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Conformation of 3'CMP bound to RNase A using TrNOESY.

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 < or = P < or =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 (1 rpf) except that a C3'-endo conformation for the ribose ring (rather than C2'-exo conformation) was found in the TrNOESY structure.

journal_name

Arch Biochem Biophys

journal_title

Archives of biochemistry and biophysics

authors

Lee YC,Jackson PL,Jablonsky MJ,Muccio DD

doi

10.1016/j.abb.2007.02.034

subject

Has Abstract

pub_date

2007-07-01 00:00:00

pages

37-46

issue

1

eissn

0003-9861

issn

1096-0384

pii

S0003-9861(07)00098-7

journal_volume

463

pub_type

杂志文章

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