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Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [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: 04/02/2024]
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
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Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
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2
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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3
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Hamidli N, Pajaziti B, Andrási M, Nagy C, Gáspár A. Determination of human insulin and its six therapeutic analogues by capillary electrophoresis - mass spectrometry. J Chromatogr A 2022; 1678:463351. [PMID: 35905683 DOI: 10.1016/j.chroma.2022.463351] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/18/2022]
Abstract
In this work, human insulin and its 6 analogues were separated and determined using CZE-MS. Three different capillaries (bare fused silica, successive multiple ionic-polymer layer (SMIL) and static linear polyacrylamide (LPA) coated) were compared based on their separation performances in their optimal operating conditions. Coated capillaries demonstrated slightly better separation of the components, although some components showed wide, distorted peaks. The highest plate number could be obtained in the SMIL capillary (192 000/m). For UV and ESI-MS detection relatively similar LOD values were obtained (0.3-1.2 mg/L and 1.0-3.4 mg/L, respectively). The application of MS detection provided useful structural information and unambiguous identification for insulins having similar or the same molecular mass. This work is considered to be important not only for the investigation of insulins but also for its potential contribution to the top-down analysis of proteins using CE-MS.
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Affiliation(s)
- Narmin Hamidli
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Blerta Pajaziti
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Melinda Andrási
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Cynthia Nagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Attila Gáspár
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.
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Kumar S, Venkatesha MA, Lall S, Prakash S, Balaram P. Mechanistic Insights into an Unusual Side-Chain-Mediated N-C α Bond Cleavage under Collision-Induced Dissociation Conditions in the Disulfide-Containing Peptide Conopressin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1083-1092. [PMID: 32175740 DOI: 10.1021/jasms.0c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Conopressin, a nonapeptide disulfide CFIRNCPKG amide present in cone snail venom, undergoes a facile cleavage at the Cys6-Pro7 peptide bond to yield a disulfide bridged b6 ion. Analysis of the mass spectral fragmentation pattern reveals the presence of a major fragment ion, which is unambiguously assigned as the tripeptide sequence IRN amide. The sequence dependence of this unusual fragmentation process has been investigated by comparing it with the fragmentation patterns of related peptides, oxytocin (CYIQNCPLG amide), Lys-vasopressin (CYFQNCPKG amide), and a series of synthetic analogues. The results establish the role of the Arg4 residue in facilitating the unusual N-Cα bond cleavage at Cys6. Structures are proposed for a modified disulfide bridged fragment containing the Cys1 and Cys6 residues. Gas-phase molecular dynamics simulations provide evidence for the occurrence of conformational states that permit close approach of the Arg4 side chain to the Cys6 Cβ methylene protons.
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Affiliation(s)
- Sanjeev Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - M Achanna Venkatesha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sahil Lall
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
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Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics 2017; 14:931-939. [DOI: 10.1080/14789450.2017.1377613] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Samuel D. Robinson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
| | | | | | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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Maes E, Dyer JM, McKerchar HJ, Deb-Choudhury S, Clerens S. Protein-protein cross-linking and human health: the challenge of elucidating with mass spectrometry. Expert Rev Proteomics 2017; 14:917-929. [PMID: 28759730 DOI: 10.1080/14789450.2017.1362336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.
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Affiliation(s)
- Evelyne Maes
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand
| | - Jolon M Dyer
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand.,c Riddet Institute, Massey University , Palmerston North , New Zealand.,d Wine, Food & Molecular Biosciences , Lincoln University , Lincoln , New Zealand
| | - Hannah J McKerchar
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
| | | | - Stefan Clerens
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
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Structural space of intramolecular peptide disulfides: Analysis of peptide toxins retrieved from venomous peptide databases. Comput Biol Chem 2017; 68:194-203. [DOI: 10.1016/j.compbiolchem.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/21/2017] [Accepted: 03/06/2017] [Indexed: 01/22/2023]
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Verdes A, Anand P, Gorson J, Jannetti S, Kelly P, Leffler A, Simpson D, Ramrattan G, Holford M. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins. Toxins (Basel) 2016; 8:117. [PMID: 27104567 PMCID: PMC4848642 DOI: 10.3390/toxins8040117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022] Open
Abstract
Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa.
