| Literature DB >> 28681360 |
Lissa C Anderson1, Maria Håkansson2, Björn Walse2, Carol L Nilsson3,4.
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.Entities:
Keywords: Collisionally induced dissociation; Electron-transfer dissociation; High field Fourier transform mass spectrometry; High resolution; Precision medicine; Protein sequence variant; Protein structure; X Ray crystallography
Mesh:
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Year: 2017 PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0
Source DB: PubMed Journal: J Am Soc Mass Spectrom ISSN: 1044-0305 Impact factor: 3.109
Figure 1Sequences of expressed BCAT2 and BCAT2 T186R protein constructs. The location of the amino acid and variant (enlarged and in bold) is given as the number in the UniProt database (O15382). The His tag is in green and the TEV protease site in in purple bold text
Figure 2(a) Broadband high resolution mass spectrum of BCAT2 T186R using 0.76 s transients (three microscans/spectrum; post-FT average of 10 spectra). Inset shows region of chromatogram over which data shown was acquired. (b) Expanded view of the +45 charge indicated in (a). Inset shows the three most abundant species observed in the Xtract deconvolved spectrum derived from (a). (c) Expanded view showing the 10 most abundant isotopologues of BCAT2 T186R. (d) Table of theoretical and observed m/z for the 10 isotopologues displayed in (c) as well as mass error (ppm). The RMS error for the 10 peaks shown was 1. 9 ppm
Figure 3(a) Mass spectrum of the isolated BCAT2 WT [M + 45H]45+ acquired with four 0.76 s transients. Total data acquisition time was approximately 5.4 s (four fills of multipole storage device; 7.5 × 105 precursor AGC target; 3 × 106 charges detected). Inset shows expanded view of the 10 most abundant isotopologues of the distribution (shaded red). (b) Table of theoretical and observed m/z for the 10 isotopologues displayed in (a) as well as mass error (ppm). RMS error for the 10 peaks shown was 2.3 ppm. (c) CID MS/MS spectrum of BCAT2 WT [M + 45H]44+ precursor using 0.76 s transients (four microscans/spectrum; post-FT average of three spectra). Total data acquisition time was approximately 16 s (~5.4 s/spectrum; four fragment ion fills; 7.5 × 105 precursor AGC target). (d) Sequence coverage derived from the spectrum and the position of the single amino acid substitution are indicated
Figure 4(a) (top) CID MS/MS spectrum of BCAT2 T186R [M + 45H]45+ precursor using 0.76 s transients (four microscans/spectrum; post-FT average of three spectra). Total data acquisition time was approximately 21 s (~7 s/spectrum; six fragment ion fills; 7.5 × 105 precursor automatic gain control (AGC) target). (b) (Top) 5 ms ETD MS/MS spectrum of BCAT2 T186R [M + 45H]45+ precursor using 0.76 s transients (four microscans/spectrum; post-FT average of three spectra). Total data acquisition time was approximately 42 s (~14 s/spectrum; 15 fragment ion fills; 2 × 105 precursor AGC target). Zoom insets of the regions shaded in color are shown center with fragment ions labeled. Sequence coverage derived from each spectrum and the position of the single amino acid substitution are indicated (bottom)
Examples of BCAT 2 T186R ETD Fragment Mass Errors from Monoisotopic Peaks (Prior to Deconvolution) and Xtract Deconvolution
| Ion type | Observed | Monoisotopic peak error (ppm) | Xtract deconvolution error (ppm) |
|---|---|---|---|
| C4 | 320.1567 | 0.6 | – |
| C5 | 407.1887 | 0.5 | – |
| C6 | 554.2572 | 0.5 | – |
| C7 | 682.3521 | 0.3 | – |
| C9 | 824.4267 | 0.7 | 1.0 |
| C10 2+ | 470.2304 | 0.4 | 0.8 |
| C13 | 1293.6826 | 2.2 | 2.4 |
| C14 | 1422.2772 | 3.4 | 3.6 |
| C14 2+ | 711.8652 | 0.6 | |
| C15 2+ | 777.3855 | 0.6 | – |
| C17 2+ | 891.9388 | 0.7 | 0.9 |
| C19 2+ | 1004.513 | 1.0 | – |
| C20 2+ | 1073.0431 | 1.5 | 1.2 |
| C20 3+ | 715.6971 | 0.4 | |
| C21 2+ | 1137.0919 | 2.6 | 2.7 |
| C21 3+ | 758.3955 | 0.5 | |
| C23 3+ | 833.4448 | 0.6 | 1.2 |
| C25 3+ | 884.8025 | 0.1 | – |
| C26 3+ | 903.8102 | 0.7 | 0.8 |
| Z7 | 929.4108 | 0.9 | 0.9 |
| Z12 2+ | 745.3626 | 0.5 | – |
| Z13 2+ | 809.392 | 0.6 | – |
| Z15 2+ | 930.4556 | 0.9 | – |
| Z16 2+ | 994.5033 | 1.0 | – |
| Z19 2+ | 1179.6148 | 1.4 | 1.5 |
| Z20 3+ | 829.4312 | 0.6 | 2.2 |
| Z21 3+ | 878.4538 | 0.3 | 0.4 |
| Z28 3+ | 1137.9461 | 2.3 | 2.3 |
The RMS errors are 1.2 and 1.8 ppm, respectively.
– = Not observed upon deconvolution.
Figure 5The T186R variant structure (T159R for numbering in the PDB file). The two monomers of the T186R mutant are colored in coral and orange, respectively. Compared with the non-variant BCAT2, it crystallizes in a different space group at exactly the same condition (pH 6.5)
Figure 6The T186R variant structure (T159R for numbering in the PDB file) overlaid on the BCAT2 inhibitor bound structure (PDB code 5CR5) described in [37]. The two different monomers of the T186R mutant are colored in coral and orange, respectively. The 5CR5 structure is colored in shades of green. The T186 loop is colored in cyan with R186 in magenta and the inhibitor in yellow