IN SILICO ANALYSIS OF INTERACTIONS IN HEME BINDING PROTEINS
Keywords:
Heme proteins, Iron-porphyrin complex, Non-covalent interactions, Stabilizing residues, Solvent accessibility, Ion-pairsAbstract
Objective: Heme cofactors are essential molecule found in almost all forms of life. Biological systems depend on heme-protein interactions to carry out basic functions required for their survival. The objective of the present work is to analyse the various non-covalent interactions and also focus on amino acid preferences in heme binding environment.
Methods: Various interactions like hydrophobic, aromatic and hydrogen bonds between heme and binding site of non-redundant dataset of 33 heme proteins were analysed to understand the characteristics of different type of interactions. Also the relative preference of amino acids participating in forming secondary structure, solvent accessibility, stabilizing residues and ion-pairs in heme binding environment was analysed.
Results: The analysis of heme binding protein environment revealed some important findings, which include the dominant role of non-polar contacts. 12% of the predicted stabilizing residues were also involved in forming interaction with heme. The secondary structure preference analysis showed that 41% of interacting residues preferred to be in helix. The frequency of non-polar amino acids in the buried region was predominant. The preference of amino acid Arg to form complete ion-pair was higher and these ion-pairs formed strong interactions. This provides insights into the better understanding of the heme environment.
Conclusion: The present findings through in silico analysis provide valuable information on natural heme binding proteins. These studies will contribute useful information regarding structural stability and its interaction in future designs of novel heme proteins.
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References
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