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Conformation of 3'CMP bound to RNase a using TrNOESY

  1. Author:
    Lee, Y. C.
    Jackson, P. L.
    Jablonsky, M. J.
    Muccio, D. D.

  2. Author Address

    Univ Alabama, Dept Chem, Birmingham, AL 35294 USA. NCI, Med Chem Lab, Frederick, MD 21702 USA. Univ Alabama, Dept Physiol & Biophys, Birmingham, AL 35294 USA.;Muccio, DD, Univ Alabama, Dept Chem, 901 14th St S, Birmingham, AL 35294 USA.;muccio@uab.edu
    1. Year: 2007
    2. Date: Jul
  2. Journal: Archives of Biochemistry and Biophysics
    1. 463
    2. 1
    3. Pages: 37-46
  4. Type of Article: Article
  5. ISSN: 0003-9861
  1. Abstract:

    The conditions for accurately determining distance constraints from TrNOESY data on a small ligand (3'CMP) bound to a small protein (RNase A, <14 kDa) are described. For small proteins, normal TrNOESY conditions of 10:1 ligand:protein or greater can lead to inaccurate structures for the ligand-bound conformation due to the contribution of the free ligand to the TrNOESY signals. By using two ligand:protein ratios (2:1 and 5:1), which give the same distance constraints, a conformation of 3'CMP bound to RNase A was determined (glycosidic torsion angle, chi= -166 degrees; pseudorotational phase angle, 0 degrees <= P <= 36 degrees). Ligand-protein NOESY cross peaks were also observed and used to dock 3'CMP into the binding pocket of the apo-protein (7rsa). After energy minimization, the conformation of the 3'CMP:RNase A complex was similar to the X-ray structure (1rpf) except that a C3'-endo conformation for the ribose ring (rather than C2'-exo conformation) was found in the TrNOESY structure. (c) 2007 Elsevier Inc. All rights reserved.

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External Sources

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  2. DOI: 10.1016/j.abb.2007.02.034
  3. View record in Web of Science®
  4. WOS: 000247419100005

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