Automated Protein NMR Structure Determination in Solution

Abstract

The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has been almost or in a few cases fully reached for favorable cases such as well-behaved, stably folding smaller proteins below the 25 kDa range. For larger and/or more difficult molecules, the input of a human expert is still required. However, even here, automated routines will substantially speed up the structure determination process. In this report, we will summarize recent developments in this field and especially emphasize practical aspects important for a successful automated protein structure determination in solution. An important aspect closely related to structure determination is structure validation. Therefore, we devote a section to automated approaches for this topic.

The evolution of protein NMR

“…The incorporation of 15 N and 13 C brought the long-term goal of developing robust and effective automation procedures for assignment and structure determination closer but manual intervention is often still required because of experimental imperfections, especially for larger, less well-behaved proteins (frequently the more interesting ones!) [62,63].…”

Structure-based prediction of protein-protein interaction sites

“…Unlike X-ray crystallography, NMR spectroscopy can produce different models of a protein, which provides some insights into its dynamics. NMR spectroscopy methods are generally used to determine the structure of proteins with molecular weight lower than 50 kDa (152) and low to moderate flexibility (66). Around 11% of the proteins structures deposited in the PDB have been determined using NMR as of February 2012.…”