Evaluation of the Utility of NMR Structures Determined from Minimal NOE-Based Restraints for Structure-Based Drug Design,Using MMP-1 as an Example

摘要

The application of deuterium labeling and residula dipolar constants in combination with other structural information has demonstrated the potential for significantly expanding the range of viable protein targets for structural analysis by NMR.A previous study by Clore et al.[(1999) J.Am,Chem.Soc.121,6513-6514] demonstrated that a significant improvement in the overall protein structure occurs with the combination of residual dipolar coupling constants and minimal tertiary long-range distance restraints.The analysis of NMR protein structures determined with minimal structural information is extended with a particular interest in the utility of these structures for a structure-based drgu design program. As an example,the catalytic fragment of human fibroblast collagenase (MMP-1) was used to follow the effect of minimal restraint restraint sets on the protein structure and its utility in drgu design with a particular interest in the effect on the active site conformation.An MMP-1 structure that a particular protein was shown to be very similar to a high-quality MMP-1 structure that was calculated from a complete set of restraints.The superposition of the active site backbone atoms for the high-quality and minimal restraint MMP-1 structres yielded an rmsd of 0.68 A where the size and shape of the S1' pocket are nearly identical.Additionally,an MMP-1-CGS-27023A complex based on a minimal set of NOE-based restraints restraints reliably reproduced the structure of the complex.estabishing the usefuless of the structures for drug design.