Simulation expansion and structural realization of the 1985 sulfur-SAS phasing insight
Habel, Jeffery Edward
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The Achilles’ heel of a protein crystal diffraction experiment is the loss of phase information necessary in the Fourier transform calculation of electron density. Traditionally, this “phase problem” was overcome by the incorporation of a heavy metal atom into the crystal. In the mid-1980’s, phasing proteins from the anomalous scattering of naturally occurring sulfur atoms in amino acids was realized on a small peptide scale (Hendrickson, 1981) and then hypothesized and simulated for a larger protein (Wang, 1985). Technological advances in X-ray generation and detection over the next fifteen years culminated in the de novo structure solution of obelin from Obelia longissima in 2000 (Liu et al., 2000). This led to the era of “direct crystallography,” where anomalous scattering from the atoms inherent in a protein are used to phase the protein structure. A new statistic, Ras (Fu et al., 2004), derived solely for measured data was developed to monitor the anomalous signal. In a simulation study of a large protein, Ras was used to monitor the incorporation of error and affect of redundancy in rescuing the data to phase the protein, elucidating a minimum Ras threshold value of 1.6. Comparison to synchrotron data was unsuccessful, but the value was later validated through the structure solution of a Southeast Collaboratory for Structural Genomics (SECSG) protein, Pfu-542154, from multiple crystals and different X-ray sources. This new structure pushes the current limits of de novo phasing with sulfur single-wavelength anomalous scattering (SAS) and verifies the original simulation of phasing approximately 50 amino acids per sulfur atom. At the same time, the simulation presented here raises the bar set by the original 1985 sulfur-SAS simulation to new heights for crystallographers to attain. This research has the possibility of helping every member of crystallographic community and with the continued technological advancement in X-ray sources and detectors; sulfur-SAS will become a more commonplace solution to the phase problem.