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

• Published in: Journal of biomolecular NMR Vol. 38; no. 2; pp. 107 - 123
• Main Authors: Massad, Tariq, Jarvet, Jüri, Tanner, Risto, Tomson, Katrin, Smirnova, Julia, Palumaa, Peep, Sugai, Mariko, Kohno, Toshiyuki, Vanatalu, Kalju, Damberg, Peter
• Format: Journal Article
• Language: English
• Published: Netherlands Dordrecht : Kluwer Academic Publishers 01.06.2007
• Subjects: Circular Dichroism; Entropy; Humans; J-couplings; Maximum entropy; Medicin och hälsovetenskap; motilin; Motilin - chemistry; NMR; Nuclear Magnetic Resonance, Biomolecular - methods; Protein Structure, Secondary; Random coil; Solutions; Nuclear Magnetic Resonance; Secondary; Biomolecular/methods; Protein Structure
• ISSN: 0925-2738; 1573-5001; 1573-5001
• DOI: 10.1007/s10858-007-9150-1

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 [graphic removed] and [graphic removed] 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 [graphic removed] 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.