Maximum entropy reconstruction of joint φ, ψ-distribution with a coil-library prior: the backbone conformation of the peptide hormone motilin in aqueous solution from φ and ψ-dependent J-couplings

Autor: Toshiyuki Kohno, Mariko Sugai, Katrin Tomson, Peter Damberg, Risto Tanner, Jüri Jarvet, Kalju Vanatalu, Julia Smirnova, Peep Palumaa, Tariq Massad
Rok vydání: 2007
Předmět:
Zdroj: Journal of Biomolecular NMR. 38:107-123
ISSN: 1573-5001
0925-2738
DOI: 10.1007/s10858-007-9150-1
Popis: In this paper, we present a new method for structure determination of flexible “random-coil” peptides. A numerical method is described, where the experimentally measured \({^{3}\hbox{J}^{{\rm H}^{\rm N} {\rm H}^{\alpha}}}\) and \({^{3}\hbox{J}^{{\rm H}^{\alpha}{\rm N}^{\rm i+1}}}\) couplings, which depend on the φ and ψ dihedral angles, are analyzed jointly with the information from a coil-library through a maximum entropy approach. The coil-library is the distribution of dihedral angles found outside the elements of the secondary structure in the high-resolution protein structures. The method results in residue specific joint φ,ψ-distribution functions, which are in agreement with the experimental J-couplings and minimally committal to the information in the coil-library. The 22-residue human peptide hormone motilin, uniformly 15N-labeled was studied. The \({^{3}\hbox{J}^{{\rm H}^{\alpha}{\rm N}^{\rm i+1}}}\) were measured from the E.COSY pattern in the sequential NOESY cross-peaks. By employing homodecoupling and an in-phase/anti-phase filter, sharp Hα-resonances (about 5 Hz) were obtained enabling accurate determination of the coupling with minimal spectral overlap. Clear trends in the resulting φ,ψ-distribution functions along the sequence are observed, with a nascent helical structure in the central part of the peptide and more extended conformations of the receptor binding N-terminus as the most prominent characteristics. From the φ,ψ-distribution functions, the contribution from each residue to the thermodynamic entropy, i.e., the segmental entropies, are calculated and compared to segmental entropies estimated from 15N-relaxation data. Remarkable agreement between the relaxation and J-couplings based methods is found. Residues belonging to the nascent helix and the C-terminus show segmental entropies, of approximately −20 J K−1 mol−1 and −12 J K−1 mol−1, respectively, in both series. The agreement between the two estimates of the segmental entropy, the agreement with the observed J-couplings, the agreement with the CD experiments, and the assignment of population to sterically allowed conformations show that the φ,ψ-distribution functions are indeed meaningful and useful descriptions of the conformational preferences for each residue in this flexible peptide.
Databáze: OpenAIRE
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