1
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Zhang J, Phetsanthad A, Li L. Investigating Anion Effects on Metal Ion Binding Interactions With Amyloid β Peptide by Ion Mobility Mass Spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5090. [PMID: 39328006 DOI: 10.1002/jms.5090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 09/28/2024]
Abstract
The study of metal ion's role in the biological processes of Alzheimer's disease has spurred investigations into the coordination chemistry of amyloid beta peptide and its fragments. Nano-electrospray ionization mass spectrometry (nESI-MS) has been utilized to examine the stabilization of bound anions on multiprotein complexes without bulk solvent. However, the effects of anions on metal ion binding interactions with amyloid beta peptide have not been explored. This study directly examined metal-peptide complexes using nESI-MS and investigated the effects of various anions on the binding ratio and stability of these complexes from ammonium salt solutions. The results indicate that different anions have distinct effects on the binding ratio and stability of various metal-peptide complexes. Of these, the bicarbonate ion exhibits the highest binding ratios for metal-peptide complexes, while binding ratios for these complexes in phosphate are comparatively low. Our results suggest that acetate, formate, bicarbonate, and phosphate have weak affinities and act as weak stabilizers of the metal-peptide complex structure in the gas phase. Intriguingly, chloride and sulfate act as stabilizers of the metal-peptide complex in the gas phase. The rank order determined from these data is substantially different from the Hofmeister salt series in solution. Although this outcome was anticipated due to the reduced influence of anions and water solvation, our findings correlate well with expected anion binding in solution and emphasize the importance of both hydration layer and anion-metal-peptide binding effects for Hofmeister-type stabilization in solution. This approach proved useful in examining the interactions between metal ions and amyloid beta peptide, which are relevant to Alzheimer's disease, using direct ESI-MS.
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Affiliation(s)
- Jingwei Zhang
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin, USA
- School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin, USA
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2
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Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD. FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Data Sets Built on FragPipe. J Proteome Res 2024; 23:2332-2342. [PMID: 38787630 DOI: 10.1021/acs.jproteome.3c00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiP-MS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a data merging scheme and a protein-centric multiple hypothesis correction scheme, enabling processed LiP-MS data sets to be more robust and less redundant. These improvements strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.
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Affiliation(s)
- Edgar Manriquez-Sandoval
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joy Brewer
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Gabriela Lule
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Samanta Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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3
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Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD. FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569947. [PMID: 38106106 PMCID: PMC10723326 DOI: 10.1101/2023.12.04.569947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiP-MS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage the fast, sensitive, and accurate search and label-free quantification algorithms in FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a new data merging scheme (from ions to cut-sites) and a protein-centric multiple hypothesis correction scheme, collectively enabling processed LiP-MS datasets to be more robust and less redundant. These improvements substantially strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. As a final feature, FLiPPR facilitates the collection of structural metadata to identify correlations between experiments and structural features. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.
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Affiliation(s)
- Edgar Manriquez-Sandoval
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joy Brewer
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Gabriela Lule
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Samanta Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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4
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Huang Z, Cai Z, Zhang J, Gu Y, Wang J, Yang J, Lv G, Yang C, Zhang Y, Ji C, Jiang S. Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken. Poult Sci 2023; 102:103118. [PMID: 37862870 PMCID: PMC10590753 DOI: 10.1016/j.psj.2023.103118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/22/2023] Open
Abstract
Inosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.
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Affiliation(s)
- Zengwen Huang
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China; College of Animal Science, Xichang University, Sichuan, Xichang 615012, China; Xinjiang Taikun Group Co., Ltd., Xinjiang, Changji 831100, China
| | - Zhengyun Cai
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China
| | - Juan Zhang
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China.
| | - Yaling Gu
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China
| | - Jing Wang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food & Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Manoa, HI 96822
| | - Gang Lv
- Xinjiang Taikun Group Co., Ltd., Xinjiang, Changji 831100, China
| | - Chaoyun Yang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Yi Zhang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Chen Ji
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Shengwang Jiang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
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5
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Liu FC, Cropley TC, Bleiholder C. Elucidating Structures of Protein Complexes by Collision-Induced Dissociation at Elevated Gas Pressures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2247-2258. [PMID: 37729591 PMCID: PMC11162217 DOI: 10.1021/jasms.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Ion activation methods carried out at gas pressures compatible with ion mobility separations are not yet widely established. This limits the analytical utility of emerging tandem-ion mobility spectrometers that conduct multiple ion mobility separations in series. The present work investigates the applicability of collision-induced dissociation (CID) at 1 to 3 mbar in a tandem-trapped ion mobility spectrometer (tandem-TIMS) to study the architecture of protein complexes. We show that CID of the homotetrameric protein complexes streptavidin (53 kDa), neutravidin (60 kDa), and concanavalin A (110 kDa) provides access to all subunits of the investigated protein complexes, including structurally informative dimers. We report on an "atypical" dissociation pathway, which for concanavalin A proceeds via symmetric partitioning of the precursor charges and produces dimers with the same charge states that were previously reported from surface induced dissociation. Our data suggest a correlation between the formation of subunits by CID in tandem-TIMS/MS, their binding strengths in the native tetramer structures, and the applied activation voltage. Ion mobility spectra of in situ-generated subunits reveal a marked structural heterogeneity inconsistent with annealing into their most stable gas phase structures. Structural transitions are observed for in situ-generated subunits that resemble the transitions reported from collision-induced unfolding of natively folded proteins. These observations indicate that some aspects of the native precursor structure is preserved in the subunits generated from disassembly of the precursor complex. We rationalize our observations by an approximately 100-fold shorter activation time scale in comparison to traditional CID in a collision cell. Finally, the approach discussed here to conduct CID at elevated pressures appears generally applicable also for other types of tandem-ion mobility spectrometers.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Tyler C. Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
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6
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Luan M, Hou Z, Zhang B, Ma L, Yuan S, Liu Y, Huang G. Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations. Anal Chem 2023; 95:8798-8806. [PMID: 37309130 DOI: 10.1021/acs.analchem.2c05630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The mechanisms whereby protein ions are released from nanodroplets at the liquid-gas interface have continued to be controversial since electrospray ionization (ESI) mass spectrometry was widely applied in biomolecular structure analysis in solution. Several viable pathways have been proposed and verified for single-domain proteins. However, the ESI mechanism of multi-domain proteins with more complicated and flexible structures remains unclear. Herein, dumbbell-shaped calmodulin was chosen as a multi-domain protein model to perform molecular dynamics simulations to investigate the structural evolution during the ESI process. For [Ca4CAM], the protein followed the classical charge residue model. As the inter-domain electrostatic repulsion increased, the droplet was found to split into two sub-droplets, while stronger-repulsive apo-calmodulin unfolded during the early evaporation stage. We designated this novel ESI mechanism as the domain repulsion model, which provides new mechanistic insights into further exploration of proteins containing more domains. Our results suggest that greater attention should be paid to the effect of domain-domain interactions on structure retention during liquid-gas interface transfer when mass spectrometry is used as the developing technique in gas phase structural biology.
