Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling

Peter V Dubovskii; Kira M Dubova; Gleb Bourenkov; Vladislav G Starkov; Anastasia G Konshina; Roman G Efremov; Yuri N Utkin; Valeriya R Samygina

doi:10.3390/toxins14020149

Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling

Toxins (Basel). 2022 Feb 18;14(2):149. doi: 10.3390/toxins14020149.

Authors

Peter V Dubovskii¹, Kira M Dubova^{2

3}, Gleb Bourenkov⁴, Vladislav G Starkov¹, Anastasia G Konshina¹, Roman G Efremov^{1

5

6}, Yuri N Utkin¹, Valeriya R Samygina^{2

3}

Affiliations

¹ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia.
² FSRC "Crystallography and Photonics", Russian Academy of Sciences, 111933 Moscow, Russia.
³ NRC "Kurchatov Institute", 123182 Moscow, Russia.
⁴ European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, 22607 Hamburg, Germany.
⁵ Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141700 Dolgoprudny, Russia.
⁶ Higher School of Economics, National Research University, 20 Myasnitskaya str., 101000 Moscow, Russia.

Abstract

Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from Naja naja cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both "water" and "membrane" conformations of the central loop (loop-2) were determined by X-ray crystallography. The "water" conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The "membrane" conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from N. oxiana (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step-the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their "water" NMR models. We found that the both toxins transform their "water" conformation of loop-2 into the "membrane" one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.

Keywords: Highly Mimetic Membrane Model; Naja naja venom; X-ray crystallography; cis–trans isomerism of X-Pro peptide bond; cobra cytotoxin; molecular dynamics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cobra Cardiotoxin Proteins / chemistry*
Crystallography, X-Ray / methods*
Cytotoxins / chemistry*
Models, Molecular*
Molecular Structure*
Protein Conformation*

Substances

Cobra Cardiotoxin Proteins
Cytotoxins