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Cited by 2Mass Spectrometry Techniques and ApplicationsAdvanced Proteomics Techniques and ApplicationsProtein Structure and Dynamics

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Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

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Luo, Jie, Ranish, Jeff·2024·eLife
DOI 10.7554/elife.99809PMC PMC11563578

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Abstract

Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here, we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry. Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ~10 Å, which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II complexes.

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Figure 1. The isobaric Qlinker quantitative crosslinking-mass spectrometry (CLMS) approach for studying conformational and structural changes in proteins and protein complexes. (a) The structure of Q2linkers and the general scheme for qCLMS using Q2linkers. The 13C atom in C1q2 or C2q2 is indicated by red font. (b–e) Experiment to evaluate the ability of Q2linkers to quantify the relative abundances of crosslinks and monolinks derived from Q2linker modification of TAP-tag affinity-purified pol I at designated ratios (~20 ug for each mixing ratio). Example spectra of a monolinked peptide (b) and a crosslinked peptide (c) with the observed reporter ion intensities at each mixing ratio. (d) Observed vs. expected log2 (127/126) reporter ion ratios for monolinks. (e) Observed vs. expected log2 (127/126) reporter ion ratios for crosslinks. Boxplot in R was used to create the graphs in (d) and (e). Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. The experiment was performed once.
Figure 1. The isobaric Qlinker quantitative crosslinking-mass spectrometry (CLMS) approach for studying conformational and structural changes in proteins and protein complexes. (a) The structure of Q2linkers and the general scheme for qCLMS using Q2linkers. The 13C atom in C1q2 or C2q2 is indicated by red font. (b–e) Experiment to evaluate the ability of Q2linkers to quantify the relative abundances of crosslinks and monolinks derived from Q2linker modification of TAP-tag affinity-purified pol I at designated ratios (~20 ug for each mixing ratio). Example spectra of a monolinked peptide (b) and a crosslinked peptide (c) with the observed reporter ion intensities at each mixing ratio. (d) Observed vs. expected log2 (127/126) reporter ion ratios for monolinks. (e) Observed vs. expected log2 (127/126) reporter ion ratios for crosslinks. Boxplot in R was used to create the graphs in (d) and (e). Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. The experiment was performed once.CC BY · PubMed Central
Figure 1—figure supplement 1. Synthesis of Q2linkers. The 13C atom in C1q2 or C2q2 is indicated by red font.
Figure 1—figure supplement 1. Synthesis of Q2linkers. The 13C atom in C1q2 or C2q2 is indicated by red font.CC BY · PubMed Central
Figure 1—figure supplement 2. Experimental procedure to evaluate the ability of Q2linkers to quantify the relative abundances of crosslinks and monolinks derived from Q2linker modification of affinity-purified pol I. M = molecular weight markers.
Figure 1—figure supplement 2. Experimental procedure to evaluate the ability of Q2linkers to quantify the relative abundances of crosslinks and monolinks derived from Q2linker modification of affinity-purified pol I. M = molecular weight markers.CC BY · PubMed Central
Figure 1—figure supplement 3. Observed vs. expected log2 (126/127) reporter ion ratios for individual monolinks (A) and crosslinks (B) at different mixing ratios. There are 298 monolinks and 32 crosslinks identified in all runs.
Figure 1—figure supplement 3. Observed vs. expected log2 (126/127) reporter ion ratios for individual monolinks (A) and crosslinks (B) at different mixing ratios. There are 298 monolinks and 32 crosslinks identified in all runs.CC BY · PubMed Central
Figure 1—figure supplement 4. The ratio distributions for interlinks, intralinks, and monolinks from the pol II +/-a-amanitin experiment.
Figure 1—figure supplement 4. The ratio distributions for interlinks, intralinks, and monolinks from the pol II +/-a-amanitin experiment.CC BY · PubMed Central
Figure 2. Q2linkers detect conformational changes in protein biosensors. (a) Quantification of a monolinked peptide from maltose binding protein (MBP) with or without maltose. Structures of MBP in the open, ligand-free conformation (green, 1mpb.pdb) and the closed, maltose-bound conformation (brown, 1n3w.pdb) are shown on the left. A close-up view of the ‘balancing interface’ is shown on the right. In the closed conformation, the sequence between amino acids 301–312 forms an alpha helix (gray) and K313 forms a salt bridge with E310. The helix and the salt bridge are disrupted in the open conformation (cyan). A crosslinker swapping experiment was performed on the same preparation of MBP; a technical replicate. (b) Quantification of monolinked and crosslinked peptides involving K78 and K95 from apo-CaM and CaM with Ca2+ and CBP. Structures of apo-CaM (left) and CaM + CBP (blue) + Ca2+ (right) are shown with key lysine residues space filled and magenta. The experiment was performed once.
