Hydrophobic interactions in the stability of porphyrin-containing proteins
Апстракт
This study aims to systematically characterize hydrophobic interactions 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 hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions 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.
Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic interactions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.
Кључне речи:
hydrophobic interactions / porphyrin containing proteins / PDBИзвор:
Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia, 2008, II, 707-709Издавач:
- Society of Physical Chemists of Serbia
Финансирање / пројекти:
- Проучавање односа реактивности, нековалентних интеракција и структуре молекула и моделовање хемијских система (RS-MESTD-MPN2006-2010-142037)
- Аутоматско резоновање и напредне обраде великих количина података и текста (RS-MESTD-MPN2006-2010-144030)
Институција/група
IHTMTY - CONF AU - Stojanović, Srđan AU - Zarić, Snežana PY - 2008 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/6529 AB - This study aims to systematically characterize hydrophobic interactions 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 hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions 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. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic interactions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score. PB - Society of Physical Chemists of Serbia C3 - Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia T1 - Hydrophobic interactions in the stability of porphyrin-containing proteins VL - II SP - 707 EP - 709 UR - https://hdl.handle.net/21.15107/rcub_cer_6529 ER -
@conference{ author = "Stojanović, Srđan and Zarić, Snežana", year = "2008", abstract = "This study aims to systematically characterize hydrophobic interactions 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 hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions 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. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic interactions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.", publisher = "Society of Physical Chemists of Serbia", journal = "Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia", title = "Hydrophobic interactions in the stability of porphyrin-containing proteins", volume = "II", pages = "707-709", url = "https://hdl.handle.net/21.15107/rcub_cer_6529" }
Stojanović, S.,& Zarić, S.. (2008). Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia Society of Physical Chemists of Serbia., II, 707-709. https://hdl.handle.net/21.15107/rcub_cer_6529
Stojanović S, Zarić S. Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia. 2008;II:707-709. https://hdl.handle.net/21.15107/rcub_cer_6529 .
Stojanović, Srđan, Zarić, Snežana, "Hydrophobic interactions in the stability of porphyrin-containing proteins" in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia, II (2008):707-709, https://hdl.handle.net/21.15107/rcub_cer_6529 .