Considering the effect of Leptin Receptor (LR) polymorphisms on their binding affinity to Leptin in dairy cow with docking method

Binding of leptin to its specific receptor (LR) is the first step in its effect on production and reproductive functions in dairy. Therefore, one of the main regulatory pathways of leptin function is its binding pattern to LR. The aim of this study was to compare the tertiary structure of different LR polymorphisms and their binding affinity to leptin in dairy cows. For this purpose, LR amino acid sequences were obtained from Gene bank. Firstly, Polymorphisms were identified by alignment analysis. Their related third structures were predicted by homology modeling technique using Modeller software. The created structures were observed and evaluated using PyMol 2.5.1 graphics software, Ramachandran plot, Provean and I-MUTANT softwars. Also, different physico-chemical parameters of the modeled proteins such as isoelectric point, molecular weight, and number of negative and positive sequences and Grand Average of hydropathicity (GRAVY) were calculated using ProtParam tool in Expasy database. Then, the affinity of leptin to each of the LR polymorphism was evaluated using molecular docking technique based on binding energy and spatial position indices. Based on the results, only two polymorphisms (LR1 and LR2) were identified among the studied sequences in which serine has been replaced by arginine. There was no difference in structural and physicochemical parameters between two polymorphisms. Ramachandran and I-MUTANT diagram evaluations showed that serine replacement with arginine had a limited effect on LR2 stability. However, according to Provean results, this effect is not sufficient to affect its structure and performance. Docking results showed that the binding affinity of leptin to LR1 is higher compared to LR2 and from a theoretical point of view it is expected that LR1 will have a better performance than LR2 in transmitting leptin messages. In general, the results of this study can play an effective role in understanding the relationship between polymorphism and physiological activity.