title: Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds.
abstract: The pi electron cloud of aromatic centers is known to be involved in several noncovalent interactions such as C--H...pi, O--H...pi, and pi...pi interactions in biomolecules. Lone-pair (lp) ... pi interactions have gained attention recently and their role in biomolecular structures is being recognized. In this article, we have carried out systematic analysis of high-resolution protein structures and identified more than 400 examples in which water oxygen atoms are in close contact (distance < 3.5 A) with the aromatic centers of aromatic residues. Three different methods were used to build hydrogen atoms and we used a consensus approach to find out potential candidates for lp...pi interactions between water oxygen and aromatic residues. Quantum mechanical calculations at MP2/6-311++G(d,p) level on model systems based on protein structures indicate that majority of the identified examples have energetically favorable interactions. The influence of water hydrogen atoms was investigated by sampling water orientations as a function of two parameters: distance from the aromatic center and the angle between the aromatic plane and the plane formed by the three water atoms. Intermolecular potential surfaces were constructed using six model compounds representing the four aromatic amino acids and 510 different water orientations for each model compound. Ab initio molecular orbital calculations at MP2/6-311++G(d,p) level show that the interaction energy is favorable even when hydrogen atoms are farthest from the aromatic plane while water oxygen is pointing toward the aromatic center. The strength of such interaction depends upon the distance of water hydrogen atoms from the aromatic substituents. Our calculations clearly show that the lp...pi interactions due to the close approach of water oxygen and aromatic center are influenced by the positions of water hydrogen atoms and the aromatic substituents.
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India.
authors.forename: Alok
authors.initials: A
authors.lastname: Jain
authors.forename: Venkatnarayan
authors.initials: V
authors.lastname: Ramanathan
authors.forename: Ramasubbu
authors.initials: R
authors.lastname: Sankararamakrishnan
mesh_terms: D024322:Amino Acids, Aromatic / Q000737:chemistry*; D001554:Benzene / Q000737:chemistry; D018360:Crystallography, X-Ray; D004583:Electrons; D006860:Hydrogen Bonding; D007211:Indoles / Q000737:chemistry; D008956:Models, Chemical; D010100:Oxygen / Q000737:chemistry*; D019800:Phenol / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
chemical_list: D024322:Amino Acids, Aromatic; D007211:Indoles; D011506:Proteins; D014867:Water; D019800:Phenol; D001554:Benzene; D010100:Oxygen