Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry–based structural proteomics tool

Johnson, Danté T.; Stefano, Luciano H Di; Jones, Lisa M.

doi:10.1074/jbc.rev119.006218

Cited by 74 publications

(89 citation statements)

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“…Although label-dependent methods can provide information on how the local environment of the probe changes as the protein folds, other methods, including NMR, pulsed oxidative labeling coupled to MS (133,134), and hydrogen-deuterium exchange MS (HDX-MS) or NMR (135), provide conformationally sensitive data with peptide to single-residue resolution. Particularly for NMR experiments, experimental data may be incorporated into simulations to help provide a molecular interpretation of the experimental results (e.g.…”

Section: Harnessing the Predictive Power Of Folding Simulationsmentioning

confidence: 99%

“…In addition, conformational distributions from folding simulations may be used to predict time-resolved experimental results. For example, oxidative labeling of amino acid side chains depends on side-chain solvent accessibility (133,134), and the time evolution of the probability that a given residue is solvent-accessible may be simply computed from conformational ensembles along the folding trajectory.…”

Section: Harnessing the Predictive Power Of Folding Simulationsmentioning

confidence: 99%

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Successes and challenges in simulating the folding of large proteins

Gershenson

Gosavi

Faccioli

et al. 2020

Journal of Biological Chemistry

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Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structurebased models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.

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Section: Harnessing the Predictive Power Of Folding Simulationsmentioning

confidence: 99%

Section: Harnessing the Predictive Power Of Folding Simulationsmentioning

confidence: 99%

Successes and challenges in simulating the folding of large proteins

Gershenson

Gosavi

Faccioli

et al. 2020

Journal of Biological Chemistry

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“…To further interrogate receptor-PPT1 interactions, we turned to hydroxyl radical protein footprinting (HRPF) by means of fast photochemical oxidation of proteins (FPOP) 44 as a method to compare protein topography between two structural states (e.g., ligand-bound versus ligandfree). Briefly, proteins are allowed to react with a high concentration of very short-lived hydroxyl radicals generated in situ.…”

Section: Mapping Ppt1 Interactionsmentioning

confidence: 99%

“…The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. The system was then equilibrated with restraints on the Cα atoms of the protein for 1ns, prior to performing a production MD simulation for 500 ns, but with restraints applied only to the Cα atoms of residues on either sides of gaps, namely (11,12,20,21,25,26,44,45,78,79,98,99,184,185,190,191, 236 and 237. AMBER numbering).…”

