An Iris-Like Mechanism of Pore Dilation in the CorA Magnesium Transport System

被引:81
作者
Chakrabarti, Nilmadhab [1 ]
Neale, Chris [1 ,2 ]
Payandeh, Jian [3 ,5 ]
Pai, Emil F. [2 ,3 ,4 ,5 ]
Pomes, Regis [1 ,2 ]
机构
[1] Hosp Sick Children, Toronto, ON M5G 1X8, Canada
[2] Univ Toronto, Dept Biochem, Toronto, ON, Canada
[3] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada
[4] Univ Toronto, Dept Mol Genet, Toronto, ON, Canada
[5] Ontario Canc Inst, Div Canc Genom & Prote, Toronto, ON M4X 1K9, Canada
基金
加拿大健康研究院;
关键词
MOLECULAR-DYNAMICS SIMULATION; PARTICLE MESH EWALD; CRYSTAL-STRUCTURE; LIPID-BILAYERS; FREE-ENERGIES; ELECTROSTATICS;
D O I
10.1016/j.bpj.2009.11.009
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Magnesium translocation across cell membranes is essential for numerous physiological processes. Three recently reported crystal structures of the CorA magnesium transport system revealed a surprising architecture, with a bundle of giant a-helices forming a 60-angstrom-long pore that extends beyond the membrane before widening into a funnel-shaped cytosolic domain. The presence of divalent cations in putative intracellular regulation sites suggests that these structures correspond to the closed conformation of CorA. To examine the nature of the conduction pathway, we performed 110-ns molecular-dynamics simulations of two of these structures in a lipid bilayer with and without regulatory ions. The results show that a 15-angstrom-long hydrophobic constriction straddling the membrane-cytosol interface constitutes a steric bottleneck whose location coincides with an electrostatic barrier opposing cation translocation. In one of the simulations, structural relaxation after the removal of regulatory ions led to concerted changes in the tilt of the pore helices, resulting in iris-like dilation and spontaneous hydration of the hydrophobic neck. This simple and robust mechanism is consistent with the regulation of pore opening by intracellular magnesium concentration, and explains the unusual architecture of CorA.
引用
收藏
页码:784 / 792
页数:9
相关论文
共 42 条
[1]   A hydrophobic gating mechanism for nanopores [J].
Beckstein, O ;
Biggin, PC ;
Sansom, MSP .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (51) :12902-12905
[2]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[3]   Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature [J].
Berger, O ;
Edholm, O ;
Jahnig, F .
BIOPHYSICAL JOURNAL, 1997, 72 (05) :2002-2013
[4]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[5]   Structural determinants of proton blockage in aquaporins [J].
Chakrabarti, N ;
Roux, B ;
Pomès, R .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 343 (02) :493-510
[6]   Nanosecond-timescale conformational dynamics of the human α7 nicotinic acetylcholine receptor [J].
Cheng, Xiaolin ;
Ivanov, Ivaylo ;
Wang, Hailong ;
Sine, Steven M. ;
McCammon, J. Andrew .
BIOPHYSICAL JOURNAL, 2007, 93 (08) :2622-2634
[7]   INCORPORATION OF SURFACE-TENSION INTO MOLECULAR-DYNAMICS SIMULATION OF AN INTERFACE - A FLUID-PHASE LIPID BILAYER-MEMBRANE [J].
CHIU, SW ;
CLARK, M ;
BALAJI, V ;
SUBRAMANIAM, S ;
SCOTT, HL ;
JAKOBSSON, E .
BIOPHYSICAL JOURNAL, 1995, 69 (04) :1230-1245
[8]   An energy-efficient gating mechanism in the acetylcholine receptor channel suggested by molecular and Brownian dynamics [J].
Corry, B .
BIOPHYSICAL JOURNAL, 2006, 90 (03) :799-810
[9]   Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer [J].
Cymes, Gisela D. ;
Grosman, Claudio .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2008, 15 (04) :389-396
[10]   PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].
DARDEN, T ;
YORK, D ;
PEDERSEN, L .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092