Figure 2. Q2linkers detect conformational changes in protein biosensors. (a) Quantification of a monolinked peptide from maltose binding protein (MBP) with or without maltose. Structures of MBP in the open, ligand-free conformation (green, 1mpb.pdb) and the closed, maltose-bound conformation (brown, 1n3w.pdb) are shown on the left. A close-up view of the ‘balancing interface’ is shown on the right. In the closed conformation, the sequence between amino acids 301–312 forms an alpha helix (gray) and K313 forms a salt bridge with E310. The helix and the salt bridge are disrupted in the open conformation (cyan). A crosslinker swapping experiment was performed on the same preparation of MBP; a technical replicate. (b) Quantification of monolinked and crosslinked peptides involving K78 and K95 from apo-CaM and CaM with Ca2+ and CBP. Structures of apo-CaM (left) and CaM + CBP (blue) + Ca2+ (right) are shown with key lysine residues space filled and magenta. The experiment was performed once.CC BY · PubMed Central
Figure 3. Q2linkers detect structural changes during TFIIA/TBP/TFIIB ternary complex formation. (a, b) The distribution of log2 (127/126) ratios for interlinks (a) and intralinks (b) from the Qlinker experiment comparing the TFIIA/TBP/TFIIB ternary complex (127) to the TFIIA/TBP and TFIIB/TBP binary complexes (126). The x-axis is the ranking of the log2 (127/126) ratios. Crosslinks with the highest ratios are labeled. (c) The structure of TFIIA, TBP, and TFIIB in the pol II PIC complex (5fmf) is shown. TFIIB is rainbow colored with blue at the N-terminus and red at the C-terminus. Residues in the central region of TFIIB that are involved in crosslinks with high ratios are shown as space filled. The regions of TFIIB that interact with the Rpb1 clamp and Rpb2 protrusion are also shown. The experiment was performed once.
Figure 3. Q2linkers detect structural changes during TFIIA/TBP/TFIIB ternary complex formation. (a, b) The distribution of log2 (127/126) ratios for interlinks (a) and intralinks (b) from the Qlinker experiment comparing the TFIIA/TBP/TFIIB ternary complex (127) to the TFIIA/TBP and TFIIB/TBP binary complexes (126). The x-axis is the ranking of the log2 (127/126) ratios. Crosslinks with the highest ratios are labeled. (c) The structure of TFIIA, TBP, and TFIIB in the pol II PIC complex (5fmf) is shown. TFIIB is rainbow colored with blue at the N-terminus and red at the C-terminus. Residues in the central region of TFIIB that are involved in crosslinks with high ratios are shown as space filled. The regions of TFIIB that interact with the Rpb1 clamp and Rpb2 protrusion are also shown. The experiment was performed once.CC BY · PubMed Central
Figure 4. Q2linkers detect conformational changes in large protein complexes. (a) The SDS-PAGE gel of affinity-purified pol II from WT and ∆Rpb4 strains and experimental design for studying conformational changes in RNA polymerase II due to deletion of Rpb4. (b–d) The log2(126/127) ratio comparisons in experiment I and II for holo-Pol II and ∆Rpb4-pol II. x-axis is ΔRpb4-pol II (126)/holo-pol II (127). y-axis is holo-pol II (126)/ΔRpb4-pol II (127). Enrichment in the holo-pol II sample (labeled with C2q2 in experiment I) will have a smaller log2(126/127) ratio on the x-axis; enrichment in the holo-pol II (labeled with C1q2 in experiment II) will have a higher log2(126/127) ratio on the y-axis. Each green dot corresponds to one unique pair of crosslinking sites identified in both experiments. Each blue dot on the x-axis corresponds to one unique pair of crosslinking sites identified only in experiment I and each yellow dot on the y-axis corresponds to one unique pair of crosslinking sites identified only in experiment II. Only the green dots are used for the linear regression analysis. (b) Interlinks, (c) intralinks, and (d) monolinks. Dashed lines indicate log2 ratio = 1. The same preparation of each protein complex was used in a crosslinker swapping experiment; a technical replicate.
