Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking

Abstract

Hybrid methods combine experimental data and computational modeling to analyze protein structures that are elusive to structure determination. To spur the development of hybrid methods, we propose to test them in the context of the CASP experiment and would like to invite experimental groups to participate in this initiative.

Figure 1

Cross-Linking/Mass Spectrometry Data Used in Critical Assessment of protein Structure Prediction 11 (CASP11). (A–D) Left panels show the C-alpha pair distance distribution of observed constraints at 5% false discovery rate (FDR) against the random constraint distribution. Middle panels show the cross-link networks for four CASP targets shown for estimated 5% FDR cut-off. Gray outer lines represent target sequences. Constraints missing from the crystal structure and, therefore, unverifiable are represented in black. Right panels show the observed constraints at 5% FDR against the X-ray structure. In all panels, constraints with Cα–Cα cross-linking distances less than 25 Å are shown in purple and constraints with distances 25 Å and over are shown in green. (A) Cross-linked residue pairs of Tx781 in Protein Data Bank (PDB)|4qan, N = 305. (B) Cross-linked residue pairs of Tx808 in PDB|4qhw, N = 265. (C) Cross-linked residue pairs of Tx767 in PDB|4qpv, N = 381. (D) Cross-linked residue pairs of Tx812 in crystal structure (structure not deposited in PDB), N = 201. Note, Tx781 was compromised during shipment and showed aggregates upon cross-linking that led to the pronounced presence of constraints not fitting the X-ray structure of that protein.