1
|
Chaturvedi S, Bawake S, Sharma N. Recent advancements in disulfide bridge characterization: Insights from mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9713. [PMID: 38361473 DOI: 10.1002/rcm.9713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024]
Abstract
RATIONALE Disulfide bridges (DSB) play an important role in stabilizing three-dimensional structures of biopharmaceuticals, single purified proteins, and various cyclic peptide drugs that contain disulfide in their structures. Incorrect cross-linking known as DSB scrambling results in misfolded structures that can be inactive, immunogenic, and susceptible to aggregation. Very few articles have been published on the experimental annotation of DSBs in proteins and cyclic peptide drugs. Accurate characterization of the disulfide bond is essential for understanding protein confirmation. METHODS Characterizing DSBs using mass spectrometry (MS) involves the chemical and enzymatic digestion of samples to obtain smaller peptide fragments, in both reduced and nonreduced forms. Subsequently, these samples are analyzed using MS to locate the DSB, either through interpretation or by employing various software tools. RESULTS The main challenge in DSB analysis methods using sample preparation is to obtain a sample solution in which nonnative DSBs are not formed due to high pH, temperature, and presence of free sulfhydryl groups. Formation of nonnative DSBs can lead to erroneous annotation of disulfide bond. Sample preparation techniques, fragmentation methods for DSB analysis, and contemporary approaches for DSB mapping using this fragmentation were discussed. CONCLUSIONS This review presents the latest advancement in MS-based characterization; also a critical perspective is presented for further annotation of DSBs using MS, primarily for single purified proteins or peptides that are densely connected and rich in cysteine. Despite significant breakthroughs resulting from advancements in MS, the analysis of disulfide bonds is not straightforward; it necessitates expertise in sample preparation and interpretation.
Collapse
Affiliation(s)
- Sachin Chaturvedi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Sanket Bawake
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Nitish Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| |
Collapse
|
2
|
Espiritu MJ, Taylor JK, Sugai CK, Thapa P, Loening NM, Gusman E, Baoanan ZG, Baumann MH, Bingham JP. Characterization of the Native Disulfide Isomers of the Novel χ-Conotoxin PnID: Implications for Further Increasing Conotoxin Diversity. Mar Drugs 2023; 21:61. [PMID: 36827103 PMCID: PMC9964023 DOI: 10.3390/md21020061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
χ-Conotoxins are known for their ability to selectively inhibit norepinephrine transporters, an ability that makes them potential leads for treating various neurological disorders, including neuropathic pain. PnID, a peptide isolated from the venom of Conus pennaceus, shares high sequence homology with previously characterized χ-conotoxins. Whereas previously reported χ-conotoxins seem to only have a single native disulfide bonding pattern, PnID has three native isomers due to the formation of different disulfide bond patterns during its maturation in the venom duct. In this study, the disulfide connectivity and three-dimensional structure of these disulfide isomers were explored using regioselective synthesis, chromatographic coelution, and solution-state nuclear magnetic resonance spectroscopy. Of the native isomers, only the isomer with a ribbon disulfide configuration showed pharmacological activity similar to other χ-conotoxins. This isomer inhibited the rat norepinephrine transporter (IC50 = 10 ± 2 µM) and has the most structural similarity to previously characterized χ-conotoxins. In contrast, the globular isoform of PnID showed more than ten times less activity against this transporter and the beaded isoform did not display any measurable biological activity. This study is the first report of the pharmacological and structural characterization of an χ-conotoxin from a species other than Conus marmoreus and is the first report of the existence of natively-formed conotoxin isomers.