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Affiliation(s)
- Moujun Luan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Zhuanghao Hou
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Buchun Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Likun Ma
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Siming Yuan
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Yangzhong Liu
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Guangming Huang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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7
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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8
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Proteomics: Application of next-generation proteomics in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00016-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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9
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Cancer proteomics, current status, challenges, and future outlook. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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10
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Cancer proteomics: Application of case studies in diverse cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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11
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Albokhari D, Ng BG, Guberinic A, Daniel EJP, Engelhardt NM, Barone R, Fiumara A, Garavelli L, Trimarchi G, Wolfe L, Raymond KM, Morava E, He M, Freeze HH, Lam C, Edmondson AC. ALG8-CDG: Molecular and phenotypic expansion suggests clinical management guidelines. J Inherit Metab Dis 2022; 45:969-980. [PMID: 35716054 PMCID: PMC9474684 DOI: 10.1002/jimd.12527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022]
Abstract
Congenital disorders of glycosylation are a continuously expanding group of monogenic disorders of glycoprotein and glycolipid glycan biosynthesis. These disorders mostly manifest with multisystem involvement. Individuals with ALG8-CDG commonly present with hypotonia, protein-losing enteropathy, and hepatic involvement. Here, we describe seven unreported individuals diagnosed with ALG8-CDG based on biochemical and molecular testing and we identify nine novel variants in ALG8, bringing the total to 26 individuals with ALG8-CDG in the medical literature. In addition to the typical multisystem involvement documented in ALG8-CDG, our cohort includes the two oldest patients reported and further expands the phenotype of ALG8-CDG to include stable intellectual disability, autism spectrum disorder and other neuropsychiatric symptoms. We further expand the clinical features in a variety of organ systems including ocular, musculoskeletal, dermatologic, endocrine, and cardiac abnormalities and suggest a comprehensive evaluation and monitoring strategy to improve clinical management.
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Affiliation(s)
- Daniah Albokhari
- Department of Pediatrics, Division of Human Genetics, Section of Metabolism, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Taibah University College of Medicine, Medina, Saudi Arabia
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, California, USA
| | - Alis Guberinic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Earnest James Paul Daniel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicole M Engelhardt
- Department of Pediatrics, Division of Human Genetics, Section of Metabolism, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rita Barone
- Department of Clinical and Experimental Medicine, Division of Child Neurology and Psychiatry, University of Catania, Catania, Italy
| | - Agata Fiumara
- Department of Clinical and Experimental Medicine, Pediatric Clinic, University of Catania, Catania, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Mother and Child Department, Local Health Authority (AUSL) of Reggio Emilia Research Unit (IRCCS), Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Medical Genetics Unit, Mother and Child Department, Local Health Authority (AUSL) of Reggio Emilia Research Unit (IRCCS), Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Kimiyo M Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, California, USA
| | - Christina Lam
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Center of Integrated Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Andrew C Edmondson
- Department of Pediatrics, Division of Human Genetics, Section of Metabolism, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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12
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Huang Z, Zhang J, Gu Y, Cai Z, Wei D, Feng X, Yang C. Analysis of the molecular mechanism of inosine monophosphate deposition in Jingyuan chicken muscles using a proteomic approach. Poult Sci 2022; 101:101741. [PMID: 35259688 PMCID: PMC8904228 DOI: 10.1016/j.psj.2022.101741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/24/2021] [Accepted: 01/12/2022] [Indexed: 12/03/2022] Open
Abstract
Inosine monophosphate (IMP) is an indicator of meat taste, and the molecular mechanism underlying IMP deposition in muscle tissues is important to developing superior poultry breeds. The aim of this study was to identify the key proteins regulating IMP deposition in different muscle groups of 180-day-old Jingyuan chickens (Hen) using a proteomics-based approach. We identified 1,300 proteins in the muscle tissues of Jingyuan chickens, of which 322 were differentially expressed between the breast and leg muscles (129 proteins were highly expressed in breast muscles and 193 proteins were highly expressed in leg muscles). PGM1, PKM2, AK1, AMPD1, and PurH/ATIC were among the differentially expressed proteins (DEPs) involved in the purine metabolism pathway, of which purH was highly expressed in leg muscles, while the others were highly expressed in breast muscles. The proteomics screening results were verified by PRM, qPCR, and western blotting, showing consistency with the proteomics results. Our findings are not only significant in terms of protecting the Jingyuan chicken germplasm resources, but also provide the molecular basis for generating high-quality broiler chicken breeds.
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Affiliation(s)
- Zengwen Huang
- Agriculture College, Ningxia University, Yinchuan, China; Xichang University, Sichuan 615012, China
| | - Juan Zhang
- Agriculture College, Ningxia University, Yinchuan, China
| | - Yaling Gu
- Agriculture College, Ningxia University, Yinchuan, China.
| | - Zhengyun Cai
- Agriculture College, Ningxia University, Yinchuan, China
| | - Dawei Wei
- Agriculture College, Ningxia University, Yinchuan, China
| | - Xiaofang Feng
- Agriculture College, Ningxia University, Yinchuan, China
| | - Chaoyun Yang
- Agriculture College, Ningxia University, Yinchuan, China
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13
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Yazhini A, Srinivasan N, Sandhya S. Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. Front Genet 2022; 12:747344. [PMID: 35082828 PMCID: PMC8785561 DOI: 10.3389/fgene.2021.747344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Multi-protein assemblies are complex molecular systems that perform highly sophisticated biochemical functions in an orchestrated manner. They are subject to changes that are governed by the evolution of individual components. We performed a comparative analysis of the ancient and functionally conserved spliceosomal SF3b complex, to recognize molecular signatures that contribute to sequence divergence and functional specializations. For this, we recognized homologous sequences of individual SF3b proteins distributed across 10 supergroups of eukaryotes and identified all seven protein components of the complex in 578 eukaryotic species. Using sequence and structural analysis, we establish that proteins occurring on the surface of the SF3b complex harbor more sequence variation than the proteins that lie in the core. Further, we show through protein interface conservation patterns that the extent of conservation varies considerably between interacting partners. When we analyze phylogenetic distributions of individual components of the complex, we find that protein partners that are known to form independent subcomplexes are observed to share similar profiles, reaffirming the link between differential conservation of interface regions and their inter-dependence. When we extend our analysis to individual protein components of the complex, we find taxa-specific variability in molecular signatures of the proteins. These trends are discussed in the context of proline-rich motifs of SF3b4, functional and drug binding sites of SF3b1. Further, we report key protein-protein interactions between SF3b1 and SF3b6 whose presence is observed to be lineage-specific across eukaryotes. Together, our studies show the association of protein location within the complex and subcomplex formation patterns with the sequence conservation of SF3b proteins. In addition, our study underscores evolutionarily flexible elements that appear to confer adaptive features in individual components of the multi-protein SF3b complexes and may contribute to its functional adaptability.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, M. S. Ramaiah University of Applied Sciences, Bengaluru, India
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14
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Abstract
Recent advancements place a comprehensive catalog of protein structure, oligomeric state, sequence, and modification status tentatively within reach, thus providing an unprecedented roadmap to therapies for many human diseases. To achieve this goal, revolutionary technologies capable of bridging key gaps in our ability to simultaneously measure protein composition and structure must be developed. Much of the current progress in this area has been catalyzed by mass spectrometry (MS) tools, which have become an indispensable resource for interrogating the structural proteome. For example, methods associated with native proteomics seek to comprehensively capture and quantify the endogenous assembly states for all proteins within an organism. Such technologies have often been partnered with ion mobility (IM) separation, from which collision cross section (CCS) information can be rapidly extracted to provide protein size information. IM technologies are also being developed that utilize CCS values to enhance the confidence of protein identification workflows derived from liquid chromatography-IM-MS analyses of enzymatically produced peptide mixtures. Such parallel advancements in technology beg the question: can CCS values prove similarly useful for the identification of intact proteins and their complexes in native proteomics? In this perspective, I examine current evidence and technology trends to explore the promise and limitations of such CCS information for the comprehensive analysis of multiprotein complexes from cellular mixtures.
