Anisotropic Local Motions and Location of Amide Protons in Proteins

• Published in: Journal of the American Chemical Society Vol. 127; no. 14; pp. 5180 - 5185
• Main Authors: Bytchenkoff, Dimitri, Pelupessy, Philippe, Bodenhausen, Geoffrey
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 13.04.2005
• Subjects: Amides - chemistry; Anisotropy; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; Intermolecular dynamics; Intermolecular phenomena; Models, Chemical; Molecular biophysics; Proteins - chemistry; Protons; Quantum Theory; Ubiquitin - chemistry; Dipole dipole interaction; Molecular flexibility; Overhauser effect; Molecular dynamics; Theoretical study; Molecular interaction; Biological macromolecule; NMR spectrometry; Experimental study; Molecular fluctuation; Three dimensional model; Molecular mobility; One dimensional model
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja043575v

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(HNN/NC‘) that are due to concerted fluctuations of the HN−N and N−C‘ dipole−dipole interactions and stronger long-range cross-correlation rates R(C‘HN/HNN) and R(NHN/HNCα). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of HN atoms with respect to peptide planes in ubiquitin were determined. Most N−HN bonds were found not to lie exactly along the bisector of the N−C‘ and N−Cα bonds but to be slightly tilted toward the carbon-terminal side of the peptide.