Packing of aromatic rings against tryptophan residues in proteins.

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp-Trp pair. While parallel stacking is the dominant feature of Trp-His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH-pi interaction.

[1]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[2]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[3]  Richard E. Dickerson,et al.  The DNA Helix and How it is Read , 1983 .

[4]  P. Taylor,et al.  Crystal environments and geometries of leucine, isoleucine, valine and phenylalanine provide estimates of minimum nonbonded contact and preferred van der Waals interaction distances , 1985 .

[5]  G A Petsko,et al.  Aromatic-aromatic interaction: a mechanism of protein structure stabilization. , 1985, Science.

[6]  Stephen K. Burley,et al.  Dimerization energetics of benzene and aromatic amino acid side chains , 1986 .

[7]  J. F. Stoddart,et al.  Noncovalent Bonding Interactions between Tetraphenylborate Anions and Paraquat and Diquat Dications , 1987 .

[8]  Andrew D. Hamilton,et al.  Aromatic-aromatic interactions in molecular recognition: a family of artificial receptors for thymine that shows both face-to-face and edge-to-face orientations , 1988 .

[9]  T. Ishida,et al.  Specific ring stacking interaction on the tryptophan-7-methylguanine system: comparative crystallographic studies of indole derivatives-7-methylguanine base, nucleoside, and nucleotide complexes , 1988 .

[10]  T. Benzing,et al.  Recognition and transport of adenine derivatives with synthetic receptors. , 1988, Science.

[11]  William L. Jorgensen,et al.  Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene , 1990 .

[12]  Christopher A. Hunter,et al.  The nature of .pi.-.pi. interactions , 1990 .

[13]  J M Thornton,et al.  Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins. , 1991, Journal of molecular biology.

[14]  F. Diederich,et al.  Cyclophane-arene inclusion complexation in protic solvents: solvent effects versus electron donor-acceptor interactions , 1991 .

[15]  S. Zimmerman,et al.  Complexation of nucleotide bases by molecular tweezers with active site carboxylic acids: effects of microenvironment , 1991 .

[16]  Per Linse,et al.  Stacked or T-shaped benzene dimer in aqueous solution? A molecular dynamic study , 1992 .

[17]  H. Whitlock,et al.  pi. Hydrogen bonds as a design principal in molecular recognition , 1992 .

[18]  Jeffrey S. Moore,et al.  Aggregation of Hexa(phenylacetylene) Macrocycles in Solution: A Model System for Studying π-π Interactions , 1992 .

[19]  Roger E Bumgarner,et al.  Benzene Forms Hydrogen Bonds with Water , 1992, Science.

[20]  F. Vögtle,et al.  Molecules with Large Cavities in Supramolecular Chemistry , 1992 .

[21]  A. Fersht,et al.  Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability. , 1992, Journal of molecular biology.

[22]  A. Cheetham,et al.  Conformational studies of dihydrotetraphenylmethanes. 2. X-ray crystallographic and solution proton NMR studies of cis-1,4-dihydro-4-tritylbiphenyl and its 4'-bromo derivative: conformational control by an intramolecular edge-to-face aromatic interaction , 1993 .

[23]  Pavel Hobza,et al.  Potential Energy Surface of the Benzene Dimer: Ab Initio Theoretical Study , 1994 .

[24]  P. Willett,et al.  A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. , 1994, Journal of molecular biology.

[25]  Christian Pedersen,et al.  The nature of stacking interactions between organic molecules elucidated by analysis of crystal structures , 1994 .

[26]  C. Wilcox,et al.  MOLECULAR TORSION BALANCE FOR WEAK MOLECULAR RECOGNITION FORCES. EFFECTS OF TILTED-T EDGE-TO-FACE AROMATIC INTERACTIONS ON CONFORMATIONAL SELECTION AND SOLID-STATE STRUCTURE , 1994 .

[27]  S. Gellman,et al.  Aromatic Stacking Interactions in Aqueous Solution: Evidence That neither Classical Hydrophobic Effects nor Dispersion Forces Are Important , 1994 .

[28]  Christopher A. Hunter,et al.  Meldola Lecture. The role of aromatic interactions in molecular recognition , 1994 .

[29]  J. Rademacher,et al.  .pi.-Complexation in the Solid State Induced by Intermolecular Hydrogen Bonding , 1994 .

[30]  K. Watanabe,et al.  Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity. , 1995, Journal of molecular biology.

[31]  R. Laatikainen,et al.  NMR Study of for Benzene and Some Other Fundamental Aromatic Systems Using Alignment of Aromatics in Strong Magnetic Field , 1995 .

[32]  D. Wemmer,et al.  Complexes of the minor groove of DNA. , 1995, Annual review of biophysics and biomolecular structure.

[33]  R. Kodandapani,et al.  A new pattern for helix–turn–helix recognition revealed by the PU.l ETS–domain–DNA complex , 1996, Nature.

[34]  Juan Fernández-Recio,et al.  The Tryptophan/Histidine interaction in α-helices , 1997 .

[35]  J. Malone,et al.  X[mdash ]H[middot][middot][middot][pi ] (phenyl) interactions Theoretical and crystallographic observations , 1997 .

[36]  W. DeGrado,et al.  Solution Structure of α2D, a Nativelike de Novo Designed Protein , 1998 .

[37]  J. Trauger,et al.  RECOGNITION OF 16 BASE PAIRS IN THE MINOR GROOVE OF DNA BY A PYRROLE-IMIDAZOLE POLYAMIDE DIMER , 1998 .

[38]  J. Ziller,et al.  PHENYL-PERFLUOROPHENYL STACKING INTERACTIONS : TOPOCHEMICAL 2+2 PHOTODIMERIZATION AND PHOTOPOLYMERIZATION OF OLEFINIC COMPOUNDS , 1998 .

[39]  J. Chandrasekhar,et al.  Ab Initio Study of Energetics of X-H···π (X = N, O, and C) Interactions Involving a Heteroaromatic Ring , 1998 .

[40]  M. Saraste,et al.  FEBS Lett , 2000 .