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Affiliation(s)
- Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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16
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Alsharhan H, He M, Edmondson AC, Daniel EJP, Chen J, Donald T, Bakhtiari S, Amor DJ, Jones EA, Vassallo G, Vincent M, Cogné B, Deb W, Werners AH, Jin SC, Bilguvar K, Christodoulou J, Webster RI, Yearwood KR, Ng BG, Freeze HH, Kruer MC, Li D, Raymond KM, Bhoj EJ, Sobering AK. ALG13 X-linked intellectual disability: New variants, glycosylation analysis, and expanded phenotypes. J Inherit Metab Dis 2021; 44:1001-1012. [PMID: 33734437 PMCID: PMC8720508 DOI: 10.1002/jimd.12378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022]
Abstract
Pathogenic variants in ALG13 (ALG13 UDP-N-acetylglucosaminyltransferase subunit) cause an X-linked congenital disorder of glycosylation (ALG13-CDG) where individuals have variable clinical phenotypes that include developmental delay, intellectual disability, infantile spasms, and epileptic encephalopathy. Girls with a recurrent de novo c.3013C>T; p.(Asn107Ser) variant have normal transferrin glycosylation. Using a highly sensitive, semi-quantitative flow injection-electrospray ionization-quadrupole time-of-flight mass spectrometry (ESI-QTOF/MS) N-glycan assay, we report subtle abnormalities in N-glycans that normally account for <0.3% of the total plasma glycans that may increase up to 0.5% in females with the p.(Asn107Ser) variant. Among our 11 unrelated ALG13-CDG individuals, one male had abnormal serum transferrin glycosylation. We describe seven previously unreported subjects including three novel variants in ALG13 and report a milder neurodevelopmental course. We also summarize the molecular, biochemical, and clinical data for the 53 previously reported ALG13-CDG individuals. We provide evidence that ALG13 pathogenic variants may mildly alter N-linked protein glycosylation in both female and male subjects, but the underlying mechanism remains unclear.
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Affiliation(s)
- Hind Alsharhan
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Miao He
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew C. Edmondson
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Earnest J. P. Daniel
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Tyhiesia Donald
- Pediatrics Ward, Grenada General Hospital, St. George’s, Grenada
- Clinical Teaching Unit, St. George’s University, St. George’s, Grenada
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, Arizona
- Department of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, Arizona
| | - David J. Amor
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, and Department of Pediatrics, University of Melbourne, Melbourne, Australia
| | - Elizabeth A. Jones
- Manchester Centre for Genomic Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Grace Vassallo
- Department of Pediatric Neurology, Royal Manchester Children’s Hospital, Manchester University Foundation Trust, Manchester, UK
| | - Marie Vincent
- Service de génétique médicale, CHU de Nantes, Nantes, France
| | - Benjamin Cogné
- Service de génétique médicale, CHU de Nantes, Nantes, France
| | - Wallid Deb
- Service de génétique médicale, CHU de Nantes, Nantes, France
| | - Arend H. Werners
- Department of Anatomy, Physiology and Pharmacology, St. George University School of Veterinary Medicine, St. George’s, Grenada
| | - Sheng C. Jin
- Department of Genetics and Pediatrics, Washington University, St. Louis, Missouri
| | - Kaya Bilguvar
- Department of Genetics, Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, and Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Richard I. Webster
- Institute for Neuroscience and Muscle Research, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | | | - Bobby G. Ng
- Human Genetics Program, Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Michael C. Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, Arizona
- Department of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, Arizona
| | - Dong Li
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kimiyo M. Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Elizabeth J. Bhoj
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew K. Sobering
- Department of Biochemistry, St. George’s University School of Medicine, St. George’s, Grenada
- Windward Islands Research and Education Foundation, True Blue, St. George’s, Grenada
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17
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Alsharhan H, Ng BG, Daniel EJP, Friedman J, Pivnick EK, Al-Hashem A, Faqeih EA, Liu P, Engelhardt NM, Keller KN, Chen J, Mazzeo PA, Rosenfeld JA, Bamshad MJ, Nickerson DA, Raymond KM, Freeze HH, He M, Edmondson AC, Lam C. Expanding the phenotype, genotype and biochemical knowledge of ALG3-CDG. J Inherit Metab Dis 2021; 44:987-1000. [PMID: 33583022 PMCID: PMC8282734 DOI: 10.1002/jimd.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/15/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Congenital disorders of glycosylation (CDGs) are a continuously expanding group of monogenic disorders of glycoprotein and glycolipid biosynthesis that cause multisystem diseases. Individuals with ALG3-CDG frequently exhibit severe neurological involvement (epilepsy, microcephaly, and hypotonia), ocular anomalies, dysmorphic features, skeletal anomalies, and feeding difficulties. We present 10 unreported individuals diagnosed with ALG3-CDG based on molecular and biochemical testing with 11 novel variants in ALG3, bringing the total to 40 reported individuals. In addition to the typical multisystem disease seen in ALG3-CDG, we expand the symptomatology of ALG3-CDG to now include endocrine abnormalities, neural tube defects, mild aortic root dilatation, immunodeficiency, and renal anomalies. N-glycan analyses of these individuals showed combined deficiencies of hybrid glycans and glycan extension beyond Man5 GlcNAc2 consistent with their truncated lipid-linked precursor oligosaccharides. This spectrum of N-glycan changes is unique to ALG3-CDG. These expanded features of ALG3-CDG facilitate diagnosis and suggest that optimal management should include baseline endocrine, renal, cardiac, and immunological evaluation at the time of diagnosis and with ongoing monitoring.
