghan; Marcus Schewe; Prafulla Aryal; Elisabeth P. Carpenter; Thomas Baukrowitz; Stephen J. Tucker

2016-05-30 (online) – 2016-06-01 (print)

The Journal of General Physiology (J. Gen. Physiol.). 147, 6, 497-505. doi:10.1085/jgp.201611601

Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance

2016-melcr-membrane-compare

Josef Melcr; Daniel Bonhenry; Štěpán Timr; Pavel Jungwirth

2016-05-10 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 12, 5, 2418-2425. doi:10.1021/acs.jctc.5b01202

Description

Compare external electric field with ion imbalance.

Allosteric coupling between proximal C-terminus and selectivity filter is facilitated by the movement of transmembrane segment 4 in TREK-2 channel

ren2016allosteric

Ren-Gong Zhuo; Peng Peng; Xiao-Yan Liu; Hai-Tao Yan; Jiang-Ping Xu; Jian-Quan Zheng; Xiao-Li Wei; Xiao-Yun Ma

2016-02-16 (online) – 2016-08-01 (print)

Scientific Reports (Sci. Rep.). 6, 1, doi:10.1038/srep21248

A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K+ Channels

schewe2016non

Marcus Schewe; Ehsan Nematian-Ardestani; Han Sun; Marianne Musinszki; Sönke Cordeiro; Giovanna Bucci; Bert L. de Groot; Stephen J. Tucker; Markus Rapedius; Thomas Baukrowitz

2016-02-01 (print)

Cell (Cell). 164, 5, 937-949. doi:10.1016/j.cell.2016.02.002

K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac

2015-carpenter-structures

Y. Y. Dong; A. C. W. Pike; A. Mackenzie; C. McClenaghan; P. Aryal; L. Dong; A. Quigley; M. Grieben; S. Goubin; S. Mukhopadhyay; G. F. Ruda; M. V. Clausen; L. Cao; P. E. Brennan; N. A. Burgess-Brown; M. S. P. Sansom; S. J. Tucker; E. P. Carpenter

2015-03-12 (online) – 2015-03-13 (print)

Science (Science). 347, 6227, 1256-1259. doi:10.1126/science.1261512

Description

Structures of up and down trek2.

Cites 2010-k2p-review (ref. 1) for background.

PDB codes

4XDJ (down state), 4BW5 (up state), 4XDL (Br-fluoxetine complex, down), 4XDK (norfluoxetine complex, down)

kchan structures

State-independent intracellular access of quaternary ammonium blockers to the pore of TREK-1

rapedius2012state

Markus Rapedius; Matthias R. Schmidt; Chetan Sharma; Phillip J. Stansfeld; Mark S.P. Sansom; Thomas Baukrowitz; Stephen J. Tucker

2014-10-31 (online) – 2012-11-18 (print)

Channels (Channels). 6, 6, 473-478. doi:10.4161/chan.22153

Molecular regulations governing TREK and TRAAK channel functions

noel2011molecular

Jacques Noël; Guillaume Sandoz; Florian Lesage

2014-10-27 (online) – 2011-09-01 (print)

Channels (Channels). 5, 5, 402-409. doi:10.4161/chan.5.5.16469

Potassium ions line up

hummer2014potassium

G. Hummer

2014-10-16 (online) – 2014-10-17 (print)

Science (Science). 346, 6207, 303-303. doi:10.1126/science.1260555

Ion permeation in K+ channels occurs by direct Coulomb knock-on

2014-kopfer-hard-knock

D. A. Kopfer; C. Song; T. Gruene; G. M. Sheldrick; U. Zachariae; B. L. de Groot

2014-10-16 (online) – 2014-10-17 (print)

Science (Science). 346, 6207, 352-355. doi:10.1126/science.1254840

Description

Introduces a new way of simulating a membrane potential: They stack two membranes on top of one another, creating an "inside" between the two. This doesn't hurt simulation throughput, because you get twice as much protein motion data in the same amount of simulation time (ignore extra factor of log n in system size). This seems to be a refinement on their earlier work in 2011-kutzner-double-membrane (ref. 25).

They hide the startling fact that every time an ion moves through the channel, they have to instantaneously move it back inside. Benoit has argued that this instantaneous jump, which can be a 100 mV difference is rediculous.

The main point of this paper is that ions translocate through the four sites of potassium channel without any waters between them. This "hard knock" mechanism is in contrast to a "soft knock" mechanism where the ion-ion interactions are softened by interviening waters.

They re-refine the xray data to show it is consistent with the hard-knock mechanism.

kchan md-applications

A hydrophobic barrier deep within the inner pore of the TWIK-1 K2P potassium channel

aryal2014hydrophobic

Prafulla Aryal; Firdaus Abd-Wahab; Giovanna Bucci; Mark S. P. Sansom; Stephen J. Tucker

2014-07-08 (online)

Nature Communications (Nat. Commun.). 5, doi:10.1038/ncomms5377

Constant electric field simulations of the membrane potential illustrated with simple systems

2012-roux-efield

James Gumbart; Fatemeh Khalili-Araghi; Marcos Sotomayor; Benoît Roux

2012-02-01 (print)

Biochimica et Biophysica Acta (BBA) - Biomembranes (Biochimica et Biophysica Acta (BBA) - Biomembranes). 1818, 2, 294-302. doi:10.1016/j.bbamem.2011.09.030

Description

Constant electric field

The pore structure and gating mechanism of K2P channels

piechotta2011pore

Paula L Piechotta; Markus Rapedius; Phillip J Stansfeld; Murali K Bollepalli; Gunter Erhlich; Isabelle Andres-Enguix; Hariolf Fritzenschaft; Niels Decher; Mark S P Sansom; Stephen J Tucker; Thomas Baukrowitz

2011-08-05 (online) – 2011-08-31 (print)

The EMBO Journal (EMBO J.). 30, 17, 3607-3619. doi:10.1038/emboj.2011.268

Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail

2011-kutzner-double-membrane

Carsten Kutzner; Helmut Grubmüller; Bert L. de Groot; Ulrich Zachariae

2011-08-01 (print)

Biophysical Journal (Biophys. J.). 101, 4, 809-817. doi:doi:10.1016/j.bpj.2011.06.010

Description

They introduce the double-membrane scheme for measuring ion conductance. They do it on a big ol' beta barrel.