Figure 4. Q2linkers detect conformational changes in large protein complexes. (a) The SDS-PAGE gel of affinity-purified pol II from WT and ∆Rpb4 strains and experimental design for studying conformational changes in RNA polymerase II due to deletion of Rpb4. (b–d) The log2(126/127) ratio comparisons in experiment I and II for holo-Pol II and ∆Rpb4-pol II. x-axis is ΔRpb4-pol II (126)/holo-pol II (127). y-axis is holo-pol II (126)/ΔRpb4-pol II (127). Enrichment in the holo-pol II sample (labeled with C2q2 in experiment I) will have a smaller log2(126/127) ratio on the x-axis; enrichment in the holo-pol II (labeled with C1q2 in experiment II) will have a higher log2(126/127) ratio on the y-axis. Each green dot corresponds to one unique pair of crosslinking sites identified in both experiments. Each blue dot on the x-axis corresponds to one unique pair of crosslinking sites identified only in experiment I and each yellow dot on the y-axis corresponds to one unique pair of crosslinking sites identified only in experiment II. Only the green dots are used for the linear regression analysis. (b) Interlinks, (c) intralinks, and (d) monolinks. Dashed lines indicate log2 ratio = 1. The same preparation of each protein complex was used in a crosslinker swapping experiment; a technical replicate.CC BY · PubMed Central
Figure 4—figure supplement 1. Structural comparison of holo-pol II (5u5q) and core-pol II (li3q). Core-pol II without Rpb4/Rpb7 is colored brown and holo-pol II is colored gray with Rpb4 and Rpb7 in light blue. The five switches that cause the movement of the clamp are colored in magenta.
Figure 4—figure supplement 1. Structural comparison of holo-pol II (5u5q) and core-pol II (li3q). Core-pol II without Rpb4/Rpb7 is colored brown and holo-pol II is colored gray with Rpb4 and Rpb7 in light blue. The five switches that cause the movement of the clamp are colored in magenta.CC BY · PubMed Central
Figure 5. Q2linkers detect conformational changes in pol II complexes. (a) Switch 2 (Rpb1:328–346) conformational changes in ∆Rpb4-pol II (cyan) and holo-pol II (gray). The crosslinked lysine residues are shown as spheres. Cα−Cα distances between crosslinked lysines are indicated. (b) Structural comparison of crosslinks involving Switch 5 (red, Rpb1:1431–1433) for ∆Rpb4-pol II (cyan, left), holo-pol II (gray, right), and the merged structures (middle). In the holo-pol II structure (right), Switch 5 bending pulls Rpb1:D1442 away from K15, breaking the salt bridge that is formed in the core pol II structure (left). The increase in the abundances of the Rpb1:15-Rpb6:76 and Rpb1:15-Rpb6:72 crosslinks in holo-pol II is likely attributed to the salt bridge between K15 and D1442 in core pol II, which impedes the NHS ester-based reaction between the epsilon amino group of K15 and the crosslinker. (c) Structural comparison of the region of Rpb5 involving the crosslink between K161 and K171 in ∆Rpb4-pol II and holo-pol II. A salt bridge (not shown) is formed between K161 and E172 in both structures. (d) Structure of Rpb1 near the crosslink between Rpb1:K689 and Rpb1:K728 in ∆Rpb4-pol II and holo-pol II. In all structures, ∆Rpb4-pol II is cyan and holo-pol II is gray. NZ−NZ distances between crosslinked lysines are indicated.
Figure 5. Q2linkers detect conformational changes in pol II complexes. (a) Switch 2 (Rpb1:328–346) conformational changes in ∆Rpb4-pol II (cyan) and holo-pol II (gray). The crosslinked lysine residues are shown as spheres. Cα−Cα distances between crosslinked lysines are indicated. (b) Structural comparison of crosslinks involving Switch 5 (red, Rpb1:1431–1433) for ∆Rpb4-pol II (cyan, left), holo-pol II (gray, right), and the merged structures (middle). In the holo-pol II structure (right), Switch 5 bending pulls Rpb1:D1442 away from K15, breaking the salt bridge that is formed in the core pol II structure (left). The increase in the abundances of the Rpb1:15-Rpb6:76 and Rpb1:15-Rpb6:72 crosslinks in holo-pol II is likely attributed to the salt bridge between K15 and D1442 in core pol II, which impedes the NHS ester-based reaction between the epsilon amino group of K15 and the crosslinker. (c) Structural comparison of the region of Rpb5 involving the crosslink between K161 and K171 in ∆Rpb4-pol II and holo-pol II. A salt bridge (not shown) is formed between K161 and E172 in both structures. (d) Structure of Rpb1 near the crosslink between Rpb1:K689 and Rpb1:K728 in ∆Rpb4-pol II and holo-pol II. In all structures, ∆Rpb4-pol II is cyan and holo-pol II is gray. NZ−NZ distances between crosslinked lysines are indicated.CC BY · PubMed Central

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Authors
Luo, J., & Ranish, J.
Affiliations
  • Institute for Systems Biology (US)
  • Institute for Systems Biology
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2024-11-14
Volume
13
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.99809
PMC
PMC11563578
OpenAlex
W4402596750
Cited by
2
References
3
Citations by year
2026: 1 · 2025: 1
Type
posted content
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Institutes of Health (RO1GM136974, RO1GM108908, R01GM144559)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
protein conformational change, protein complexes, general transcription factors, TATA-binding protein, TFIIA, TFIIB, RNA polymerase II, biosensors, ternary complex
MeSH terms
Cross-Linking Reagents, Humans, Protein Conformation, Proteins, RNA Polymerase II, Mass Spectrometry, Multiprotein Complexes

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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