Blind testing cross-linking/mass spectrometry under the auspices of the 11thcritical assessment of methods of protein structure prediction (CASP11).
Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination withab initiostructure prediction determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.5 Å, or 3.4 Å in the context of blood serum. This paper reports the blind test on the readiness of this technology through the help of Critical Assessment of protein Structure Prediction (CASP). We identified between 201-381 unique residue pairs at an estimated 5% FDR (at link level albeit with missing site assignment precision evaluation), for four target proteins. HD-CLMS proved reliable once crystal structures were released. However, improvements in structure prediction using cross-link data were slight. We identified two reasons for this. Spread of cross-links along the protein sequence and the tightness of the spatial constraints must be improved. However, for the selected targets even ideal contact data derived from crystal structures did not allow modellers to arrive at the observed structure. Consequently, the progress of HD-CLMS in conjunction with computational modeling methods as a structure determination method, depends on advances on both arms of this hybrid approach.
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
Adam
0000-0002-8442-4964
A
Belsom
Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.|Institute of Biotechnology, Technische Universität Berlin, Berlin, 13355, Germany.
Michael
M
Schneider
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
Lutz
L
Fischer
Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Mahmoud
M
Mabrouk
Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Kolja
K
Stahl
Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Oliver
O
Brock
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.|Institute of Biotechnology, Technische Universität Berlin, Berlin, 13355, Germany.
Juri
0000-0001-5999-1310
J
Rappsilber
CASP; High-density cross-linking/mass spectrometry; chemical biology; computational biology; protein cross-linking; protein modeling; protein structure; structural biology