[11] Heuristic refinement method for determination of solution structure of proteins from nuclear magnetic resonance data

• Published in: Methods in Enzymology Vol. 177; pp. 218,IN1,231 - 230,IN4,246
• Main Authors: Altman, Russ B., Jardetzky, Oleg
• Format: Book Chapter Journal Article
• Language: English
• Published: United States Elsevier Science & Technology 1989
• Subjects: Amino Acid Sequence; Analysis of Variance; Computer Simulation; Escherichia coli - enzymology; Magnetic Resonance Spectroscopy - methods; Models, Molecular; Molecular Sequence Data; Muramidase; Protein Conformation; Proteins; Software; Solutions; T-Phages - enzymology
• ISBN: 9780121820787; 0121820785
• ISSN: 0076-6879; 1557-7988
• DOI: 10.1016/0076-6879(89)77013-0

This chapter discusses the heuristic refinement method for determination of solution structure of proteins from nuclear magnetic resonance data. This chapter discusses various methods for interpretation of NMR that is the adjustment or exclusion is described. Methods within the adjustment paradigm generate starting structures, usually at random, and then search the neighboring conformational space until the mismatch between the data predicted from the adjusted structure and the experimental data is minimized, in terms of the chosen target function. The method described in this chapter is based on the exclusion paradigm. Simply stated, its purpose is to sample the conformational space systematically and to determine the entire set of positions for each atom that is compatible with the given set of constraints. In its design, it falls into the general class of constraint satisfaction methods, which are the subject of a sizeable literature. The method is coded in a program called PROTEAN. With the aim of accurately defining the spatial distribution of atomic positions allowed by the given data, the value of using a systematic search of conformational space and the exclusion paradigm is almost self evident.