Unconventional interactions between water and heterocyclic nitrogens in protein structures

Proteins: Structure, Function and Genetics

Volumn 57, Issue 1, 2004, Pages 1-8

  Stollar, Elliott J ^a   Gelpí, Jose Luis ^b,c   Velankar, Sameer ^d   Golovin, Adel ^d   Orozco, Modesto ^b,c   Luisi, Ben F ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

^d EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Italy)

Author keywords

Aromatic hydrogen bonds; Molecular simulations; Protein structure; Tryptophan fluorescence; Water protein interactions

Indexed keywords

AROMATIC HYDROCARBON; HETEROCYCLIC NITRO COMPOUND; HISTIDINE; IMIDAZOLE DERIVATIVE; INDOLE; NITROGEN; TRYPTOPHAN; WATER;

ARTICLE; BETA SHEET; CALCULATION; COMPLEX FORMATION; CRYSTAL STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; WATER PROTEIN INTERACTION;

AMINO ACIDS; ANIMALS; CONSERVED SEQUENCE; DATABASES, PROTEIN; DROSOPHILA PROTEINS; ELECTROSTATICS; HOMEODOMAIN PROTEINS; HYDROGEN BONDING; IMIDAZOLES; INDOLES; NITROGEN; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SPECTROMETRY, FLUORESCENCE; THERMODYNAMICS; TRANSCRIPTION FACTORS; TRYPTOPHAN; WATER;

EID: 4444228189     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20216     Document Type: Article

References (17)

1. Levitt M, Perutz MF. Aromatic rings act as hydrogen bond acceptors. J Mol Biol 1988;201:751-754.
2. Burley SK, Petsko GA. Amino-aromatic interactions in proteins. FEBS Lett 1986;203:139-143.
3. van Mourik T, Price SL, Clary DC. Ab initio calculations on indole-water, 1-methylindole-water and indole-(water)2. Chem Phys Lett 2000;311:253.
4. Sarkhel S, Rich A, Egli M. Water-nucleobase "stacking": H-pi and lone pair-pi interactions in the atomic resolution crystal structure of an RNA pseudoknot. J Am Chem Soc 2003;125:8998-8999.
5. Stollar EJ, Mayor U, Lovell SC, Federici L, Freund SM, Fersht AR, Luisi BF. Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics. J Biol Chem 2003;278:43699-43708.
6. Gelpi JL, Kalko SG, Barril X, Cirera J, de La Cruz X, Luque FJ, Orozco M. Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins. Proteins 2001;45:428-437.
7. Case DA, Pearlman DA, Caldwell JW, Cheatham TE, Ross WS, Simmerling CL, Darden TL, Marz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER. 6.0; 1999.
8. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz K, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179.
9. Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 1998;37:785.
10. Boys SF, Bernardi F. Calculation of small molecular interactions by differences of separate total energies. Some procedures with reduced errors. Mol Phys 1970;19:553.
11. Orozco M, Luque FJ. Molecular Interaction Potential (MIP). A new tool for the study of chemical reactivity. J Comp Chem 1993;14:587-603.
12. Boutselakis H, Dimitropoulos D, Fillon J, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res 2003;31:458-462.
13. Adams PD, Chen Y, Ma K, Zagorski MG, Sonnichsen FD, McLaughlin ML, Barkley MD. Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc 2002;124:9278-9286.
14. Nanda V, Brand L. Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan. Proteins 2000;40:112-125.
15. Subramaniam V, Jovin TM, Rivera-Pomar RV. Aromatic amino acids are critical for stability of the bicoid homeodomain. J Biol Chem 2001;276:21506-21511.
16. Thanki N, Thornton JM, Goodfellow JM. Distributions of water around amino acid residues in proteins. J Mol Biol 1988;202:637-657.
17. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acid Res 2004;32:D138-D141.