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Affiliation(s)
- Hind Alsharhan
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Faculty of Medicine, Kuwait
University, Kuwait City, Kuwait
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical
Discovery Institute, La Jolla, California
| | - Earnest James Paul Daniel
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jennifer Friedman
- Division of Neurosciences and Pediatrics, University of
California San Diego and Rady Children’s Hospital, San Diego,
California
| | - Eniko K. Pivnick
- Department of Pediatrics, Division of Medical Genetics,
University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee
| | - Amal Al-Hashem
- Department of Pediatrics, Prince Sultan Military Medical
City, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi
Arabia
| | - Eissa Ali Faqeih
- Section of Medical Genetics, Children’s Specialist
Hospital King Fahad Medical City, Riyadh, Saudi Arabia
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor
College of Medicine, Houston, Texas
- Baylor Genetics Laboratories, Houston, Texas
| | - Nicole M. Engelhardt
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Kierstin N. Keller
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pamela A. Mazzeo
- Department of Pediatrics, The Children’s Hospital
of Philadelphia, Philadelphia, Pennsylvania
| | | | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor
College of Medicine, Houston, Texas
- Baylor Genetics Laboratories, Houston, Texas
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of Pediatrics,
University of Washington School of Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington,
Seattle, Washington
- Brotman-Baty Institute, Seattle, Washington
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington,
Seattle, Washington
- Brotman-Baty Institute, Seattle, Washington
| | - Kimiyo M. Raymond
- Department of Laboratory Medicine and Pathology, Mayo
Clinic, Rochester, Minnesota
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical
Discovery Institute, La Jolla, California
| | - Miao He
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew C. Edmondson
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Christina Lam
- Division of Genetic Medicine, Department of Pediatrics,
University of Washington School of Medicine, Seattle, Washington
- Center of Integrated Brain Research, Seattle
Children’s Research Institute, Seattle, Washington
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18
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Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
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Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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19
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Mitra R, Gadkari VV, Meinen BA, van Mierlo CPM, Ruotolo BT, Bardwell JCA. Mechanism of the small ATP-independent chaperone Spy is substrate specific. Nat Commun 2021; 12:851. [PMID: 33558474 PMCID: PMC7870927 DOI: 10.1038/s41467-021-21120-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy's action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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20
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Jayasundara K, Li C, DeBastiani A, Sharif D, Li P, Valentine SJ. Physicochemical Property Correlations with Ionization Efficiency in Capillary Vibrating Sharp-Edge Spray Ionization (cVSSI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:84-94. [PMID: 32856909 PMCID: PMC8130659 DOI: 10.1021/jasms.0c00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The relative contributions to ionization efficiency by three molecular chemical properties have been examined for field-free and field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) using mass spectrometry (MS) analysis. Ion intensities have been recorded for model compounds under each operational ionization mode as well as for aqueous and nonaqueous (methanol) solvent systems. Multiple regression analysis suggests that for field-free cVSSI, ion intensity is mostly associated with the log of the base dissociation constant (pKb) and proton affinity (PA) for both aqueous and methanol solutions. Comparatively, for field-enabled cVSSI using aqueous solutions, the dominant factor correlated with ion intensity is the log of the partition coefficient (log P). To a lesser degree, this is observed for methanol solutions as well. For ESI, pKb is the dominant factor associated with ion signal levels from methanol and aqueous solutions. These results are supported by studies conducted on two different mass spectrometers employing different cVSSI emitter tips. The relationship of ion intensity and pKb in ESI is supported by multiple studies; however, the shift to other chemical properties with the addition of cVSSI suggests the possibility that a different (or combinations of) ionization mechanism(s) may be operative for these ionization modes. These results are briefly considered in light of the different ESI mechanisms.
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Affiliation(s)
| | | | | | | | - Peng Li
- To whom correspondence should be addressed: , and .
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21
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Gadkari VV, Ramírez CR, Vallejo DD, Kurulugama RT, Fjeldsted JC, Ruotolo BT. Enhanced Collision Induced Unfolding and Electron Capture Dissociation of Native-like Protein Ions. Anal Chem 2020; 92:15489-15496. [PMID: 33166123 PMCID: PMC7861131 DOI: 10.1021/acs.analchem.0c03372] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is capable of revealing much that remains unknown within the structural proteome, promising such information on refractory protein targets. Here, we report the development of a unique drift tube IM-MS (DTIM-MS) platform, which combines high-energy source optics for improved collision induced unfolding (CIU) experiments and an electromagnetostatic cell for electron capture dissociation (ECD). We measured a series of high precision collision cross section (CCS) values for protein and protein complex ions ranging from 6-1600 kDa, exhibiting an average relative standard deviation (RSD) of 0.43 ± 0.20%. Furthermore, we compare our CCS results to previously reported DTIM values, finding strong agreement across similarly configured instrumentation (average RSD of 0.82 ± 0.73%), and systematic differences for DTIM CCS values commonly used to calibrate traveling-wave IM separators (-3% average RSD). Our CIU experiments reveal that the modified DTIM-MS instrument described here achieves enhanced levels of ion activation when compared with any previously reported IM-MS platforms, allowing for comprehensive unfolding of large multiprotein complex ions as well as interplatform CIU comparisons. Using our modified DTIM instrument, we studied two protein complexes. The enhanced CIU capabilities enable us to study the gas phase stability of the GroEL 7-mer and 14-mer complexes. Finally, we report CIU-ECD experiments for the alcohol dehydrogenase tetramer, demonstrating improved sequence coverage by combining ECD fragmentation integrated over multiple CIU intermediates. Further improvements for such native top-down sequencing experiments were possible by leveraging IM separation, which enabled us to separate and analyze CID and ECD fragmentation simultaneously.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Daniel D Vallejo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Ruwan T Kurulugama
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 98051, United States
| | - John C Fjeldsted
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 98051, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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22
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Mehaffey MR, Xia Q, Brodbelt JS. Uniting Native Capillary Electrophoresis and Multistage Ultraviolet Photodissociation Mass Spectrometry for Online Separation and Characterization of Escherichia coli Ribosomal Proteins and Protein Complexes. Anal Chem 2020; 92:15202-15211. [PMID: 33156608 PMCID: PMC7788560 DOI: 10.1021/acs.analchem.0c03784] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With an overarching goal of characterizing the structure of every protein within a cell, identifying its interacting partners, and quantifying the dynamics of the states in which it exists, key developments are still necessary to achieve comprehensive native proteomics by mass spectrometry (MS). In practice, much work remains to optimize reliable online separation methods that are compatible with native MS and improve tandem MS (MS/MS) approaches with respect to when and how energy is deposited into proteins of interest. Herein, we utilize native capillary zone electrophoresis coupled with MS to characterize the proteoforms in the Escherichia coli 70S ribosome. The capabilities of 193 nm ultraviolet photodissociation (UVPD) to yield informative backbone sequence ions are compared to those of higher-energy collisional dissociation (HCD). To further improve sequence coverage values, a multistage MS/MS approach is implemented involving front-end collisional activation to disassemble protein complexes into constituent subunits that are subsequently individually isolated and activated by HCD or UVPD. In total, 48 of the 55 known E. coli ribosomal proteins are identified as 84 unique proteoforms, including 22 protein-metal complexes and 10 protein-protein complexes. Additionally, mapping metal-bound holo fragment ions resulting from UVPD of protein-metal complexes offers insight into the metal-binding sites.
