Protein Structure Determination Using Protein Threading and Sparse NMR Data

摘要

It is well known that the NMR method for protein structure determination applies211u001eto small proteins and that its effectiveness decreases very rapidly as the 211u001emolecular weight increases beyond about 30 kD. We have recently developed a 211u001emethod for protein structure determination that can fully utilize partial NMR 211u001edata as calculation constraints. The core of the method is a threading algorithm 211u001ethat guarantees to find a globally optimal alignment between a query sequence and 211u001ea template structure, under distance constraints specified by NMR/NOE data. Our 211u001epreliminary tests have demonstrated that a small number of NMR/NOE distance 211u001erestraints can significantly improve threading performance in both fold 211u001erecognition and threading-alignment accuracy, and can possibly extend threading's 211u001escope of applicability from structural homologs to structural analogs. An 211u001eaccurate backbone structure generated by NMR-constrained threading can then 211u001eprovide a significant amount of structural information, equivalent to that 211u001eprovided by the NMR method with many NMR/NOE restraints; and hence can greatly 211u001ereduce the amount of NMR data typically required for accurate structure 211u001edetermination. Our preliminary study suggests that a small number of NMR/NOE 211u001erestraints may suffice to determine adequately the all-atom structure when those 211u001erestraints are incorporated in a procedure combining threading, modeling of loops 211u001eand sidechains, and molecular dynamics simulation. Potentially, this new 211u001etechnique can expand NMR's capability to larger proteins.