金属离子-质膜相互作用的分子动力学模拟研究
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摘要
为研究植物根表质膜与土壤溶液界面上的双电层结构对金属离子在质膜上吸附以及吸收的影响,从分子水平探讨质膜表面电势下金属离子与质膜的相互作用,建立了质膜与金属溶液的界面模型,采用分子动力学方法模拟了质膜界面K~+、Na~+、Ca~(2+)、Mg~(2+)等碱/碱土金属阳离子与Cu~(2+)、Cd~(2+)等重金属离子的结合与分布过程。通过对吸附构型、浓度分布等统计分析,发现阳离子在质膜表面主要与质膜头部的羰基和磷酸基团等极性基团结合;二价阳离子吸附作用比一价阳离子更为强烈,并造成质膜表面电势的反转,直接控制着扩散层中离子的分布特征。分子动力学模拟结果与描述界面双电层结构的Gouy-Chapman-Stern(GCS)经典理论很好地吻合,可以从分子水平预测和解释金属阳离子与质膜相互作用的动态过程。
The electric double layer at the soil solution-plant root membrane interface plays an important role in adsorption and uptake of metal ions.Molecular level investigation on the interaction between metal ions and root plasma membrane under the surface potential of membrane was conducted using molecular dynamics(MD)simulation of a model lipid bilayer equilibrating with different electrolyte solutions including K~+,Na~+,Ca~(2+),Mg~(2+),and heavy metals such as Cu~(2+),Cd~(2+).Statistical analysis of simulation results,including adsorption configurations and concentration profiles,revealed that cations mainly binded to the carbonyl and phosphate groups of lipids.The stronger binding for divalent cations than monovalent cations,especially divalent heavy metals,resulted in the sign changes of the surface potential which directly controlled the distribution of ions in the diffuse layer.The molecular dynamics simulation correctly predicted the distribution of ions consistent with the classical Gouy-Chapman-Stern(GCS)model of the electric double layer.We demonstrated that molecular dynamics simulation could quantitatively characterize the dynamic processes of metal ions binding and distribution at the surface of the membrane.
The electric double layer at the soil solution-plant root membrane interface plays an important role in adsorption and uptake of metal ions.Molecular level investigation on the interaction between metal ions and root plasma membrane under the surface potential of membrane was conducted using molecular dynamics(MD)simulation of a model lipid bilayer equilibrating with different electrolyte solutions including K~+,Na~+,Ca~(2+),Mg~(2+),and heavy metals such as Cu~(2+),Cd~(2+).Statistical analysis of simulation results,including adsorption configurations and concentration profiles,revealed that cations mainly binded to the carbonyl and phosphate groups of lipids.The stronger binding for divalent cations than monovalent cations,especially divalent heavy metals,resulted in the sign changes of the surface potential which directly controlled the distribution of ions in the diffuse layer.The molecular dynamics simulation correctly predicted the distribution of ions consistent with the classical Gouy-Chapman-Stern(GCS)model of the electric double layer.We demonstrated that molecular dynamics simulation could quantitatively characterize the dynamic processes of metal ions binding and distribution at the surface of the membrane.
引文
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[24]Jo S,Lim J B,Klauda J B,et al.CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes[J].Biophysical Journal,2009,97(1):50-58.
[25]Lee J,Patel D S,St?hle J,et al.CHARMM-GUI membrane builder for complex biological membrane simulations with glycolipids and lipoglycans[J].Journal of Chemical Theory and Computation,2018,15(1):775-786.
[26]Brooks B R,Brooks C L,Mackerell A D,et al.CHARMM:The biomolecular simulation program[J].Journal of Computational Chemistry,2009,30(10):1545-1614.
[27]Lee J,Cheng X,Swails J M,et al.CHARMM-GUI input generator for NAMD,GROMACS,AMBER,OpenMM,and CHARMM/OpenMMsimulations using the CHARMM36 additive force field[J].Journal of Chemical Theory and Computation,2015,12(1):405-413.
