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