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Methods. 2015 Nov 1;89:79-90. doi: 10.1016/j.ymeth.2015.05.014. Epub 2015 May 15.

Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length.

Author information

1
Department of Proteomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig D-04318, Germany.
2
Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
3
Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: jens@meilerlab.org.
4
Department of Proteomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig D-04318, Germany; Department of Bioanalytics, University of Applied Sciences and Arts of Coburg, D-96450 Coburg, Germany. Electronic address: stefan.kalkhof@ufz.de.

Abstract

Recent development of high-resolution mass spectrometry (MS) instruments enables chemical crosslinking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein-protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein's tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal crosslinker type and length for protein structure determination. While a longer crosslinker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space. In this study, the number of crosslinks and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys, and Arg-Arg reactive crosslinkers between 1 and 60Å. Depending on the protein size a heuristic was developed that determines the optimal crosslinker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct crosslinker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.

KEYWORDS:

Crosslinking; De novo folding; Mass spectrometry; Protein modeling; Protein structure prediction

PMID:
25986934
PMCID:
PMC4803439
DOI:
10.1016/j.ymeth.2015.05.014
[Indexed for MEDLINE]
Free PMC Article

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