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Affiliation(s)
- Aida Verdes
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Prachi Anand
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Juliette Gorson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Stephen Jannetti
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Patrick Kelly
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Abba Leffler
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine 550 1st Avenue, New York, NY 10016, USA.
| | - Danny Simpson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Tandon School of Engineering, New York University 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Girish Ramrattan
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Mandë Holford
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
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10
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Structure and function of μ-conotoxins, peptide-based sodium channel blockers with analgesic activity. Future Med Chem 2015; 6:1677-98. [PMID: 25406007 DOI: 10.4155/fmc.14.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
μ-Conotoxins block voltage-gated sodium channels (VGSCs) and compete with tetrodotoxin for binding to the sodium conductance pore. Early efforts identified µ-conotoxins that preferentially blocked the skeletal muscle subtype (NaV1.4). However, the last decade witnessed a significant increase in the number of µ-conotoxins and the range of VGSC subtypes inhibited (NaV1.2, NaV1.3 or NaV1.7). Twenty µ-conotoxin sequences have been identified to date and structure-activity relationship studies of several of these identified key residues responsible for interactions with VGSC subtypes. Efforts to engineer-in subtype specificity are driven by in vivo analgesic and neuromuscular blocking activities. This review summarizes structural and pharmacological studies of µ-conotoxins, which show promise for development of selective blockers of NaV1.2, and perhaps also NaV1.1,1.3 or 1.7.
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11
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Tran TTN, Brinkworth CS, Bowie JH. The identification of disulfides in ricin D using proteolytic cleavage followed by negative-ion nano-electrospray ionization mass spectrometry of the peptide fragments. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:182-190. [PMID: 25641493 DOI: 10.1002/rcm.7088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/30/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE To use negative-ion nano-electrospray ionization mass spectrometry of peptides from the tryptic digest of ricin D, to provide sequence information; in particular, to identify disulfide position and connectivity. METHODS Negative-ion fragmentations of peptides from the tryptic digest of ricin D was studied using a Waters QTOF2 mass spectrometer operating in MS and MS(2) modes. RESULTS Twenty-three peptides were obtained following high-performance liquid chromatography and studied by negative-ion mass spectrometry covering 73% of the amino-acid residues of ricin D. Five disulfide-containing peptides were identified, three intermolecular and two intramolecular disulfide-containing peptides. The [M-H](-) anions of the intermolecular disulfides undergo facile cleavage of the disulfide units to produce fragment peptides. In negative-ion collision-induced dissociation (CID) these source-formed anions undergo backbone cleavages, which provide sequencing information. The two intramolecular disulfides were converted proteolytically into intermolecular disulfides, which were identified as outlined above. CONCLUSIONS The positions of the five disulfide groups in ricin D may be determined by characteristic negative-ion cleavage of the disulfide groups, while sequence information may be determined using the standard negative-ion backbone cleavages of the resulting cleaved peptides. Negative-ion mass spectrometry can also be used to provide partial sequencing information for other peptides (i.e. those not containing Cys) using the standard negative-ion backbone cleavages of these peptides.
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Affiliation(s)
- T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia, Australia, 5005
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12
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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13
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Huang SY, Chen SF, Chen CH, Huang HW, Wu WG, Sung WC. Global Disulfide Bond Profiling for Crude Snake Venom Using Dimethyl Labeling Coupled with Mass Spectrometry and RADAR Algorithm. Anal Chem 2014; 86:8742-50. [DOI: 10.1021/ac501931t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sheng Yu Huang
- Mithra Biotechnology
Inc., 7F, No. 104, Sec. 1, Xintai 5th
Road, Xizhi Dist., New Taipei City 221, Taiwan
| | - Sung Fang Chen
- National Taiwan Normal University, Department of
Chemistry, No. 88, Sec.
