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Halogen bonding in complexes of proteins and non-natural amino acids
dc.creator | Borozan, Sunčica | |
dc.creator | Stojanović, Srđan | |
dc.date.accessioned | 2019-01-30T17:35:23Z | |
dc.date.available | 2019-01-30T17:35:23Z | |
dc.date.issued | 2013 | |
dc.identifier.issn | 1476-9271 | |
dc.identifier.uri | https://cer.ihtm.bg.ac.rs/handle/123456789/1235 | |
dc.description.abstract | In this work, we have analyzed the influence of halogen bonding to the stability of 44 complexes of proteins and non-natural amino acids. Fluorine- and chlorine-containing non-natural amino acids are more prevalent in the dataset, and an even larger number of contacts made by iodine-containing ligands are found. Only few halogen bonds with the hydroxyl oxygens and carboxylate side chains are found in the dataset. Halogen bonds with the nitrogen-containing side chains have higher occurrence than other acceptors. Backbone carbonyl oxygens and nitrogens are to a substantial extent involved in our dataset We have observed a small percentage of interactions involving water as hydrogen bond donors. Additionally, most of the interacting residues comprising the interfaces also show a great degree of conservation. There is a clear interaction hot spot at distances of 3.5-3.7 angstrom and Theta(1) angles of 100-120 degrees. There is also a cluster of contacts featuring short distances (2.6-2.9 angstrom) but only nearly optimal Theta(1) angles (140-160 degrees). 51.3% of stabilizing residues are involved in building halogen bonds with the non-natural amino acids. We discovered three types of structural motifs significantly over-represented: beta-turn-ir, beta-turn-il and niche-4r. The halogen-bonding statistics of the dataset do not show any preference for alpha-helices (36%), beta-sheets (36%), or turns/coils (28%) structures. Most of the amino acid residues that were involved in halogen bonds prefer to be in the solvent excluded environment (buried). Furthermore, we have shown that in amino acid-protein complexes halogen atoms can sometimes be involved in hydrogen bonding interactions with hydrogen bonding-donors. The results from this study might be used for the rational design of halogenated ligands as inhibitors and drugs, and in biomolecular engineering. | en |
dc.publisher | Elsevier Sci Ltd, Oxford | |
dc.relation | info:eu-repo/grantAgreement/MESTD/Basic Research (BR or ON)/172001/RS// | |
dc.relation | info:eu-repo/grantAgreement/MESTD/Basic Research (BR or ON)/173034/RS// | |
dc.rights | restrictedAccess | |
dc.source | Computational Biology and Chemistry | |
dc.subject | Halogen bonding | en |
dc.subject | Proteins | en |
dc.subject | Non-natural amino acids | en |
dc.subject | Complexes | en |
dc.subject | Stabilization centers | en |
dc.title | Halogen bonding in complexes of proteins and non-natural amino acids | en |
dc.type | article | |
dc.rights.license | ARR | |
dcterms.abstract | Борозан, Сунцица З.; Стојановић, Срђан; | |
dc.citation.volume | 47 | |
dc.citation.spage | 231 | |
dc.citation.epage | 239 | |
dc.citation.other | 47: 231-239 | |
dc.citation.rank | M22 | |
dc.identifier.pmid | 24200696 | |
dc.identifier.doi | 10.1016/j.compbiolchem.2013.10.002 | |
dc.identifier.scopus | 2-s2.0-84887443028 | |
dc.identifier.wos | 000329270700029 | |
dc.type.version | publishedVersion |