Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart

Caudal, Arianne; Tang, Xiaoting; Chavez, Juan D.; Keller, Andrew; Mohr, Jared P.; Bakhtina, Anna; Villet, Outi; Chen, Hongye; Zhou, Bo; Walker, M.; Tian, Rong; Bruce, James E.

doi:10.1038/s44161-022-00127-4

Cited by 15 publications

(19 citation statements)

References 74 publications

(77 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although its protein levels are not altered in TAC versus Sham mice, several of its intraprotein cross-links are increased in abundance. Because both c-state and m-state specific cross-links were increased in heart failure samples, an open channel AlphaFold model ADT1 conformation compatible with all increased cross-links was proposed to be increased in TAC mice . This conformation is consistent with the previously proposed existence of a “P state” of ADT1 described by Karch et al and Bround et al…”

Section: Resultssupporting

confidence: 83%

“…The automatically generated hypotheses for the decreased cross-link abundances propose reduced accessibility of CX6B1 residue 13 and NDUA4 residues 74 and 76 or increased reported PTMs on CX6B1 peptide IKNY K 13 TAPFDSR residue 13 and NDUA4 peptide FYSVNVDYS K 74 LK residues 64, 66, 67, 72, 73, or 74. Complex IV activity was reduced in TAC mice, and the observed change of interaction between CX6B1 and NDUA4 was proposed to possibly play a role. Therefore, it is of great interest that the quantitation of DE peptides indicates conformational changes of both proteins localized to their cross-linked residues.…”

Section: Resultsmentioning

confidence: 96%

“…Previously described heart mitochondrial quantitative XL-MS data obtained from 6 pairs of TAC versus Sham mice 28 was used for this study. Raw data and search results are available at the ProteomeXchange Consortium via the PRIDE 29 partner repository with the data set identifier PXD027757.…”

Section: Tac Versus Sham Heart Mitochondrial Cross-link and De Datamentioning

confidence: 99%

See 2 more Smart Citations

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS

2023

Self Cite

View full text Add to dashboard Cite

Chemical cross-linking with mass spectrometry provides low-resolution structural information on proteins in cells and tissues.Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells or young and old mice. A difference can originate from protein conformational changes that alter the solvent-accessible distance separating the crosslinked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or posttranslational modifications of the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein with the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified crosslinks and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences in cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.

show abstract

Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 96%

See 1 more Smart Citation

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS

2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…47,48,55 Increased multimerization among oligomeric units of SCOT in mouse hearts exposed to TAC, which could augment SCOT enzymatic activity, suggests that multiple myocardium-autonomous mechanisms contribute to enhanced ketone oxidation in the failing heart. 56 This and other prospective mechanisms require further validation.…”

Section: Ketone Metabolism In the Hypertrophied And Failing Heart Car...mentioning

confidence: 95%

Ketones and the Heart: Metabolic Principles and Therapeutic Implications

Matsuura

Puchalska

Crawford

et al. 2023

Circulation Research

View full text Add to dashboard Cite

The ketone bodies beta-hydroxybutyrate and acetoacetate are hepatically produced metabolites catabolized in extrahepatic organs. Ketone bodies are a critical cardiac fuel and have diverse roles in the regulation of cellular processes such as metabolism, inflammation, and cellular crosstalk in multiple organs that mediate disease. This review focuses on the role of cardiac ketone metabolism in health and disease with an emphasis on the therapeutic potential of ketosis as a treatment for heart failure (HF). Cardiac metabolic reprogramming, characterized by diminished mitochondrial oxidative metabolism, contributes to cardiac dysfunction and pathologic remodeling during the development of HF. Growing evidence supports an adaptive role for ketone metabolism in HF to promote normal cardiac function and attenuate disease progression. Enhanced cardiac ketone utilization during HF is mediated by increased availability due to systemic ketosis and a cardiac autonomous upregulation of ketolytic enzymes. Therapeutic strategies designed to restore high-capacity fuel metabolism in the heart show promise to address fuel metabolic deficits that underpin the progression of HF. However, the mechanisms involved in the beneficial effects of ketone bodies in HF have yet to be defined and represent important future lines of inquiry. In addition to use as an energy substrate for cardiac mitochondrial oxidation, ketone bodies modulate myocardial utilization of glucose and fatty acids, two vital energy substrates that regulate cardiac function and hypertrophy. The salutary effects of ketone bodies during HF may also include extra-cardiac roles in modulating immune responses, reducing fibrosis, and promoting angiogenesis and vasodilation. Additional pleotropic signaling properties of beta-hydroxybutyrate and AcAc are discussed including epigenetic regulation and protection against oxidative stress. Evidence for the benefit and feasibility of therapeutic ketosis is examined in preclinical and clinical studies. Finally, ongoing clinical trials are reviewed for perspective on translation of ketone therapeutics for the treatment of HF.

show abstract

“…The inter-residue qXL-MS readout provides direct information on the proximity of two amino acid sites during protein folding or unfolding in the absence of any model or known structure. XL-MS has been applied to protein complexes, 8 as well as living cells, 9 to probe protein topologies, protein−ligand conformational changes as detailed in an extended review, 10 and more recently used to identify phenotypic tissue interactome differences in heart failure 11 and aging. 12 However, the use of XL-MS to quantify ligandinduced structural stability shifts, to our knowledge, has not been documented.…”

Section: ■ Introductionmentioning

confidence: 99%

Studying Protein–Ligand Interactions by Protein Denaturation and Quantitative Cross-Linking Mass Spectrometry

2023

Self Cite

View full text Add to dashboard Cite

Recently, several mass spectrometry methods have utilized protein structural stability for the quantitative study of protein–ligand engagement. These protein-denaturation approaches, which include thermal proteome profiling (TPP) and stability of proteins from rates of oxidation (SPROX), evaluate ligand-induced denaturation susceptibility changes with a MS-based readout. The different techniques of bottom-up protein-denaturation methods each have their own advantages and challenges. Here, we report the combination of protein-denaturation principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link relative ratios across chemical denaturation. As a proof of concept, we found ligand-stabilized cross-linked lysine pairs in well-studied bovine serum albumin and ligand bilirubin. These links map to the known binding sites Sudlow Site I and subdomain IB. We propose that protein denaturation and qXL-MS can be combined with similar peptide-level quantification approaches, like SPROX, to increase the coverage information profiled for facilitating protein–ligand engagement efforts.

show abstract

Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart

Cited by 15 publications

References 74 publications

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS

Ketones and the Heart: Metabolic Principles and Therapeutic Implications

Studying Protein–Ligand Interactions by Protein Denaturation and Quantitative Cross-Linking Mass Spectrometry

Contact Info

Product

Resources

About