Gold clusters as Spatial Probes of Residue Position on Protein in Small Angle X-ray Scattering

Abstract

We are developing a new method for using proteins labeled with one or two gold clusters in small angle X-ray scattering. Gold cluster labeling provides strong cluster-cluster (for double-label) and cluster-protein (for single and double-labels) interference. Analysis of the former provides the distance between gold clusters, while the analysis of the latter provides the distance and relative orientation between gold cluster and protein.Here, we have investigated what structural information can be extracted from labeled protein. Simulated scattering curves of single or double-cluster labeled hypothetical template structures (PDB models modified with monomaleimido undecagold) were generated by the Debye formula using effective-atomic-scattering factors in solution. The template scattering curve is compared to the simulated scattering curves of trial structures generated by exhaustive rigid body searches for a fixed protein with rotated and translated gold cluster(s). For both single and double-labeled rigid body modeling (RBM), inter-body distance information was predicted within 1-2 A error. However, the prediction of gold cluster position(s) was inaccurate (20-40 A error for double-label, 5-50 A error for single-label) presumably because inter-body distance information dominates over the relative orientation of gold cluster and protein. To predict accurate gold cluster position(s), we corrected inter-body distance(s) of trial structure by moving gold cluster(s) along the vector from protein to cluster during RBM. Gold cluster position(s) were improved significantly by correcting to the simulated template distance (2-7 A for double-label, 2-5 A for single-label), although the accuracy was reduced when using distance(s) determined by RBM (5-70 A double-label, 2-12 A single-label). Combining single and double-labeled data is being pursued.This technique is being developed for two main applications: (1) discrimination of threading structures, (2) protein-protein docking model prediction.