4, Tingchow Road, Taipei 116, Taiwan
| | - Chun Hao Chen
- National Taiwan Normal University, Department of
Chemistry, No. 88, Sec.
4, Tingchow Road, Taipei 116, Taiwan
| | - Hsuan Wei Huang
- National Health
Research Institutes, National Institute of Infectious Diseases and
Vaccinology, No. 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan
- National Tsing Hua University, Institute of Bioinformatics
and Structural Biology, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 330, Taiwan
| | - Wen Guey Wu
- National Tsing Hua University, Institute of Bioinformatics
and Structural Biology, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 330, Taiwan
| | - Wang Chou Sung
- National Health
Research Institutes, National Institute of Infectious Diseases and
Vaccinology, No. 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan
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Borges CR, Sherma ND. Techniques for the analysis of cysteine sulfhydryls and oxidative protein folding. Antioxid Redox Signal 2014; 21:511-31. [PMID: 24383618 PMCID: PMC4076987 DOI: 10.1089/ars.2013.5559] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Modification of cysteine thiols dramatically affects protein function and stability. Hence, the abilities to quantify specific protein sulfhydryl groups within complex biological samples and map disulfide bond structures are crucial to gaining greater insights into how proteins operate in human health and disease. RECENT ADVANCES Many different molecular probes are now commercially available to label and track cysteine residues at great sensitivity. Coupled with mass spectrometry, stable isotope-labeled sulfhydryl-specific reagents can provide previously unprecedented molecular insights into the dynamics of cysteine modification. Likewise, the combined application of modern mass spectrometers with improved sample preparation techniques and novel data mining algorithms is beginning to routinize the analysis of complex protein disulfide structures. CRITICAL ISSUES Proper application of these modern tools and techniques, however, still requires fundamental understanding of sulfhydryl chemistry as well as the assumptions that accompany sample preparation and underlie effective data interpretation. FUTURE DIRECTIONS The continued development of tools, technical approaches, and corresponding data processing algorithms will, undoubtedly, facilitate site-specific protein sulfhydryl quantification and disulfide structure analysis from within complex biological mixtures with ever-improving accuracy and sensitivity. Fully routinizing disulfide structure analysis will require an equal but balanced focus on sample preparation and corresponding mass spectral dataset reproducibility.
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Affiliation(s)
- Chad R Borges
- Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University , Tempe, Arizona
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15
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Sharma IM, Prakash S, Dhanaraman T, Chatterji D. Characterization of a dual-active enzyme, DcpA, involved in cyclic diguanosine monophosphate turnover in Mycobacterium smegmatis. MICROBIOLOGY-SGM 2014; 160:2304-2318. [PMID: 25037163 DOI: 10.1099/mic.0.080200-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have reported previously that the long-term survival of Mycobacterium smegmatis is facilitated by a dual-active enzyme MSDGC-1 (renamed DcpA), which controls the cellular turnover of cyclic diguanosine monophosphate (c-di-GMP). Most mycobacterial species possess at least a single copy of a DcpA orthologue that is highly conserved in terms of sequence similarity and domain architecture. Here, we show that DcpA exists in monomeric and dimeric forms. The dimerization of DcpA is due to non-covalent interactions between two protomers that are arranged in a parallel orientation. The dimer shows both synthesis and hydrolysis activities, whereas the monomer shows only hydrolysis activity. In addition, we have shown that DcpA is associated with the cytoplasmic membrane and exhibits heterogeneous cellular localization with a predominance at the cell poles. Finally, we have also shown that DcpA is involved in the change in cell length and colony morphology of M. smegmatis. Taken together, our study provides additional evidence about the role of the bifunctional protein involved in c-di-GMP signalling in M. smegmatis.
