pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures
Abstract
In this study we have described the pi-pi and cation-pi interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pi-pi interactions was higher than that of cation-pi interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in pi-pi interactions with pi systems of another porphyrin in the protein. We have found 5.1% cation-pi interactions between porphyrin Fe2+ metal cations and pi systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the pi-pi interactions have an energy in the range -0.5 to -2.0 kcal mol(-1), while the cation-pi interactions showed an energy in the range 22 to -4 kcal mol(-1). Further, an appreciable number of metal/cation-pi interaction pairs have an energy in the range -6 to -13 kcal mol(-1). The preferred parallel-stacked orientation is found to be more stable than a T-sh...aped structure for the full set of pi-pi interaction pairs. In the case of cation-pi interactions, it was found that 44% of the cation-pi interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of pi residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.
Source:
RSC Advances, 2012, 2, 33, 12963-12972Publisher:
- The Royal Society of Chemistry
Funding / projects:
- Management of sustainable farming of organic lamb production as a support to rural development (RS-31085)
- The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences (RS-172001)
- Cell Cycle Aberrations and the Impact of Oxidative Stress in Neurodegenerative Processes and Malignant Transformation of the Cell (RS-173034)
DOI: 10.1039/c2ra21937a
ISSN: 2046-2069
WoS: 000312149600063
Scopus: 2-s2.0-84870030299
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IHTMTY - JOUR AU - Dimitrijević, Blagoje P. AU - Borozan, Sunčica AU - Stojanović, Srđan PY - 2012 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/1119 AB - In this study we have described the pi-pi and cation-pi interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pi-pi interactions was higher than that of cation-pi interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in pi-pi interactions with pi systems of another porphyrin in the protein. We have found 5.1% cation-pi interactions between porphyrin Fe2+ metal cations and pi systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the pi-pi interactions have an energy in the range -0.5 to -2.0 kcal mol(-1), while the cation-pi interactions showed an energy in the range 22 to -4 kcal mol(-1). Further, an appreciable number of metal/cation-pi interaction pairs have an energy in the range -6 to -13 kcal mol(-1). The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of pi-pi interaction pairs. In the case of cation-pi interactions, it was found that 44% of the cation-pi interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of pi residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design. PB - The Royal Society of Chemistry T2 - RSC Advances T1 - pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures VL - 2 IS - 33 SP - 12963 EP - 12972 DO - 10.1039/c2ra21937a ER -
@article{ author = "Dimitrijević, Blagoje P. and Borozan, Sunčica and Stojanović, Srđan", year = "2012", abstract = "In this study we have described the pi-pi and cation-pi interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pi-pi interactions was higher than that of cation-pi interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in pi-pi interactions with pi systems of another porphyrin in the protein. We have found 5.1% cation-pi interactions between porphyrin Fe2+ metal cations and pi systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the pi-pi interactions have an energy in the range -0.5 to -2.0 kcal mol(-1), while the cation-pi interactions showed an energy in the range 22 to -4 kcal mol(-1). Further, an appreciable number of metal/cation-pi interaction pairs have an energy in the range -6 to -13 kcal mol(-1). The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of pi-pi interaction pairs. In the case of cation-pi interactions, it was found that 44% of the cation-pi interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of pi residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.", publisher = "The Royal Society of Chemistry", journal = "RSC Advances", title = "pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures", volume = "2", number = "33", pages = "12963-12972", doi = "10.1039/c2ra21937a" }
Dimitrijević, B. P., Borozan, S.,& Stojanović, S.. (2012). pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures. in RSC Advances The Royal Society of Chemistry., 2(33), 12963-12972. https://doi.org/10.1039/c2ra21937a
Dimitrijević BP, Borozan S, Stojanović S. pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures. in RSC Advances. 2012;2(33):12963-12972. doi:10.1039/c2ra21937a .
Dimitrijević, Blagoje P., Borozan, Sunčica, Stojanović, Srđan, "pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures" in RSC Advances, 2, no. 33 (2012):12963-12972, https://doi.org/10.1039/c2ra21937a . .