title: Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue.
abstract: The intrinsic conformational preferences of the nonproteinogenic amino acids constructed by incorporating the arginine side chain in the beta position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated by using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c(5)Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N'-methylamide derivatives of cis- and trans-c(5)Arg have been examined in the gas phase and in solution by using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented.
authors.affiliation: Departament d'Enginyeria Quimica, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
authors.forename: Guillem
authors.initials: G
authors.lastname: Revilla-López
authors.forename: Juan
authors.initials: J
authors.lastname: Torras
authors.forename: Ana I
authors.initials: AI
authors.lastname: Jiménez
authors.forename: Carlos
authors.initials: C
authors.lastname: Cativiela
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.forename: Carlos
authors.initials: C
authors.lastname: Alemán
mesh_terms: D001120:Arginine / Q000031:analogs & derivatives* / Q000737:chemistry*; D003198:Computer Simulation; D003517:Cyclopentanes; D005740:Gases; D008958:Models, Molecular; D008968:Molecular Conformation; D012996:Solutions
chemical_list: D003517:Cyclopentanes; D005740:Gases; D012996:Solutions; D001120:Arginine