Structure refinement of a cyclic peptide from two-dimensional NMR data and molecular modeling

• Published in: Biochemistry (Easton) Vol. 26; no. 7; pp. 1851 - 1859
• Main Authors: Fesik, Stephen W, Bolis, Giorgio, Sham, Hing L, Olejniczak, Edward T
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 07.04.1987
• Subjects: Algorithms; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Humans; Magnetic Resonance Spectroscopy - methods; Models, Molecular; Molecular biophysics; Peptides, Cyclic - pharmacology; Protein Conformation; Renin - antagonists & inhibitors; Structure in molecular biology; Tridimensional structure; Renin; Cyclic peptides; Refinement; Inhibitor; Models; NMR spectrum; Conformation; Two dimension spectrometry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00381a010

The conformational and dynamic properties of a cyclic peptide designed to inhibit human renin have been examined by using NMR and molecular modeling. From a quantitative analysis of a series of two-dimensional NOE data sets, proton-proton distances were calculated. Several different methods were explored and compared to incorporate these distance constraints as well as those derived from vicinal spin-spin coupling constants into computer-generated three-dimensional structures. These methods included interactive manual manipulation of the structures to fit the NMR-determined distance constraints, distance geometry, constrained energy minimizations, and constrained molecular dynamics. The advantages and disadvantages of the methods are discussed. In addition, to gain insight into the conformations accessible to the cyclic peptide and the relative flexibility of the different parts of the molecule, molecular dynamics calculations were performed at three different temperatures. Average interproton distances and dihedral angles were obtained from the structures generated in the dynamics trajectories and compared to those obtained from the NMR experiments. Despite the four methylene groups and ether linkage contained in the cyclic portion of the peptide, our NMR results indicated a preferred conformation for the macrocyclic ring of the peptide and supported the presence of a cis Phe-Ala peptide bond. In contrast, both the molecular dynamics and NMR data indicated a considerable amount of flexibility for the remaining noncyclic portion of the molecule. These results are used to propose an explanation for the cyclic peptide's inability to inhibit human renin.