Collapse
Affiliation(s)
- Michael J. Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Jonathan K. Taylor
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Christopher K. Sugai
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Nikolaus M. Loening
- Department of Chemistry, Lewis & Clark College, 615 S Palatine Hill Road, Portland, OR 97219, USA
| | - Emma Gusman
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Zenaida G. Baoanan
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- Department of Biology, College of Science, University of the Philippines Baguio, Baguio City 2600, Philippines
| | - Michael H. Baumann
- Designer Drug Research Unit, Intramural Research Program, National Institute on Drug Abuse (NIDA), National Institutes of Health (NIH), 333 Cassell Drive Suite 4400, Baltimore, MD 21224, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| |
Collapse
|
3
|
Yadavalli NS, Borodinov N, Choudhury CK, Quiñones-Ruiz T, Laradji AM, Tu S, Lednev IK, Kuksenok O, Luzinov I, Minko S. Thermal Stabilization of Enzymes with Molecular Brushes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nataraja S. Yadavalli
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Nikolay Borodinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Chandan K. Choudhury
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Tatiana Quiñones-Ruiz
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Amine M. Laradji
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Sidong Tu
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor K. Lednev
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Olga Kuksenok
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor Luzinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
4
|
Spit J, Philips A, Wynant N, Santos D, Plaetinck G, Vanden Broeck J. Knockdown of nuclease activity in the gut enhances RNAi efficiency in the Colorado potato beetle, Leptinotarsa decemlineata, but not in the desert locust, Schistocerca gregaria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 81:103-116. [PMID: 28093313 DOI: 10.1016/j.ibmb.2017.01.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 05/21/2023]
Abstract
The responsiveness towards orally delivered dsRNA and the potency of a subsequent environmental RNA interference (RNAi) response strongly differs between different insect species. While some species are very sensitive to dsRNA delivery through the diet, others are not. The underlying reasons for this may vary, but degradation of dsRNA by nucleases in the gut lumen is believed to play a crucial role. The Colorado potato beetle, Leptinotarsa decemlineata, is a voracious defoliator of potato crops worldwide, and is currently under investigation for novel control methods based on dsRNA treatments. Here we describe the identification and characterization of two nuclease genes exclusively expressed in the gut of this pest species. Removal of nuclease activity in adults increased the sensitivity towards dsRNA and resulted in improved protection of potato plants. A similar strategy in the desert locust, Schistocerca gregaria, for which we show a far more potent nuclease activity in the gut juice, did however not lead to an improvement of the RNAi response. Possible reasons for this are discussed. Taken together, the present data confirm a negative effect of nucleases in the gut on the environmental RNAi response, and further suggest that interfering with this activity is a strategy worth pursuing for improving RNAi efficacy in insect pest control applications.
Collapse
Affiliation(s)
- Jornt Spit
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium; Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium.
| | - Annelies Philips
- Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium
| | - Niels Wynant
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
| | - Dulce Santos
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
| | - Geert Plaetinck
- Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium
| | - Jozef Vanden Broeck
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Chad R Borges
- Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University , Tempe, Arizona
| | | |
Collapse
|
6
|
Stinson CA, Xia Y. Reactions of hydroxyalkyl radicals with cysteinyl peptides in a nanoESI plume. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1192-1201. [PMID: 24793576 DOI: 10.1007/s13361-014-0898-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
In biological systems, carbon-centered small molecule radicals are primarily formed via external radiation or internal radical reactions. These radical species can react with a variety of biomolecules, most notably nucleic acids, the consequence of which has possible links to gene mutation and cancer. Sulfur-containing peptides and proteins are reactive toward a variety of radical species and many of them behave as radical scavengers. In this study, the reactions between alkyl alcohol carbon-centered radicals (e.g., •CH2OH for methanol) and cysteinyl peptides within a nanoelectrospray ionization (nanoESI) plume were explored. The reaction system involved ultraviolet (UV) irradiation of a nanoESI plume using a low pressure mercury lamp consisting of 185 and 254 nm emission bands. The alkyl alcohol was added as solvent into the nanoESI solution and served as the precursor of hydroxyalkyl radicals upon UV irradiation. The hydroxyalkyl radicals subsequently reacted with cysteinyl peptides either containing a disulfide linkage or free thiol, which led to the formation of peptide-S-hydroxyalkyl product. This radical reaction coupled with subsequent MS/MS was shown to have analytical potential by cleaving intrachain disulfide linked peptides prior to CID to enhance sequence information. Tandem mass spectrometry via collision-induced dissociation (CID), stable isotope labeling, and accurate mass measurement were employed to verify the identities of the reaction products.
Collapse
Affiliation(s)
- Craig A Stinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | | |
Collapse
|