Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: A molecular modeling study

Abstract

BNIP3 is a mitochondrial 19-kDa proapoptotic protein, a member of the Bcl-2 family. It has a single COOH-terminal transmembrane (TM) alpha-helical domain, which is required for membrane targeting, proapoptotic activity, hetero- and homo-dimerization in membrane. The role and the molecular details of association of TM helices of BNIP3 are yet to be established. Here, we present a molecular modeling study of helix interactions in its membrane domain. The approach combines Monte Carlo conformational search in an implicit hydrophobic slab followed by molecular dynamics simulations in a hydrated full-atom lipid bilayer. The former technique was used for exhaustive sampling of the peptides' conformational space and for generation of putative "native-like" structures of the dimer. The latter ones were taken as realistic starting points to assess stability and dynamic behavior of the complex in explicit lipid-water surrounding. As a result, several groups of tightly packed right-handed structures of the dimer were proposed. They have almost similar helix-helix interface, which includes the motif A(176)xxxG(180)xxxG(184) and agrees well with previous mutagenesis data and preliminary NMR analysis. Molecular dynamics simulations of these structures reveal perfect adaptation of most of them to heterogeneous membrane environment. A remarkable feature of the predicted dimeric structures is the occurrence of a cluster of H-bonded histidine 173 and serines 168 and 172 on the helix interface, near the N-terminus. Because of specific polar interactions between the monomers, this part of the dimer has no such dense packing as the C-terminal one, thus allowing penetration of water from the extramembrane side into the membrane interior. We propose that the ionization state of His(173) can mediate structural and dynamic properties of the dimer. This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions.

Structure and dimerization of the teleost transmembrane immunoglobulin region

“…This result is not surprising since spontaneous helix-helix aggregations were already observed in nanosecond time simulations, providing that the starting configurations are not too far away [13,14]. On the other hand, 4 out of 10 simulations performed in water, for a total of about 120 ns, did not produce a parallel pairing of the two helices.…”

“…In particular, MD simulations can provide useful insights into the factors governing helix-helix association in lipid bilayers. Although incomplete sampling, inaccurate force fields, and approximate treatment of long-range interactions intrinsically limit these studies, intriguing results on the mechanisms of TM helix recognition have been recently reported [13,14,[44][45][46][47].…”

Bnip3 functions as a mitochondrial sensor of oxidative stress during myocardial ischemia and reperfusion

“…Our results also suggest that the NH 2 and COOH termini of Bnip3 cooperate in the homodimerization and activation of Bnip3. Interestingly, based on structural analysis of the transmembrane domain using NMR and computational modeling, it has been proposed that the Bnip3 homodimer may be able to form a channel that is permeable to water (4,33). However, it still remains to be determined whether the activated homodimer forms a channel in the mitochondrial membrane.…”

“…Deletion of the transmembrane domain completely abrogates homodimerization and cell death (7), although this might be due to the fact that the transmembrane domain is also important for targeting Bnip3 to the mitochondria. Computational modeling and mutagenesis studies (4,29,33) have identified the histidine at residue 173 to be essential for homodimerization of Bnip3. Our study confirms the importance of the histidine at residue 173 in homodimerization and also demonstrates that this residue is essential for the cell death activity of Bnip3.…”

Structure-Functional Insight Into Transmembrane Helix Dimerization

“…Correctness of the resulting 'consensus' structures was assessed based on the information about orientation of the CO groups determined by site-specific infrared dichroism. Vereshaga et al, 2007, calculated the spatial structure of TM segment dimer of human proapoptotic protein Bnip3. In this case, Monte Carlo conformational search in an implicit membrane with subsequent MD relaxation of the best models in the full-atom DMPC bilayer was used for identification of the potential structures.…”