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      Halogen bonding in complexes of proteins and non-natural amino acids.

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          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 Å and Θ1 angles of 100-120°. There is also a cluster of contacts featuring short distances (2.6-2.9 Å) but only nearly optimal Θ1 angles (140-160°). 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 α-helices (36%), β-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.

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          Author and article information

          Journal
          Comput Biol Chem
          Computational biology and chemistry
          Elsevier BV
          1476-928X
          1476-9271
          Dec 2013
          : 47
          Affiliations
          [1 ] Department of Chemistry, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia.
          Article
          S1476-9271(13)00093-5
          10.1016/j.compbiolchem.2013.10.002
          24200696
          ee7f630d-9481-4728-b3d1-d76be7fa401c
          History

          Non-natural amino acids,Halogen bonding,Complexes,Stabilization centers,Proteins

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