Multiple modalities converge on a common gate to control K2Pchannel function

bagriantsev2011multiple

Sviatoslav N Bagriantsev; Rémi Peyronnet; Kimberly A Clark; Eric Honoré; Daniel L Minor

2011-07-15 (online) – 2011-08-31 (print)

The EMBO Journal (EMBO J.). 30, 17, 3594-3606. doi:10.1038/emboj.2011.230

Structural mechanism of C-type inactivation in K+ channels

cuello2010structural

Luis G. Cuello; Vishwanath Jogini; D. Marien Cortes; Eduardo Perozo

2010-07-08 (print)

Nature (Nature). 466, 7303, 203-208. doi:10.1038/nature09153

Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels

clarke2010domain

Oliver B. Clarke; Alessandro T. Caputo; Adam P. Hill; Jamie I. Vandenberg; Brian J. Smith; Jacqueline M. Gulbis

2010-06-01 (print)

Cell (Cell). 141, 6, 1018-1029. doi:10.1016/j.cell.2010.05.003

Molecular Background of Leak K+ Currents: Two-Pore Domain Potassium Channels

2010-k2p-review

P. Enyedi; G. Czirjak

2010-04-14 (online) – 2010-04-01 (print)

Physiological Reviews (Physiol. Rev.). 90, 2, 559-605. doi:10.1152/physrev.00029.2009

Description

Nice review of K2P two-pore potassium channels. They talk about the wide variety of regulatory stimuli

kchan

Principles of conduction and hydrophobic gating in K+ channels

jensen2010principles

M. O. Jensen; D. W. Borhani; K. Lindorff-Larsen; P. Maragakis; V. Jogini; M. P. Eastwood; R. O. Dror; D. E. Shaw

2010-03-15 (online) – 2010-03-30 (print)

Proceedings of the National Academy of Sciences (Proc. Natl. Acad. Sci. U.S.A.). 107, 13, 5833-5838. doi:10.1073/pnas.0911691107

Two-P-Domain (K2P) Potassium Channels: Leak Conductance Regulators of Excitability

goldstein2001potassium

D. Thomas; S.A.N. Goldstein

2009-01-01 (print)

Encyclopedia of Neuroscience (Encyclopedia of Neuroscience). 1207-1220. doi:10.1016/b978-008045046-9.01636-3

The Membrane Potential and its Representation by a Constant Electric Field in Computer Simulations

2008-roux-efield

Benoît Roux

2008-11-01 (print)

Biophysical Journal (Biophys. J.). 95, 9, 4205-4216. doi:10.1529/biophysj.108.136499

Description

Constant electric field

Calculating potentials of mean force from steered molecular dynamics simulations

2004-pmf

Sanghyun Park; Klaus Schulten

2004-04-01 (print)

The Journal of Chemical Physics (J. Chem. Phys.). 120, 13, 5946-5961. doi:10.1063/1.1651473

Human TREK2, a 2P Domain Mechano-sensitive K+Channel with Multiple Regulations by Polyunsaturated Fatty Acids, Lysophospholipids, and Gs, Gi, and GqProtein-coupled Receptors

lesage2000human

Florian Lesage; Cécile Terrenoire; Georges Romey; Michel Lazdunski

2000-07-03 (online) – 2000-09-15 (print)

Journal of Biological Chemistry (J. Biol. Chem.). 275, 37, 28398-28405. doi:10.1074/jbc.m002822200

Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane

2000-roux-kcsa-md

Simon Bernèche; Benoît Roux

2000-06-01 (print)

Biophysical Journal (Biophys. J.). 78, 6, 2900-2917. doi:10.1016/S0006-3495(00)76831-7

Description

They run 4ns of MD on KcsA potassium channel.

Two types of inactivation in Shaker K+ channels: Effects of alterations in the carboxy-terminal region

hoshi1991two

Toshinori Hoshi; William N. Zagotta; Richard W. Aldrich

1991-10-01 (print)

Neuron (Neuron). 7, 4, 547-556. doi:10.1016/0896-6273(91)90367-9

ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB

maier2015ff14sb

James A Maier; Carmenza Martinez; Koushik Kasavajhala; Lauren Wickstrom; Kevin E Hauser; Carlos Simmerling

Journal of chemical theory and computation (J. Chem. Theory Comput.). 11, 3696-3713.

UCSF Chimera-a visualization system for exploratory research and analysis

pettersen2004ucsf

Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin

Journal of computational chemistry (J. Comput. Chem.). 25, 1605-1612.

Amber 14

case2014amber

DA Case; V Babin; Josh Berryman; RM Betz; Q Cai; DS Cerutti; TE Cheatham Iii; TA Darden; RE Duke; H Gohlke

The potassium permeability of a giant nerve fibre

hodgkin1955potassium

A. L. Hodgkin; R. D. Keynes

1955-04-28 (online) – 1955-04-28 (print)

The Journal of Physiology (J. Physiol. (Lond.)). 128, 1, 61-88. doi:10.1113/jphysiol.1955.sp005291