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Qiangwei Xia
- CMP Scientific Corporation, Brooklyn, New York, New York 11226, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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23
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Hong J, Wu H, Zhang R, He M, Xu W. The Coupling of Taylor Dispersion Analysis and Mass Spectrometry to Differentiate Protein Conformations. Anal Chem 2020; 92:5200-5206. [DOI: 10.1021/acs.analchem.9b05745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haimei Wu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Muyi He
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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24
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Marcinko TM, Drews T, Liu T, Vachet RW. Epigallocatechin-3-gallate Inhibits Cu(II)-Induced β-2-Microglobulin Amyloid Formation by Binding to the Edge of Its β-Sheets. Biochemistry 2020; 59:1093-1103. [PMID: 32100530 DOI: 10.1021/acs.biochem.0c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) is a catechin found in green tea that can inhibit the amyloid formation of a wide variety of proteins. EGCG's ability to prevent or redirect the amyloid formation of so many proteins may reflect a common mechanism of action, and thus, greater molecular-level insight into how it exerts its effect could have broad implications. Here, we investigate the molecular details of EGCG's inhibition of the protein β-2-microglobulin (β2m), which forms amyloids in patients undergoing long-term dialysis treatment. Using size-exclusion chromatography and a collection of mass spectrometry-based techniques, we find that EGCG prevents Cu(II)-induced β2m amyloid formation by diverting the normal progression of preamyloid oligomers toward the formation of spherical, redissolvable aggregates. EGCG exerts its effect by binding with a micromolar affinity (Kd ≈ 5 μM) to the β2m monomer on the edge of two β-sheets near the N-terminus. This interaction destabilizes the preamyloid dimer and prevents the formation of a tetramer species previously shown to be essential for Cu(II)-induced β2m amyloid formation. EGCG's binding at the edge of the β-sheets in β2m is consistent with a previous hypothesis that EGCG generally prevents amyloid formation by binding cross-β-sheet aggregation intermediates.
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Affiliation(s)
- Tyler M Marcinko
- Department of Chemistry, University of Massachusetts-Amherst, 374 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Thomas Drews
- Department of Chemistry, University of Massachusetts-Amherst, 374 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts-Amherst, 374 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts-Amherst, 374 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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25
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Marcinko TM, Liang C, Savinov S, Chen J, Vachet RW. Structural Heterogeneity in the Preamyloid Oligomers of β-2-Microglobulin. J Mol Biol 2019; 432:396-409. [PMID: 31711963 DOI: 10.1016/j.jmb.2019.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 11/29/2022]
Abstract
In dialysis patients, the protein β2-microglobulin (β2m) forms amyloid fibrils in a condition known as dialysis-related amyloidosis. To understand the early stages of the amyloid assembly process, we have used native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble preamyloid oligomers. ESI-IM-MS reveals the presence of multiple conformers for the dimer, tetramer, and hexamer that precede the Cu(II)-induced amyloid assembly process, results which are distinct from β2m oligomers formed at low pH. Experimental and computational results indicate that the predominant dimer is a Cu(II)-bound structure with an antiparallel side-by-side configuration. In contrast, tetramers exist in solution in both Cu(II)-bound and Cu(II)-free forms. Selective depletion of Cu(II)-bound species results in two primary conformers-one that is compact and another that is more expanded. Molecular modeling and molecular dynamics simulations identify models for these two tetrameric conformers with unique interactions and interfaces that enthalpically compensate for the loss of Cu(II). Unlike with other amyloid systems in which conformational heterogeneity is often associated with different amyloid morphologies or off-pathway events, conformational heterogeneity in the tetramer seems to be a necessary aspect of Cu(II)-induced amyloid formation by β2m. Moreover, the Cu(II)-free models represent a new advance in our understanding of Cu(II) release in Cu(II)-induced amyloid formation, laying a foundation for further mechanistic studies as well as development of new inhibition strategies.
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Affiliation(s)
- Tyler M Marcinko
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Chungwen Liang
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States
| | - Sergey Savinov
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Jianhen Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
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Wu Z, Malty R, Moutaoufik MT, Zhang Q, Jessulat M, Babu M. A Tag-Based Affinity Purification Mass Spectrometry Workflow for Systematic Isolation of the Human Mitochondrial Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:83-100. [PMID: 31452137 DOI: 10.1007/978-981-13-8367-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mitochondria (mt) are double-membraned, dynamic organelles that play an essential role in a large number of cellular processes, and impairments in mt function have emerged as a causative factor for a growing number of human disorders. Given that most biological functions are driven by physical associations between proteins, the first step towards understanding mt dysfunction is to map its protein-protein interaction (PPI) network in a comprehensive and systematic fashion. While mass-spectrometry (MS) based approaches possess the high sensitivity ideal for such an endeavor, it also requires stringent biochemical purification of bait proteins to avoid detecting spurious, non-specific PPIs. Here, we outline a tagging-based affinity purification coupled with mass spectrometry (AP-MS) workflow for discovering new mt protein associations and providing novel insights into their role in mt biology and human physiology/pathology. Because AP-MS relies on the creation of proteins fused with affinity tags, we employ a versatile-affinity (VA) tag, consisting of 3× FLAG, 6 × His, and Strep III epitopes. For efficient delivery of affinity-tagged open reading frames (ORF) into mammalian cells, the VA-tag is cloned onto a specific ORF using Gateway recombinant cloning, and the resulting expression vector is stably introduced in target cells using lentiviral transduction. In this chapter, we show a functional workflow for mapping the mt interactome that includes tagging, stable transduction, selection and expansion of mammalian cell lines, mt extraction, identification of interacting protein partners by AP-MS, and lastly, computational assessment of protein complexes/PPI networks.