[28]Wang P,Kinraide T B,Zhou D M,et al.Plasma membrane surface potential:Dual effects upon ion uptake and toxicity[J].Plant Physiology,2011,155(2):808-820.
[29]Gurtovenko A A,Vattulainen I.Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance[J].Biophysical Journal,2007,92(6):1878-1890.
[30]Dickey A,Faller R.Examining the contributions of lipid shape and headgroup charge on bilayer behavior[J].Biophysical Journal,2008,95(6):2636-2646.
[31]Vácha R,Jurkiewicz P,Petrov M,et al.Mechanism of interaction of monovalent ions with phosphatidylcholine lipid membranes[J].The Journal of Physical Chemistry B,2010,114(29):9504-9509.
[32]Mackinnon R.Potassium channels[J].FEBS Letters,2003,555(1):62-65.
[33]Chapman D L.LI.A contribution to the theory of electrocapillarity[J].The London,Edinburgh,and Dublin Philosophical Magazine and Journal of Science,1913,25(148):475-481.
[34]Spohr E.Molecular simulation of the electrochemical double layer[J].Electrochimica Acta,1999,44(11):1697-1705.
[2]Cao Q,Hu Q H,Khan S,et al.Wheat phytotoxicity from arsenic and cadmium separately and together in solution culture and in a calcareous soil[J].Journal of Hazardous Materials,2007,148(1/2):377-382.
[3]张红振,骆永明,章海波,等.水稻,小麦籽粒砷,镉,铅富集系数分布特征及规律[J].环境科学,2010,31(2):488-495.ZHANG Hong-zhen,LUO Yong-ming,ZHANG Hai-bo,et al.Characterizing the plant uptake factor of As,Cd and Pb for rice and wheat cereal[J].Environmental Science,2010,31(2):488-495.
[4]Li L Z,Zhou D M,Wang P,et al.Predicting Cd partitioning in spiked soils and bioaccumulation in the earthworm Eisenia fetida[J].Applied Soil Ecology,2009,42(2):118-123.
[5]Li L Z,Zhou D M,Luo X S,et al.Effect of major cations and pH on the acute toxicity of cadmium to the earthworm Eisenia fetida:Implications for the biotic ligand model approach[J].Archives of Environmental Contamination and Toxicology,2008,55(1):70-77.
[6]Zhao F J,Ma J F,Meharg A A,et al.Arsenic uptake and metabolism in plants[J].New Phytologist,2009,181(4):777-794.
[7]Ma J F,Yamaji N,Mitani N,et al.Transporters of arsenite in rice and their role in arsenic accumulation in rice grain[J].Proceedings of the National Academy of Sciences,2008,105(29):9931-9935.
[8]Sui F Q,Chang J D,Tang Z,et al.Nramp5 expression and functionality likely explain higher cadmium uptake in rice than in wheat and maize[J].Plant and Soil,2018,433(1/2):377-389.
[9]Lau A,Mclaughlin A,Mclaughlin S.The adsorption of divalent cations to phosphatidylglycerol bilayer membranes[J].Biochimica et Biophysica Acta(BBA)-Biomembranes,1981,645(2):279-292.
[10]Nobel P S.Physicochemical&environmental plant physiology[M].Academic press,1999.
[11]Obi I,Ichikawa Y,Kakutani T,et al.Electrophoretic studies on plant protoplastsⅠ.pH dependence of zeta potentials of protoplasts from various sources[J].Plant and Cell Physiology,1989,30(3):439-444.
[12]Kinraide T B.Use of a Gouy-Chapman-Stern model for membranesurface electrical potential to interpret some features of mineral rhizotoxicity[J].Plant Physiology,1994,106(4):1583-1592.
[13]Kinraide T B,Ryan P R,Kochian L V.Interactive effects of Al3+,H+,and other cations on root elongation considered in terms of cell-surface electrical potential[J].Plant Physiology,1992,99(4):1461-1468.