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Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Thillaivillalan Dhanaraman
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal H3C 3J7, Québec, Canada
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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16
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Anand P, Grigoryan A, Bhuiyan MH, Ueberheide B, Russell V, Quinoñez J, Moy P, Chait BT, Poget SF, Holford M. Sample limited characterization of a novel disulfide-rich venom peptide toxin from terebrid marine snail Terebra variegata. PLoS One 2014; 9:e94122. [PMID: 24713808 PMCID: PMC3979744 DOI: 10.1371/journal.pone.0094122] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/13/2014] [Indexed: 12/19/2022] Open
Abstract
Disulfide-rich peptide toxins found in the secretions of venomous organisms such as snakes, spiders, scorpions, leeches, and marine snails are highly efficient and effective tools for novel therapeutic drug development. Venom peptide toxins have been used extensively to characterize ion channels in the nervous system and platelet aggregation in haemostatic systems. A significant hurdle in characterizing disulfide-rich peptide toxins from venomous animals is obtaining significant quantities needed for sequence and structural analyses. Presented here is a strategy for the structural characterization of venom peptide toxins from sample limited (4 ng) specimens via direct mass spectrometry sequencing, chemical synthesis and NMR structure elucidation. Using this integrated approach, venom peptide Tv1 from Terebra variegata was discovered. Tv1 displays a unique fold not witnessed in prior snail neuropeptides. The novel structural features found for Tv1 suggest that the terebrid pool of peptide toxins may target different neuronal agents with varying specificities compared to previously characterized snail neuropeptides.
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Affiliation(s)
- Prachi Anand
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
| | - Alexandre Grigoryan
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
| | - Mohammed H. Bhuiyan
- Department of Chemistry, College of Staten Island and Graduate Center, City University of New York, Staten Island, New York, United States of America
| | - Beatrix Ueberheide
- NYU Langone Medical Center, New York University, New York, New York, United States of America
| | - Victoria Russell
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
| | - Jose Quinoñez
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
| | - Patrick Moy
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
| | - Brian T. Chait
- The Rockefeller University, New York, New York, United States of America
| | - Sébastien F. Poget
- Department of Chemistry, College of Staten Island and Graduate Center, City University of New York, Staten Island, New York, United States of America
| | - Mandë Holford
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and Graduate Center, New York, New York, United States of America
- The American Museum of Natural History, New York, New York, United States of America
- * E-mail:
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17
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Robinson SD, Safavi-Hemami H, McIntosh LD, Purcell AW, Norton RS, Papenfuss AT. Diversity of conotoxin gene superfamilies in the venomous snail, Conus victoriae. PLoS One 2014; 9:e87648. [PMID: 24505301 PMCID: PMC3914837 DOI: 10.1371/journal.pone.0087648] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/28/2013] [Indexed: 12/31/2022] Open
Abstract
Animal venoms represent a vast library of bioactive peptides and proteins with proven potential, not only as research tools but also as drug leads and therapeutics. This is illustrated clearly by marine cone snails (genus Conus), whose venoms consist of mixtures of hundreds of peptides (conotoxins) with a diverse array of molecular targets, including voltage- and ligand-gated ion channels, G-protein coupled receptors and neurotransmitter transporters. Several conotoxins have found applications as research tools, with some being used or developed as therapeutics. The primary objective of this study was the large-scale discovery of conotoxin sequences from the venom gland of an Australian cone snail species, Conus victoriae. Using cDNA library normalization, high-throughput 454 sequencing, de novo transcriptome assembly and annotation with BLASTX and profile hidden Markov models, we discovered over 100 unique conotoxin sequences from 20 gene superfamilies, the highest diversity of conotoxins so far reported in a single study. Many of the sequences identified are new members of known conotoxin superfamilies, some help to redefine these superfamilies and others represent altogether new classes of conotoxins. In addition, we have demonstrated an efficient combination of methods to mine an animal venom gland and generate a library of sequences encoding bioactive peptides.