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Affiliation(s)
- Zhuoran Wu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Ramy Malty
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada.
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Exploration of variations in proteome and metabolome for predictive diagnostics and personalized treatment algorithms: Innovative approach and examples for potential clinical application. J Proteomics 2018; 188:30-40. [DOI: 10.1016/j.jprot.2017.08.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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28
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Lu M, Zhan X. The crucial role of multiomic approach in cancer research and clinically relevant outcomes. EPMA J 2018; 9:77-102. [PMID: 29515689 PMCID: PMC5833337 DOI: 10.1007/s13167-018-0128-8] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/29/2018] [Indexed: 02/06/2023]
Abstract
Cancer with heavily economic and social burden is the hot point in the field of medical research. Some remarkable achievements have been made; however, the exact mechanisms of tumor initiation and development remain unclear. Cancer is a complex, whole-body disease that involves multiple abnormalities in the levels of DNA, RNA, protein, metabolite and medical imaging. Biological omics including genomics, transcriptomics, proteomics, metabolomics and radiomics aims to systematically understand carcinogenesis in different biological levels, which is driving the shift of cancer research paradigm from single parameter model to multi-parameter systematical model. The rapid development of various omics technologies is driving one to conveniently get multi-omics data, which accelerates predictive, preventive and personalized medicine (PPPM) practice allowing prediction of response with substantially increased accuracy, stratification of particular patients and eventual personalization of medicine. This review article describes the methodology, advances, and clinically relevant outcomes of different "omics" technologies in cancer research, and especially emphasizes the importance and scientific merit of integrating multi-omics in cancer research and clinically relevant outcomes.
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Affiliation(s)
- Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- The State Key Laboratory of Medical Genetics, Central South University, 88 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
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29
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Eschweiler JD, Frank AT, Ruotolo BT. Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1991-2000. [PMID: 28752478 PMCID: PMC5693686 DOI: 10.1007/s13361-017-1757-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 05/21/2023]
Abstract
Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analysis by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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30
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Marcinko TM, Dong J, LeBlanc R, Daborowski KV, Vachet RW. Small molecule-mediated inhibition of β-2-microglobulin-based amyloid fibril formation. J Biol Chem 2017; 292:10630-10638. [PMID: 28468825 DOI: 10.1074/jbc.m116.774083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint and bone function. Recently, several small molecules have been identified as potential inhibitors of β2m amyloid formation in vitro Here we investigated whether these molecules are more broadly applicable inhibitors of β2m amyloid formation by studying their effect on Cu(II)-induced β2m amyloid formation. Using a variety of biophysical techniques, we also examined their inhibitory mechanisms. We found that two molecules, doxycycline and rifamycin SV, can inhibit β2m amyloid formation in vitro by causing the formation of amorphous, redissolvable aggregates. Rather than interfering with β2m amyloid formation at the monomer stage, we found that doxycycline and rifamycin SV exert their effect by binding to oligomeric species both in solution and in gas phase. Their binding results in a diversion of the expected Cu(II)-induced progression of oligomers toward a heterogeneous collection of oligomers, including trimers and pentamers, that ultimately matures into amorphous aggregates. Using ion mobility mass spectrometry, we show that both inhibitors promote the compaction of the initially formed β2m dimer, which causes the formation of other off-pathway and amyloid-incompetent oligomers that are isomeric with amyloid-competent oligomers in some cases. Overall, our results suggest that doxycycline and rifamycin are general inhibitors of Cu(II)-induced β2m amyloid formation. Interestingly, the putative mechanism of their activity is different depending on how amyloid formation is initiated with β2m, which underscores the complexity of how these structures assemble in vitro.
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Affiliation(s)
- Tyler M Marcinko
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Jia Dong
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Raquel LeBlanc
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kate V Daborowski
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Richard W Vachet
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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31
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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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32
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Eschweiler JD, Martini RM, Ruotolo BT. Chemical Probes and Engineered Constructs Reveal a Detailed Unfolding Mechanism for a Solvent-Free Multidomain Protein. J Am Chem Soc 2017; 139:534-540. [PMID: 27959526 PMCID: PMC5724362 DOI: 10.1021/jacs.6b11678] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and noncovalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas phase, as well as more general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and we are able to assign each unfolded form observed in our gas-phase data set to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multidomain protein unfolding in the gas phase, and highlights key similarities and differences from the known solution-phase pathway.
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Affiliation(s)
| | - Rachel M. Martini
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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33
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Zhang H, Harrington LB, Lu Y, Prado M, Saer R, Rempel D, Blankenship RE, Gross ML. Native Mass Spectrometry Characterizes the Photosynthetic Reaction Center Complex from the Purple Bacterium Rhodobacter sphaeroides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:87-95. [PMID: 27506206 PMCID: PMC5613939 DOI: 10.1007/s13361-016-1451-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) is an emerging approach to study protein complexes in their near-native states and to elucidate their stoichiometry and topology. Here, we report a native MS study of the membrane-embedded reaction center (RC) protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides. The membrane-embedded RC protein complex is stabilized by detergent micelles in aqueous solution, directly introduced into a mass spectrometer by nano-electrospray (nESI), and freed of detergents and dissociated in the gas phase by collisional activation. As the collision energy is increased, the chlorophyll pigments are gradually released from the RC complex, suggesting that native MS introduces a near-native structure that continues to bind pigments. Two bacteriochlorophyll a pigments remain tightly bound to the RC protein at the highest collision energy. The order of pigment release and their resistance to release by gas-phase activation indicates the strength of pigment interaction in the RC complex. This investigation sets the stage for future native MS studies of membrane-embedded photosynthetic pigment-protein and related complexes.Graphical Abstract.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Lucas B Harrington
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Yue Lu
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Mindy Prado
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Rafael Saer
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Don Rempel
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
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Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins. Methods Mol Biol 2017; 1635:205-232. [PMID: 28755371 DOI: 10.1007/978-1-4939-7151-0_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past years, native mass spectrometry and ion mobility have grown into techniques that are widely applicable to the study of aspects of protein structure. More recently, it has become apparent that this approach provides a very promising avenue for the investigation of integral membrane proteins in lipid or detergent environments.In this chapter, we discuss applications of native mass spectrometry and ion mobility in membrane protein research-what is important to take into consideration when working with membrane proteins, and what the requirements are for sample preparation for native mass spectrometry. Furthermore, we will discuss the types of information provided by the measurements, including the oligomeric state, subunit composition and stoichiometry, interactions with detergents or lipids, conformational transitions, and the binding and structural effect of ligands and drugs.
