scholarly journals Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

2016 ◽  
Author(s):  
Adam Belsom ◽  
Michael Schneider ◽  
Lutz Fischer ◽  
Oliver Brock ◽  
Juri Rappsilber
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Critical Assessment ◽  
Conformational Space ◽  
Cross Linking

SummaryDetermining the structure of a protein by any method requires varies contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry data in combination with ab initio structure prediction by conformational space search determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.53 Å, or 3.38 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 the four proteins that we provided data for. This equates to between 0.63-1.20 proximal residues per residue, which is comparable to that obtained in the HSA study (0.85 links per residue at 5% FDR). Nevertheless, initial results of CASP11 have suggested that improvements in structure prediction using cross-link data are slight. Most significantly, however, CASP11 revealed to us some of the current limitations of cross-linking, spelling out areas in which the method must develop in future: links spread unevenly over sequence and beta sheets both lacked links and suffered from weak definition of observed links over structure. With CASP12 taking place this year and biannually in the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking. Data are available via ProteomeXchange with identifier PXD003643.The abbreviations used areCLMScross-linking/mass spectrometry;NHSN-hydroxysuccinimide;NMRnuclear magnetic resonance;sulfo-SDAsulfo-NHSdiazirine, sulfosuccinimidyl 4,4’-azipentanoate;FDRfalse discovery rate;MBSmodel-based search;HSAhuman serum albumin;RMSDroot-mean-square deviation;CASPCritical Assessment of protein Structure Prediction;Tristris(hydroxymethyl)aminomethane;PESpolyethersulphone;IAAiodoacetamide;LTQlinear trap quadrupole;MS2tandem MS scan;LC-MSliquid chromatography mass spectrometry;FMfree modelling.

scholarly journals Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

2016 ◽  
Vol 1 ◽  
pp. 24 ◽  
Author(s):  
Adam Belsom ◽  
Michael Schneider ◽  
Lutz Fischer ◽  
Mahmoud Mabrouk ◽  
Kolja Stahl ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Crystal Structures ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Hybrid Approach ◽  
Critical Assessment ◽  
Cross Linking ◽  
Blind Test ◽  
Contact Data

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 with ab initio structure 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.

scholarly journals Probing conformational changes of human serum albumin due to unsaturated fatty acid binding by chemical cross-linking and mass spectrometry

2005 ◽  
Vol 387 (3) ◽  
pp. 695-702 ◽  
Author(s):  
Bill X. HUANG ◽  
Chhabil DASS ◽  
Hee-Yong KIM
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Conformational Changes ◽  
Cross Linking ◽  
X Ray ◽  
Chemical Cross Linking

Mass spectrometry with chemical cross-linking was used to probe the conformational changes of HSA (human serum albumin) in solution on interaction with monounsaturated OA (oleic acid) or polyunsaturated AA (arachidonic acid) or DHA (docosahexaenoic acid). Fatty acid-free or -bound HSA was modified with lysine-specific cross-linkers and digested with trypsin. Cross-linked peptides were analysed by nano-electrospray ionization MS to localize the sites of cross-linking. Our data indicated that a local conformational change involving movement of the side chains of Lys-402 of subdomain IIIA or Lys-541 of subdomain IIIB occurred upon binding of all three fatty acids. Our data also indicated that the side chains of Lys-205 (IIA) and Lys-466 (IIIA) moved closer towards each other upon binding AA or DHA, but not OA, suggesting that the conformations of HSA when bound to mono- and poly-unsaturated fatty acids are distinctively different. While these observations agreed with previous X-ray crystallographic studies, the distances between ε-amino groups of most cross-linked lysine pairs were shorter than the crystal structure predicted, possibly reflecting a discrepancy between the solution and crystal structures. This method can serve as a useful complement to X-ray crystallography, particularly in probing the structure of a protein in solution.

Critical assessment of methods of protein structure prediction (CASP): Round II

1997 ◽  
Vol 29 (S1) ◽  
pp. 2-6 ◽  
Author(s):  
John Moult ◽  
Tim Hubbard ◽  
Stephen H. Bryant ◽  
Krzysztof Fidelis ◽  
Jan T. Pedersen
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Critical Assessment
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