[14]Kinraide T B,Wang P.The surface charge density of plant cell membranes(σ):An attempt to resolve conflicting values for intrinsicσ[J].Journal of Experimental Botany,2010,61(9):2507-2518.
[15]Wang P,Zhou D M,Kinradide T B,et al.Cell membrane surface potential(ψ0)plays a dominant role in the phytotoxicity of copper and arsenate[J].Plant Physiology,2008,148(4):2134-2143.
[16]Wang P,Kinraide T B,Smolders E,et al.An electrostatic model pre-20197-dicting Cu and Ni toxicity to microbial processes in soils[J].Soil Biology and Biochemistry,2013,57:720-730.
[17]Wang Y M,Kinraide T,Wang P,et al.Surface electrical potentials of root cell plasma membranes:Implications for ion interactions,rhizotoxicity,and uptake[J].International Journal of Molecular Sciences,2014,15(12):22661-22677.
[18]Yi M,Nymeyer H,Zhou H X.Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations[J].Physical Review Letters,2008,101(3):038103.
[19]Cordomi A,Edholm O,Perez J J.Effect of ions on a dipalmitoyl phosphatidylcholine bilayer.A molecular dynamics simulation study[J].The Journal of Physical Chemistry B,2008,112(5):1397-1408.
[20]Khalili-araghi F,Gumbart J,Wen P C,et al.Molecular dynamics simulations of membrane channels and transporters[J].Current Opinion in Structural Biology,2009,19(2):128-137.
[21]Yang J,Calero C,Bonomi M,et al.Specific ion binding at phospholipid membrane surfaces[J].Journal of Chemical Theory and Computation,2015,11(9):4495-4499.
[22]Sachs J N,Woolf T B.Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers:Molecular dynamics simulations[J].Journal of the American Chemical Society,2003,125(29):8742-8743.
[23]Jo S,Kim T,Im W.Automated builder and database of protein/membrane complexes for molecular dynamics simulations[J].PLoS One,2007,2(9):e880.
[24]Jo S,Lim J B,Klauda J B,et al.CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes[J].Biophysical Journal,2009,97(1):50-58.
[25]Lee J,Patel D S,St?hle J,et al.CHARMM-GUI membrane builder for complex biological membrane simulations with glycolipids and lipoglycans[J].Journal of Chemical Theory and Computation,2018,15(1):775-786.
[26]Brooks B R,Brooks C L,Mackerell A D,et al.CHARMM:The biomolecular simulation program[J].Journal of Computational Chemistry,2009,30(10):1545-1614.
[27]Lee J,Cheng X,Swails J M,et al.CHARMM-GUI input generator for NAMD,GROMACS,AMBER,OpenMM,and CHARMM/OpenMMsimulations using the CHARMM36 additive force field[J].Journal of Chemical Theory and Computation,2015,12(1):405-413.
[28]Wang P,Kinraide T B,Zhou D M,et al.Plasma membrane surface potential:Dual effects upon ion uptake and toxicity[J].Plant Physiology,2011,155(2):808-820.
[29]Gurtovenko A A,Vattulainen I.Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance[J].Biophysical Journal,2007,92(6):1878-1890.
[30]Dickey A,Faller R.Examining the contributions of lipid shape and headgroup charge on bilayer behavior[J].Biophysical Journal,2008,95(6):2636-2646.
[31]Vácha R,Jurkiewicz P,Petrov M,et al.Mechanism of interaction of monovalent ions with phosphatidylcholine lipid membranes[J].The Journal of Physical Chemistry B,2010,114(29):9504-9509.
[32]Mackinnon R.Potassium channels[J].FEBS Letters,2003,555(1):62-65.
[33]Chapman D L.LI.A contribution to the theory of electrocapillarity[J].The London,Edinburgh,and Dublin Philosophical Magazine and Journal of Science,1913,25(148):475-481.
[34]Spohr E.Molecular simulation of the electrochemical double layer[J].Electrochimica Acta,1999,44(11):1697-1705.
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