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35
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Khakinejad M, Kondalaji SG, Donohoe GC, Valentine SJ. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:451-61. [PMID: 26802030 PMCID: PMC4814291 DOI: 10.1007/s13361-015-1304-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/17/2023]
Abstract
Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H](2-) ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H](3-) ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H](2-) ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H](3-) ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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37
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Khakinejad M, Kondalaji SG, Donohoe GC, Valentine SJ. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:462-73. [PMID: 26620531 PMCID: PMC4872623 DOI: 10.1007/s13361-015-1305-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/17/2023]
Abstract
Gas-phase hydrogen deuterium exchange (HDX), collision cross section (CCS) measurement, and molecular dynamics simulation (MDS) techniques were utilized to develop and compare three methods for estimating the relative surface area exposure of separate peptide chains within bovine insulin ions. Electrosprayed [M - 3H](3-) and [M - 5H](5-) insulin ions produced a single conformer type with respective collision cross sections of 528 ± 5 Å(2) and 808 ± 2 Å(2). [M - 4H](4-) ions were comprised of more compact (Ω = 676 ± 3 Å(2)) and diffuse (i.e., more elongated, Ω = 779 ± 3 Å(2)) ion conformer types. Ions were subjected to HDX in the drift tube using D2O as the reagent gas. Collision-induced dissociation was used to fragment mobility-selected, isotopically labeled [M - 4H](4-) and [M - 5H](5-) ions into the protein subchains. Deuterium uptake levels of each chain can be explained by limited inter-chain isotopic scrambling upon collisional activation. Using nominal ion structures from MDS and a hydrogen accessibility model, the deuterium uptake for each chain was correlated to its exposed surface area. In separate experiments, the per-residue deuterium content for the protonated and deprotonated ions of the synthetic peptide KKDDDDDIIKIIK were compared. The differences in deuterium content indicated the regional HDX accessibility for cations versus anions. Using ions of similar conformational type, this comparison highlights the complementary nature of HDX data obtained from positive- and negative-ion analysis.
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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38
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Bornschein RE, Niu S, Eschweiler J, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:41-49. [PMID: 26323618 DOI: 10.1007/s13361-015-1250-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 07/30/2015] [Accepted: 08/01/2015] [Indexed: 06/04/2023]
Abstract
Protocols that aim to construct complete models of multiprotein complexes based on ion mobility and mass spectrometry data are becoming an important element of integrative structural biology efforts. However, the usefulness of such data is predicated, in part, on an ability to measure individual subunits removed from the complex while maintaining a compact/folded state. Gas-phase dissociation of intact complexes using collision induced dissociation is a potentially promising pathway for acquiring such protein monomer size information, but most product ions produced are possessed of high charge states and elongated/string-like conformations that are not useful in protein complex modeling. It has previously been demonstrated that the collision induced dissociation of charge-reduced protein complexes can produce compact subunit product ions; however, their formation mechanism is not well understood. Here, we present new experimental evidence for the avidin (64 kDa) and aldolase (157 kDa) tetramers that demonstrates significant complex remodeling during the dissociation of charge-reduced assemblies. Detailed analysis and modeling indicates that highly compact intermediates are accessed during the dissociation process by both complexes. Here, we present putative pathways that describe the formation of such ions, as well as discuss the broader significance of such data for structural biology applications moving forward.
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Affiliation(s)
| | - Shuai Niu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Eschweiler
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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39
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Rivera-Santiago RF, Sriswasdi S, Harper SL, Speicher DW. Probing structures of large protein complexes using zero-length cross-linking. Methods 2015; 89:99-111. [PMID: 25937394 PMCID: PMC4628899 DOI: 10.1016/j.ymeth.2015.04.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/10/2015] [Accepted: 04/24/2015] [Indexed: 02/02/2023] Open
Abstract
Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed.
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Affiliation(s)
- Roland F Rivera-Santiago
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Sira Sriswasdi
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Sandra L Harper
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States
| | - David W Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States.
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40
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Characterization of top-down ETD in a travelling-wave ion guide. Methods 2015; 89:22-9. [DOI: 10.1016/j.ymeth.2015.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/30/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
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41
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Campuzano IDG, Larriba C, Bagal D, Schnier PD. Ion Mobility and Mass Spectrometry Measurements of the Humanized IgGk NIST Monoclonal Antibody. ACTA ACUST UNITED AC 2015. [DOI: 10.1021/bk-2015-1202.ch004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- Iain D. G. Campuzano
- Molecular Structure and Characterization, Amgen Inc., Thousand Oaks, California 91320, United States
- Mechanical Engineering Department, Yale University, New Haven, Connecticut 06520, United States
- Molecular Structure and Characterization, Amgen Inc., South San Francisco, California 94080, United States
| | - Carlos Larriba
- Molecular Structure and Characterization, Amgen Inc., Thousand Oaks, California 91320, United States
- Mechanical Engineering Department, Yale University, New Haven, Connecticut 06520, United States
- Molecular Structure and Characterization, Amgen Inc., South San Francisco, California 94080, United States
| | - Dhanashri Bagal
- Molecular Structure and Characterization, Amgen Inc., Thousand Oaks, California 91320, United States
- Mechanical Engineering Department, Yale University, New Haven, Connecticut 06520, United States
- Molecular Structure and Characterization, Amgen Inc., South San Francisco, California 94080, United States
| | - Paul D. Schnier
- Molecular Structure and Characterization, Amgen Inc., Thousand Oaks, California 91320, United States
- Mechanical Engineering Department, Yale University, New Haven, Connecticut 06520, United States
- Molecular Structure and Characterization, Amgen Inc., South San Francisco, California 94080, United States
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42
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Valera E, Bailey RC. Eavesdropping on interactions. Nat Chem 2015; 7:767-9. [DOI: 10.1038/nchem.2355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Dailing A, Luchini A, Liotta L. Unlocking the secrets to protein-protein interface drug targets using structural mass spectrometry techniques. Expert Rev Proteomics 2015; 12:457-67. [PMID: 26400464 DOI: 10.1586/14789450.2015.1079487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-protein interactions (PPIs) drive all biologic systems at the subcellular and extracellular level. Changes in the specificity and affinity of these interactions can lead to cellular malfunctions and disease. Consequently, the binding interfaces between interacting protein partners are important drug targets for the next generation of therapies that block such interactions. Unfortunately, protein-protein contact points have proven to be very difficult pharmacological targets because they are hidden within complex 3D interfaces. For the vast majority of characterized binary PPIs, the specific amino acid sequence of their close contact regions remains unknown. There has been an important need for an experimental technology that can rapidly reveal the functionally important contact points of native protein complexes in solution. In this review, experimental techniques employing mass spectrometry to explore protein interaction binding sites are discussed. Hydrogen-deuterium exchange, hydroxyl radical footprinting, crosslinking and the newest technology protein painting are compared and contrasted.
