Nanochemistry and biotechnology

Three-dimensional structure and folding-analogs of Ca2+ cation antiporter of Natrialba aegyptia
Venger A.1, Venger O.2, Pasternak S.3, Purich D.4, Hruzevskyi O.1
1 Department of microbiology, virology and immunology, Odessa National Medical University, Valychovski Lane, 2, Odesa-65000, Ukraine.
E-mail: venger87@ukr.net
2 Plant Breeding and Genetics Institute – National Center of Seed and Cultivar Investigation, Ovidiopol’ska doroga Str., 3, Odesa-65036, Ukraine.
3 Odessa National University of I. I. Mechnikov, Dvoryan’ska Str., 2,Odesa-65082, Ukraine.
4 Odessa National Polytechnic University, Boulevard of Shevchenko, 1, Odesa-65044, Ukraine.

The Ca2+ cation antiporter (CaCA) family (TC# 2.A.19) is a member of the cation diffusion facilitator (CDF) superfamily. Ca2+ binding to these regulatory domains activates its transport across the plasma membrane. In the absence of Ca2+, Lys585 stabilizes the structure by coordinating two acidic residues, and prevents protein unfolding [1]. The structure of CaCA is currently undescribed. The aim was the modulation of the three-dimensional structure and search of folding-analogs of CaCA of archaae Natrialba aegyptia. Models were built based on the target-template alignment using ProMod3. Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodeled using a fragment library. The geometry of the resulting model is regularized by a force field. In case loop modelling with ProMod3 fails, an alternative model is built with PROMOD-II [2]. As result, three-dimensional structure of CaCA was calculated by folding-analogs. Three of them are statistically correct: 5hxc.1.A (sodium, calcium exchanger), 3v5u.1.A (membrane protein MJ0091) and 4k1c.1.A (vacuolar Ca2+ transporter).

1.	Liao Q. S., Du Q., Lou J., Xu J. Y., Xie R. Roles of Na+/Ca2+ exchanger 1 in digestive system physiology and pathophysiology // World J Gastroenterol.-2019.-25, N 3.-P. 287-299.
2.	Guex N., Peitsch M. C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling // Electrophoresis.-1997.-18, N 15.-P. 2714-2723.