Section: Electron Microscopy (Em) On Ci-mpr Domains 1-5 In the Presenmentioning

confidence: 99%

Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor

Olson

Misra

Ishihara

et al. 2020

Preprint

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The cation-independent mannose 6-phosphate receptor (CI-MPR), also known as the IGF2 receptor or CD222, is a multifunctional type I transmembrane glycoprotein ubiquitously expressed in most eukaryotic cell types. Through the receptor's ability to bind a variety of unrelated extracellular and intracellular ligands, it is involved in a wide array of functions including protein trafficking, lysosomal biogenesis, internalization, regulation of cell growth, cell migration and apoptosis. CI-MPR has a large extracellular region comprised of 15 contiguous domains, four of which interact with phosphorylated glycans on lysosomal enzymes. Here we present a series of biophysical studies, along with crystal structures, providing information on how the N-terminal 5 domains of this receptor work in concert to bind and release carbohydrates. High-resolution electron microscopy as well as hydroxyl radical protein footprinting (HRPF) of this multifunctional multidomain construct demonstrates dynamic conformational changes occur as a consequence of ligand binding and different pH conditions, These data, coupled with surface plasmon resonance studies and molecular modeling, allow us to propose a bi-dentate oligosaccharide binding model, which could explain how high affinity carbohydrate binding is achieved through allosteric domain cooperativity. Introduction:Lysosomes are acidified organelles that carry out degradative metabolism critical to many endocytic, phagocytic, and autophagic processes, such as inactivation of pathogenic organisms and disposal of abnormal proteins 1-5 . This diverse degradative capacity depends on a collection of over 60 different soluble proteases, glycosidases, nucleases, and lipases. Delivery of these newly synthesized hydrolytic enzymes to lysosomes depends on the P-type lectins, the 300kDa cation-independent mannose 6-phosphate receptor (CI-MPR) and the 46kDa cation-dependent MPR (CD-MPR), that bind a unique carbohydrate determinant, mannose 6-phosphate (M6P), on lysosomal enzymes. However, CI-MPR is the primary receptor responsible for this trafficking 4 . Because CI-MPR binds a wide range of ligands 6,7 at the cell surface that include M6P-containing cytokines/hormones 8,9 and non-M6P-containing molecules (e.g., insulin-like growth factor 2 (IGF2) 10 , plasminogen 11 , urokinase-type plasminogen activator receptor (uPAR) 11 ) to mediate CI-MPR's roles as a tumor suppressor 12 and regulator of cell growth and differentiation 13 , it is not surprising CI-MPR is essentiel for normal development as transgenic mice lacking the CI-MPR gene die at birth 14,15 .Lysosomal storage diseases (LSDs) are caused by mutations in lysosomal proteins, mainly enzymes, that result in defective catabolism and substrate accumulation. Characteristic of the family of ~70 LSDs is their progressive and debilitating nature due to their impact on multiple organ systems. Treatment is symptomatic for most LSDs, with only 11 having FDAapproved therapies. For example, deficiency of palmitoyl-protein thioesterase 1 (PPT1), which remo...

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“…Mass spectrometry (MS) has recently become an increasingly attractive option for the structural characterization of membrane proteins due to its high sensitivity, low sample requirements, and its speed and ability to handle impure samples [1,2]. Native MS has emerged as a complementary approach to X-ray crystallography and NMR in membrane protein studies through the use of membrane mimetics such as detergent micelles, bicelles, lipodiscs, liposomes, amphipols, and nanodiscs and soft ionization techniques [3,4]. Even though native MS provides important insights into subunit stoichiometry, complex organization and interface stability, it also presents challenges due to ionization into and detection in the gas phase, which can lead to differences in the complexes detected [5].…”

Section: Introductionmentioning

confidence: 99%

Self-Organized Amphiphiles are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments

Cheng

Mobley²,

Misra³

et al. 2020

Preprint

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The analysis of membrane protein topography using fast photochemical oxidation of protein (FPOP) has been reported in recent years, but still underrepresented in literature. Based on the hydroxyl radical reactivity of lipids and other amphiphiles, it is believed that the membrane environment acts as a hydroxyl radical scavenger decreasing effective hydroxyl radical doses and resulting in less observed oxidation of proteins. Here, we investigated the effect of bulk hydroxyl radical scavenging in FPOP using both isolated cellular membranes as well as detergent micelles. We found no significant change in radical scavenging activity upon the addition of disrupted cellular membranes with the membrane concentration in the range of 0-25600 cell/μL using an inline radical dosimeter. We confirmed the non-scavenging nature of the membrane with the FPOP results of a soluble model protein in the presence of cell membranes, which showed no significant difference in oxidation with or without membranes. The use of detergents revealed that, while soluble detergent below the critical micelle concentration acts as a potent hydroxyl radical scavenger as expected, additional detergent has little to no hydroxyl radical scavenging effect once the critical micelle concentration is reached. These results suggest that any scavenging effect of membranes or organized amphiphilic membrane mimetics in FPOP experiments are not due to bulk hydroxyl radical scavenging, but may be due to a localized scavenging phenomenon.

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Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry–based structural proteomics tool

Cited by 74 publications

References 100 publications

Successes and challenges in simulating the folding of large proteins

Successes and challenges in simulating the folding of large proteins

Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor

Self-Organized Amphiphiles are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments

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