A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings

• Published in: Journal of biomolecular NMR Vol. 20; no. 3; pp. 223 - 231
• Main Authors: Dosset, P, Hus, J C, Marion, D, Blackledge, M
• Format: Journal Article
• Language: English
• Published: Netherlands 01.07.2001
• Subjects: Algorithms; Amino Acid Sequence; Bacteriophage M13 - chemistry; Capsid - chemistry; Capsid Proteins; Crystallography, X-Ray; Macromolecular Substances; Membrane Proteins - chemistry; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular - methods; Protein Conformation; Protein Structure, Tertiary; Proteins - chemistry; RNA, Catalytic - chemistry; Rotation; Software
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1023/A:1011206132740

Residual dipolar couplings (RDC), measured by dissolving proteins in dilute liquid crystal media, or by studying naturally paramagnetic molecules, have rapidly become established as routine measurements in the investigation of the structure of macromolecules by NMR. One of the most obvious applications of the previously inaccessible long-range angular information afforded by RDC is the accurate definition of domain orientation in multi-module macromolecules or complexes. In this paper we describe a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation to construct low-resolution models of macromolecular structure. For multi-domain systems the program determines the relative orientation of individual structured domains, and provides graphical user-driven rigid-body modeling of the different modules relative to the common tensorial frame. Translational freedom in the common frame, and equivalent rotations about the diagonalized (x,y,z) axes are used to position the different modules in the common frame to find a model in best agreement with experimentally measured couplings alone or in combination with additional experimental or covalent information.