Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay

Lin, Hsien-Jung L; James, Isabella; Hyer, Chad D; Haderlie, Connor T; Zackrison, Michael J; Bateman, Tyler M; Berg, Monica; Park, Jaebeom; Daley, S Anisha; Pina, Nathan R Zuniga; Tseng, Yi Jie; Moody, J. D.; Price, John C.

doi:10.1021/acs.jproteome.2c00323

Cited by 4 publications

(9 citation statements)

References 106 publications

(137 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Included with C Half are instructions for installation and operation as well as a series of tutorial videos at . C Half requires an experimental design common to chemical or thermal denaturing experiments − and that MS data be preprocessed through an MSMS identification and quantification software package such as Protein Prospector, Comet, Mascot, MaxQuant, or PEAKS Studio Figure shows the general workflow of C Half from pre-C Half processing (Figure A), C Half Initialization (Figure B), curve fitting (Figure C), quality control tools (Figure D), combined site stability (Figure E), and data visualization (Figure F).…”

Section: Methodsmentioning

confidence: 99%

“…C Half uses peptide abundances to calculate PFS by first normalizing them and plotting them against their denaturant concentration/temperature values (Figure C). These points are used to fit a sigmoid curve using the curve_fit method from the Python SciPy module and a fitting equation (eq ) that has been used almost universally across different studies of PFS. − y = B + A − B 1 + e false( prefix− 1 false) false( C 1 2 − x false) / b The parameters for the equation were normalized peptide signal intensity in each fraction ( y ), final denaturant concentration or temperature of each fraction ( x ), pretransition baseline ( A ), post-transition baseline ( B ), denature midpoint ( C 1/2 or T m ), and the slope of transition ( b ).…”

Section: Methodsmentioning

confidence: 99%

“…In this section the modules of C Half will be discussed. Three data sets were used for benchmarking the program: Lin et al, for IPSA data, Walker et al, for SPROX data, and Leijten et al, for TPP data.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

C_Half: Folding Stability Made Simple

et al. 2023

Self Cite

View full text Add to dashboard Cite

The structure of a protein defines its function and integrity and correlates with the protein folding stability (PFS). Quantifying PFS allows researchers to assess differential stability of proteins in different disease or ligand binding states, providing insight into protein efficacy and potentially serving as a metric of protein quality. There are a number of mass spectrometry (MS)-based methods to assess PFS, such as Thermal Protein Profiling (TPP), Stability of Proteins from Rates of Oxidation (SPROX), and Iodination Protein Stability Assay (IPSA). Despite the critical value that PFS studies add to the understanding of mechanisms of disease and treatment development, proteomics research is still primarily dominated by concentration-based studies. We found that a major reason for the lack of PFS studies is the lack of a user-friendly data processing tool. Here we present the first user-friendly software, CHalf , with a graphical user interface for calculating PFS. Besides calculating site-specific PFS of a given protein from chemical denature folding stability assays, CHalf is also compatible with thermal denature folding stability assays. CHalf also includes a set of data visualization tools to help identify changes in PFS across protein sequences and in between different treatment conditions. We expect the introduction of CHalf to lower the barrier of entry for researchers to investigate PFS, promoting the usage of PFS in studies. In the long run, we expect this increase in PFS research to accelerate our understanding of the pathogenesis and pathophysiology of disease.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

C_Half: Folding Stability Made Simple

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…To increase the throughput, one-point approaches of SPROX and pulse proteolysis have been developed by pooling the ligand-treated and vehicle-treated samples across all the denaturing conditions following chemical modification or proteolysis, providing powerful tools for high-throughput PECI mapping. More recently, John C. Price group introduced IPSA to monitor the surface-accessibility differences of tyrosine, histidine, methionine, and cysteine under denaturing conditions and a user-friendly data processing tool of C Half to calculate protein folding stability changes from chemical denature folding stability assays, demonstrating increased sensitivity compared with SPROX. , …”

Section: Overview Of the Methods For Peci Mappingmentioning

confidence: 99%

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Li,

Lyu,

Wang

et al. 2023

Chem. Res. Toxicol.

View full text Add to dashboard Cite

Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinitydriven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.

show abstract

“…To better understand RA pathology and changes in HSA stability, future RA studies should look for potential binding partners by extracting lipids and small molecules from purified serum HSA. Other directions to explore the mechanisms that increase HSA stability are: (1) Using more specific surface modifications or chemical crosslinking reagents to carry out indepth surface probing of HSA, collect specific information about HSA binding partners and coordination changes [93,94], and (2) comparing HSA and CRP protein binding partners in RA and non-RA patients using immunoaffinity purification together with mass spectrometry to understand how a change in CRP concentration could be contributing to HSA interactor changes. Future research into HSA and other related proteins will continue to enhance our understanding of RA-specific pathology and give insights into the development of, and potential treatments for, RA.…”

Section: Plos Onementioning

confidence: 99%

Modification of the structural stability of human serum albumin in rheumatoid arthritis

et al. 2023

Self Cite

View full text Add to dashboard Cite

Differential scanning calorimetry (DSC) can indicate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes result from either concentration changes or altered thermal stabilities for 7–10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA and the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes observed in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of some fraction of the human serum albumin (HSA) proteins in the sample. By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.

show abstract

Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay

Cited by 4 publications

References 106 publications

C_Half: Folding Stability Made Simple

C_Half: Folding Stability Made Simple

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Modification of the structural stability of human serum albumin in rheumatoid arthritis

Contact Info

Product

Resources

About

Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay

Cited by 4 publications

References 106 publications

CHalf: Folding Stability Made Simple

CHalf: Folding Stability Made Simple

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Modification of the structural stability of human serum albumin in rheumatoid arthritis

Contact Info

Product

Resources

About

C_Half: Folding Stability Made Simple

C_Half: Folding Stability Made Simple