Structural Analysis of the Globins Binding Sites
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Seyede Shideh Ghoreishi,1 Maryam Azimzade Irani,2 Hossein Askari,3,* Seyed Omid Ranaei Siadat,4
1. Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
2. Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
3. Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
4. Protein Research Center, Shahid Beheshti University, Tehran, Iran
- Introduction: Globins are a superfamily of proteins that bind to an organic molecule heme. These proteins are present during evolution from prokaryotes to eukaryotes and have important biological functions such as Oxygen transfer and storage, nitric oxide (NO) metabolism, detoxification of reactive oxygen species (ROS), protection against apoptosis, signal transduction, etc. (Keppner et al., 2020; Buemester and Hankeln , 2014). Globins are structurally in the form of a 3-on-3 Hb fold, also known as myoglobin-fold, and 2-on-2 Hb fold, which belong to the family of Truncated hemoglobins (TrHb). Each of these folds is known to provide different binding affinities to the globins target molecules. As a result, structural studies of the globins binding sites can help us to study their interactions with Oxygen in different organisms. We can also suggest strategies for optimal use of these proteins in genetic engineering and life sciences. Thus, we examined the structure of binding sites in the main 6 groups of globins that were selected from different families to find the best energetically favourable interactions between globin and heme.
- Methods: We used PDB to select the three-dimensional (3D) structures of the globins (http://www.rcsb.org/). To select the structures, we considered the best resolution heme-bound structures with the least number of missed amino acids to examine the interactions more accurately and completely. In the next step, we examined all the atomic interactions within 5 Ǻ of the heme-binding site using PYMOL biomolecular visualizer (WL, 2002).
- Results: While examining the interactions in all of the 6 selected groups of globins, we divided them into 4 categories: 1- Histidines that are known to play an essential role in heme binding 2- Charged amino acids 3- Polar amino acids 4- non-polar amino acids. The results of comparing these structures showed us that myoglobin and leghemoglobin have the best binding energy with heme molecule among all the six studied groups. The difference in the biding site is mainly driven by the number of Histidines and other charged amino acids. Both myoglobin and leghemoglobin have three Histidines which is the highest number and the highest number of charged amino acids which is two in their binding site. These are His64, His93, His97, Lys42, Lys45 For myoglobin and His63, His97, His106, Lys66, Lys100 for leghemoglobin binding sites. Based on our observations, myoglobin and leghemoglobin will have stronger interactions with heme. And these results are consistent with previous studies on globins.
- Conclusion: By studying the structural binding sites of the most important groups of globins we showed that leghemoglobin can have a stable interaction with heme molecules such as myoglobin. Thus, leghemoglobin is a potential target for myoglobin replacement in the use of industrial-scale recombinant protein production processes to improve respiratory efficiency, genetic engineering approaches involved in oxygen supply in culture medium and agriculture.
- Keywords: Globins, Heme, Binding Site
