Hydrogen bonds of porphyrins in porphyrin containing proteins

Abstract

This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen bonds are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone, or side chain, and in different secondary structural regions such as helices, strands and turns. The results revealed that the significant number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. The average conservation score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples.Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka (PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima (heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na nekoliko primera

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