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Titolo:
Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices
Autore:
Vila, JA; Ripoll, DR; Villegas, ME; Vorobjev, YN; Scheraga, HA;
Indirizzi:
Cornell Univ, Baker Lab, Dept Chem & Biol Chem, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 t Chem & Biol Chem, Ithaca, NY 14853 USA Univtinal San Luis, Fac Ciencias Fis Matemat & Nat, RA-5700 San Luis, Argen Univ Nacl San Luis San Luis Argentina RA-5700 t, RA-5700 San Luis, Argen Consejoanacl Invest Cient & Tecn, Inst Matemat Aplicada San Luis, RA-5700 S Consejo Nacl Invest Cient & Tecn San Luis Argentina RA-5700 s, RA-5700 S Cornell Univ, Cornell Theory Ctr, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 Cornell Theory Ctr, Ithaca, NY 14853 USA Univ N Carolina, Dept Biochem, FLOB, Chapel Hill, NC 27599 USA Univ N Carolina Chapel Hill NC USA 27599 FLOB, Chapel Hill, NC 27599 USA
Titolo Testata:
BIOPHYSICAL JOURNAL
fascicolo: 6, volume: 75, anno: 1998,
pagine: 2637 - 2646
SICI:
0006-3495(199812)75:6<2637:ROHASC>2.0.ZU;2-L
Fonte:
ISI
Lingua:
ENG
Soggetto:
OCCURRING AMINO-ACIDS; HYDROGEN-BOND INTERACTIONS; SHORT TEMPLATED PEPTIDES; MULTIPLE-MINIMA PROBLEM; ALANINE-BASED PEPTIDES; MONTE-CARLO METHOD; CONFORMATIONAL-ANALYSIS; NONBONDED INTERACTIONS; ENERGY PARAMETERS; SIDE-CHAIN;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
68
Recensione:
Indirizzi per estratti:
Indirizzo: Scheraga, HA Cornell Univ, Baker Lab, Dept Chem & Biol Chem, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 Chem, Ithaca, NY 14853 USA
Citazione:
J.A. Vila et al., "Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices", BIOPHYS J, 75(6), 1998, pp. 2637-2646

Abstract

A theoretical study to identify the conformational preferences of lysine-based oligopeptides has been carried out. The solvation free energy and freeenergy of ionization of the oligopeptides have been calculated by using a fast multigrid boundary element method that considers the coupling between the conformation of the molecule and the ionization equilibria explicitly, at a given pH value. It has been found experimentally that isolated alanineand lysine residues have somewhat small intrinsic helix-forming tendencies; however, results from these simulations indicate that conformations containing right handed alpha-helical turns are energetically favorable at low values of pH for lysine-based oligopeptides. Also, unusual patterns of interactions among lysine side chains with large hydrophobic contacts and close proximity (5-6 Angstrom) between charged NH3+ groups are observed. Similar arrangements of charged groups have been seen for lysine and arginine residues in experimentally determined structures of proteins available from the Protein Data Bank. The lowest-free-energy conformation of the sequence Ac-(LYS)(6)-NMe from these simulations showed large pK(alpha) shifts for some of the NH3+ groups of the lysine residues. Such large effects are not observed in the lowest-energy conformations of oligopeptide sequences with two, three, or four lysine residues. Calculations on the sequence Ac-LYS-(ALA)(4)-LYS-NMe also reveal low-energy alpha-helical conformations with interactions of one of the LYS side chains with the helix backbone in an arrangement quite similar to the one described recently by Groebke et al., 1996 (Proc. Natl. Acad. Sci. U.S.A. 93:4025-4029). The results of this study provide a sound basis with which to discuss the nature of the interactions, such as hydrophobicity, charge-charge interaction, and solvent polarization effects,that stabilize right-handed a-helical conformations.

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Documento generato il 07/07/20 alle ore 21:48:00