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Affiliation(s)
- Samuel D. Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- * E-mail: (SDR); (HSH)
| | - Helena Safavi-Hemami
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- * E-mail: (SDR); (HSH)
| | - Lachlan D. McIntosh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
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18
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Goyder MS, Rebeaud F, Pfeifer ME, Kálmán F. Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins. Expert Rev Proteomics 2013; 10:489-501. [PMID: 24087910 DOI: 10.1586/14789450.2013.837663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by mass measurement of bridged fragments. By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide assignment due to their numerous closely spaced cysteines and knotted disulfide structure, requiring creative strategies to determine their connectivity. Today, these include the use of an array of reagents for enzymatic and/or chemical cleavage, partial reduction, differential cysteine labeling and tandem MS. This review aims to describe the toolkit of techniques available to MS users approaching both straightforward and complex disulfide bridge assignments, with a particular focus on strategies utilizing standard instrumentation found in a well-equipped analytical or proteomics laboratory.
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Affiliation(s)
- Miriam S Goyder
- Institute of Life Technologies, University of Applied Sciences Western Switzerland (HES-SO Valais/Wallis), 1950 Sion, Switzerland
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19
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Kuang Z, Zhang MM, Gupta K, Gajewiak J, Gulyas J, Balaram P, Rivier JE, Olivera BM, Yoshikami D, Bulaj G, Norton RS. Mammalian neuronal sodium channel blocker μ-conotoxin BuIIIB has a structured N-terminus that influences potency. ACS Chem Biol 2013; 8:1344-51. [PMID: 23557677 DOI: 10.1021/cb300674x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Among the μ-conotoxins that block vertebrate voltage-gated sodium channels (VGSCs), some have been shown to be potent analgesics following systemic administration in mice. We have determined the solution structure of a new representative of this family, μ-BuIIIB, and established its disulfide connectivities by direct mass spectrometric collision induced dissociation fragmentation of the peptide with disulfides intact. The major oxidative folding product adopts a 1-4/2-5/3-6 pattern with the following disulfide bridges: Cys5-Cys17, Cys6-Cys23, and Cys13-Cys24. The solution structure reveals that the unique N-terminal extension in μ-BuIIIB, which is also present in μ-BuIIIA and μ-BuIIIC but absent in other μ-conotoxins, forms part of a short α-helix encompassing Glu3 to Asn8. This helix is packed against the rest of the toxin and stabilized by the Cys5-Cys17 and Cys6-Cys23 disulfide bonds. As such, the side chain of Val1 is located close to the aromatic rings of Trp16 and His20, which are located on the canonical helix that displays several residues found to be essential for VGSC blockade in related μ-conotoxins. Mutations of residues 2 and 3 in the N-terminal extension enhanced the potency of μ-BuIIIB for NaV1.3. One analogue, [d-Ala2]BuIIIB, showed a 40-fold increase, making it the most potent peptide blocker of this channel characterized to date and thus a useful new tool with which to characterize this channel. On the basis of previous results for related μ-conotoxins, the dramatic effects of mutations at the N-terminus were unanticipated and suggest that further gains in potency might be achieved by additional modifications of this region.
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Affiliation(s)
- Zhihe Kuang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade,
Parkville, Victoria, 3052, Australia
| | - Min-Min Zhang
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Kallol Gupta
- Molecular Biophysics
Unit, Indian Institute of Science, Bangalore,
560 012, India
| | - Joanna Gajewiak
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, United States
| | - Jozsef Gulyas
- The Clayton
Foundation Laboratories
for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California
92037, United States
| | - Padmanabhan Balaram
- Molecular Biophysics
Unit, Indian Institute of Science, Bangalore,
560 012, India
| | - Jean E. Rivier
- The Clayton
Foundation Laboratories
for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California
92037, United States
| | - Baldomero M. Olivera
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, United States
| | - Doju Yoshikami
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, United States
| | - Grzegorz Bulaj
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, United States
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
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