Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin

Abstract

Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from N.oxiana venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by ¹H-NMR spectroscopy. Then, via CG- and FA MD-computations, we evaluated partitioning of CT1 molecule into palmitoyloleoylphosphatidylcholine (POPC) membrane, using the toxin spatial models, obtained either in aqueous solution, or detergent micelle. The latter model exhibits minimal structural changes upon partitioning into the membrane, while the former deviates from the starting conformation, loosing the tightly bound water molecule in the loop-2. These data show that the structural changes elicited by CT1 molecule upon incorporation into DPC micelle take place likely in the lipid membrane, although the mode of the interaction of this toxin with DPC micelle (with the tips of the all three loops) is different from its mode in POPC membrane (primarily with the tip of the loop-1 and both the tips of the loop-1 and loop-2).

Keywords:

• three-finger toxins
• spatial structure
• membrane-binding modes
• NMR spectroscopy
• coarse-grained and full-atom molecular dynamics simulations

Abbreviations:

• 2D, two-dimensional
• 3D, three-dimensional
• 5-DOX, 5-doxylstearic acid
• 16-DOX, 16-doxylstearic acid
• COSY, 2D correlation spectroscopy
• FA, full-atom
• DQF-COSY, double quantum filtered correlation spectroscopy
• CG, coarse-grained
• CT, cytotoxin
• CTs, cytotoxins
• CT1, cytotoxin I from N. oxiana
• CT2, cytotoxin 2 from N. oxiana
• DPC, dodecylphosphocholine
• DPC-d₃₈, deuterated DPC
• H-bond, hydrogen bond
• MD, molecular dynamics
• NOESY, 2D nuclear Overhauser effect spectroscopy
• POPC, palmitoyloleoylphosphatidylcholine
• RMSD, root-mean-square deviation
• ROESY, 2D NOE in the rotating frame spectroscopy
• TOCSY, 2D total correlation spectroscopy

Acknowledgements

This work was supported by the Russian Science Foundation (grant 14-50-00131). D.P.V. is grateful to the Russian Foundation for Basic Research (grant 16-04-01479, MD analysis). Access to computational facilities of the Supercomputer Center ‘Polytechnical’ at the St. Petersburg Polytechnic University and the Joint Supercomputer Center of RAS (Moscow) is appreciated. Experiments were partially carried out using the equipment provided by the IBCH core facility (CKP IBCH, supported by Russian Ministry of Education and Science, grant RFMEFI62117X0018).