Unique Dimeric Structure of BNip3 Transmembrane Domain Suggests Membrane Permeabilization as a Cell Death Trigger

Eduard V Bocharov,Yulia E Pustovalova,Konstantin V Pavlov,Pavel E Volynsky,Marina V Goncharuk,Yaroslav S Ermolyuk,Dmitry V Karpunin,Alexey A Schulga,Michail P Kirpichnikov,Roman G Efremov,Innokenty V Maslennikov,Alexander S Arseniev

doi:10.1074/jbc.m701745200

Eduard V Bocharov, Yulia E Pustovalova + Show 10 more

Open Access

https://doi.org/10.1074/jbc.m701745200

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Abstract

BNip3 is a prominent representative of apoptotic Bcl-2 proteins with rather unique properties initiating an atypical programmed cell death pathway resembling both necrosis and apoptosis. Many Bcl-2 family proteins modulate the permeability state of the outer mitochondrial membrane by forming homo- and hetero-oligomers. The structure and dynamics of the homodimeric transmembrane domain of BNip3 were investigated with the aid of solution NMR in lipid bicelles and molecular dynamics energy relaxation in an explicit lipid bilayer. The right-handed parallel helix-helix structure of the domain with a hydrogen bond-rich His-Ser node in the middle of the membrane, accessibility of the node for water, and continuous hydrophilic track across the membrane suggest that the domain can provide an ion-conducting pathway through the membrane. Incorporation of the BNip3 transmembrane domain into an artificial lipid bilayer resulted in pH-dependent conductivity increase. A possible biological implication of the findings in relation to triggering necrosis-like cell death by BNip3 is discussed.

Highlights

Hydrophobic domain essential for membrane targeting [2]
It was demonstrated that the BNip3 transmembrane domain (TM)3 is crucial for pro-apoptotic activity, mitochondrial localization, and homodimerization of the protein, 3 The abbreviations used are: TM, transmembrane; BNip3tm, TM fragment 146 –190 of human pro-apoptotic protein BNip3; GpAtm, TM fragment 61–98 of human protein glycophorin A; bilayer lipid membranes (BLMs), bilayer lipid membrane; molecular hydrophobicity potential (MHP), molecular hydrophobic potential; DMPC, dimyristoyl-phosphatidylcholine; DHPC, dihexanoyl-phosphatidylcholine; DPhPC, diphytanoyl-phosphatidylcholine; NOE, nuclear Overhauser effect; MD, molecular dynamics; MES, 4-morpholineethanesulfonic acid; VDAC, voltage-dependent anionic channel
We describe the spatial structure and internal dynamics of the homodimeric TM domain of human pro-apoptotic protein BNip3 in a membrane-mimicking lipid environment obtained with the aid of a combination of NMR spectroscopic technique and molecular dynamics (MD) energy relaxation

Summary

Introduction

Hydrophobic domain essential for membrane targeting [2]. A major function of Bcl-2 family proteins is to regulate the permeability state of the outer mitochondrial membrane by forming homo- and hetero-oligomers inside the membrane that determine cell fate [3,4,5]. We describe the spatial structure and internal dynamics of the homodimeric TM domain of human pro-apoptotic protein BNip in a membrane-mimicking lipid environment obtained with the aid of a combination of NMR spectroscopic technique and molecular dynamics (MD) energy relaxation. The structure suggests a possibility that the BNip TM domain alone can form an ionconducting pathway in the membrane, as supported by direct measurements on the bilayer lipid membranes (BLMs). This property of the TM domain can help to explain the mechanism of BNip action, in particular in hypoxia acidosis-induced cell death

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