Maximum entropy reconstruction of joint phi, psi-distribution with a coil-library prior: the backbone conformation of the peptide hormone motilin in aqueous solution from phi and psi-dependent J-couplings.
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 3J(H(alpha)Nalpha) and [3J(H(alpha)Nalpha+1 couplings, which depend on the phi and psi 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 phi,psi-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 3J(H(alpha)-N(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 H(alpha)-resonances (about 5 Hz) were obtained enabling accurate determination of the coupling with minimal spectral overlap. Clear trends in the resulting phi,psi-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 phi,psi-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 phi,psi-distribution functions are indeed meaningful and useful descriptions of the conformational preferences for each residue in this flexible peptide.
Massad
Tariq
T
Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 12, 106 91, Stockholm, Sweden.
Jarvet
Jüri
J
Tanner
Risto
R
Tomson
Katrin
K
Smirnova
Julia
J
Palumaa
Peep
P
Sugai
Mariko
M
Kohno
Toshiyuki
T
Vanatalu
Kalju
K
Damberg
Peter
P
D002942:Circular Dichroism; D019277:Entropy; D006801:Humans; D009037:Motilin / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017433:Protein Structure, Secondary; D012996:Solutions
D012996:Solutions; D009037:Motilin