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Affiliation(s)
| | - Alessandra Luchini
- a Center for Applied Proteomics and Molecular Medicine, Life Sciences Lab Building, George Mason University, 10920 University Boulevard, Manassas, Virginia 20110, USA
| | - Lance Liotta
- a Center for Applied Proteomics and Molecular Medicine, Life Sciences Lab Building, George Mason University, 10920 University Boulevard, Manassas, Virginia 20110, USA
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44
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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45
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Cui W, Zhang H, Blankenship RE, Gross ML. Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly. Protein Sci 2015; 24:1325-32. [PMID: 26032343 DOI: 10.1002/pro.2712] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/19/2015] [Indexed: 12/12/2022]
Abstract
Native spray has the potential to probe biophysical properties of protein assemblies. Here we report an investigation using both ECD top-down sequencing with an FTICR mass spectrometer and ion mobility (IM) measurements on a Q-TOF to investigate the collisionally induced unfolding of a native-like heterogeneous tetrameric assembly, human hemoglobin (hHb), in the gas phase. To our knowledge, this is the first report combining ECD and ion-mobility data on the same target protein assembly to delineate the effects of collisional activation on both assembly size and the extent and location of fragmentation. Although the collision-induced unfolding of the hemoglobin assembly is clearly seen by both IMMS and ECD, the latter delineates the regions that increasingly unfold as the collision energy is increased. The results are consistent with previous outcomes for homogeneous protein assemblies and reinforce our interpretation that activation opens the structure of the protein assembly from the flexible regions to make available ECD fragmentation, without dissociating the component proteins.
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Affiliation(s)
- Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
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46
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Han L, Ruotolo BT. Ion Mobility-Mass Spectrometry Differentiates Protein Quaternary Structures Formed in Solution and in Electrospray Droplets. Anal Chem 2015; 87:6808-13. [PMID: 26075825 DOI: 10.1021/acs.analchem.5b01010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrospray ionization coupled to mass spectrometry is a key technology for determining the stoichiometries of multiprotein complexes. Despite highly accurate results for many assemblies, challenging samples can generate signals for artifact protein-protein binding born of the crowding forces present within drying electrospray droplets. Here, for the first time, we study the formation of preferred protein quaternary structures within such rapidly evaporating nanodroplets. We use ion mobility and tandem mass spectrometry to investigate glutamate dehydrogenase dodecamers and serum amyloid P decamers as a function of protein concentration, along with control experiments using carefully chosen protein analogues, to both establish the formation of operative mechanisms and assign the bimodal conformer populations observed. Further, we identify an unprecedented symmetric collision-induced dissociation pathway that we link directly to the quaternary structures of the precursor ions selected.
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Affiliation(s)
- Linjie Han
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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47
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Niu S, Ruotolo BT. Collisional unfolding of multiprotein complexes reveals cooperative stabilization upon ligand binding. Protein Sci 2015; 24:1272-81. [PMID: 25970849 DOI: 10.1002/pro.2699] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 04/13/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Abstract
Cooperative binding mechanisms are a common feature in biology, enabling a diverse range of protein-based molecular machines to regulate activities ranging from oxygen uptake to cellular membrane transport. Much, however, is not known about such cooperative binding mechanisms, including how such events typically add to the overall stability of such protein systems. Measurements of such cooperative stabilization events are challenging, as they require the separation and resolution of individual protein complex bound states within a mixture of potential stoichiometries to individually assess protein stabilities. Here, we report ion mobility-mass spectrometry results for the concanavalin A tetramer bound to a range of polysaccharide ligands. We use collision induced unfolding, a relatively new methodology that functions as a gas-phase analog of calorimetry experiments in solution, to individually assess the stabilities of concanavalin A bound states. By comparing the differences in activation voltage required to unfold different concanavalin A-ligand stoichiometries, we find evidence suggesting a cooperative stabilization of concanavalin A occurs upon binding most carbohydrate ligands. We critically evaluate this observation by assessing a broad range of ligands, evaluating the unfolding properties of multiple protein charge states, and by comparing our gas-phase results with those obtained from calorimetry experiments carried out in solution.
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Affiliation(s)
- Shuai Niu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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48
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Srinivasa S, Ding X, Kast J. Formaldehyde cross-linking and structural proteomics: Bridging the gap. Methods 2015; 89:91-8. [PMID: 25979347 DOI: 10.1016/j.ymeth.2015.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Proteins are dynamic entities constantly moving and altering their structures based on their functions and interactions inside and outside the cell. Formaldehyde cross-linking combined with mass spectrometry can accurately capture interactions of these rapidly changing biomolecules while maintaining their physiological surroundings. Even with its numerous established uses in biology and compatibility with mass spectrometry, formaldehyde has not yet been applied in structural proteomics. However, formaldehyde cross-linking is moving toward analyzing tertiary structure, which conventional cross-linkers have already accomplished. The purpose of this review is to describe the potential of formaldehyde cross-linking in structural proteomics by highlighting its applications, characteristics and current status in the field.
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Affiliation(s)
- Savita Srinivasa
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xuan Ding
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, United States
| | - Juergen Kast
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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49
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Donohoe GC, Arndt JR, Valentine SJ. Online deuterium hydrogen exchange and protein digestion coupled with ion mobility spectrometry and tandem mass spectrometry. Anal Chem 2015; 87:5247-54. [PMID: 25893550 DOI: 10.1021/acs.analchem.5b00277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Online deuterium hydrogen exchange (DHX) and pepsin digestion (PD) is demonstrated using drift tube ion mobility spectrometry (DTIMS) coupled with linear ion trap (LTQ) mass spectrometry (MS) with electron transfer dissociation (ETD) capabilities. DHX of deuterated ubiquitin, followed by subsequent quenching and digestion, is performed within ∼60 s, yielding 100% peptide sequence coverage. The high reproducibility of the IMS separation allows spectral feature matching between two-dimensional IMS-MS datasets (undeuterated and deuterated) without the need for dataset alignment. Extracted ion drift time distributions (XIDTDs) of deuterated peptic peptides are mobility-matched to corresponding XIDTDs of undeuterated peptic peptides that were identified using collision-induced dissociation (CID). Matching XIDTDs allows a straightforward identification and deuterium retention evaluation for labeled peptides. Aside from the mobility separation, the ion trapping capabilities of the LTQ, combined with ETD, are demonstrated to provide single-residue resolution. Deuterium retention for the c- series ions across residues M(1)-L(15) and N(25)-R(42) are in good agreement with the known secondary structural elements within ubiquitin.
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Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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50
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Saliou JM, Manival X, Tillault AS, Atmanene C, Bobo C, Branlant C, Van Dorsselaer A, Charpentier B, Cianférani S. Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity. Proteomics 2015; 15:2851-61. [DOI: 10.1002/pmic.201400529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/06/2015] [Accepted: 02/24/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Anne-Sophie Tillault
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Cédric Atmanene
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Claude Bobo
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
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