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Tolpina MD, Vasileva ID, Samgina TY. Modern Approaches in de novo Sequencing of Nontryptic Peptides of Ranid and Hylid Frogs by Means of Mass Spectrometry: A Review. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822130081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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2
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Rowell CER, Dobrovolny HM. Energy Requirements for Loss of Viral Infectivity. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:281-294. [PMID: 32757142 PMCID: PMC7405386 DOI: 10.1007/s12560-020-09439-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Outside the host, viruses will eventually lose their ability to infect cells due to conformational changes that occur to proteins on the viral capsid. In order to undergo a conformational change, these proteins require energy to activate the chemical reaction that leads to the conformational change. In this study, data from the literature is used to calculate the energy required for viral inactivation for a variety of different viruses by means of the Arrhenius equation. We find that some viruses (rhinovirus, poliovirus, human immunodeficiency virus, Alkhumra hemorrhagic fever virus, and hepatitis A virus) have high inactivation energies, indicative of breaking of a chemical double bond. We also find that several viruses (respiratory syncytial virus, poliovirus, and norovirus) have nonlinear Arrhenius plots, suggesting that there is more than a single pathway for inactivation of these viruses.
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Affiliation(s)
- Caroline E R Rowell
- Department of Chemistry, Wingate University, Hendersonville, NC, USA
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA.
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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Aprahamian ML, Lindert S. Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta. J Chem Theory Comput 2019; 15:3410-3424. [PMID: 30946594 DOI: 10.1021/acs.jctc.9b00101] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covalent labeling mass spectrometry experiments are growing in popularity and provide important information regarding protein structure. Information obtained from these experiments correlates with residue solvent exposure within the protein in solution. However, it is impossible to determine protein structure from covalent labeling data alone. Incorporation of sparse covalent labeling data into the protein structure prediction software Rosetta has been shown to improve protein tertiary structure prediction. Here, covalent labeling techniques were analyzed computationally to provide insight into what labeling data is needed to optimize tertiary protein structure prediction in Rosetta. We have successfully implemented a new scoring functionality that provides improved predictions. We developed two new covalent labeling based score terms that use a "cone"-based neighbor count to quantify the relative solvent exposure of each amino acid. To test our method, we used a set of 20 proteins with structures deposited in the Protein Data Bank. Decoy model sets were generated for each of these 20 proteins, and the normalized covalent labeling score versus RMSD distributions were evaluated. On the basis of these distributions, we have determined an optimal subset of residues to use when performing covalent labeling experiments in order to maximize the structure prediction capabilities of the covalent labeling data. We also investigated how much false negative and false positive data can be tolerated without meaningfully impacting protein structure prediction. Using these new covalent labeling score terms, protein models were rescored and the resulting models improved by 3.9 Å RMSD on average. New models were also generated using Rosetta's AbinitioRelax program under the guidance of covalent labeling information, and improvement in model quality was observed.
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Affiliation(s)
- Melanie L Aprahamian
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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Schuchman RM, Vancini R, Piper A, Breuer D, Ribeiro M, Ferreira D, Magliocca J, Emmerich V, Hernandez R, Brown DT. Role of the vacuolar ATPase in the Alphavirus replication cycle. Heliyon 2018; 4:e00701. [PMID: 30094371 PMCID: PMC6074608 DOI: 10.1016/j.heliyon.2018.e00701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/07/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023] Open
Abstract
We have shown that Alphaviruses can enter cells by direct penetration at the plasma membrane (R. Vancini, G. Wang, D. Ferreira, R. Hernandez, and D. Brown, J Virol, 87:4352–4359, 2013). Direct penetration removes the requirement for receptor-mediated endocytosis exposure to low pH and membrane fusion in the process of RNA entry. Endosomal pH as well as the pH of the cell cytoplasm is maintained by the activity of the vacuolar ATPase (V-ATPase). Bafilomycin is a specific inhibitor of V-ATPase. To characterize the roll of the V-ATPase in viral replication we generated a Bafilomycin A1(BAF) resistant mutant of Sindbis virus (BRSV). BRSV produced mature virus and virus RNA in greater amounts than parent virus in BAF-treated cells. Sequence analysis revealed mutations in the E2 glycoprotein, T15I/Y18H, were responsible for the phenotype. These results show that a functional V-ATPase is required for efficient virus RNA synthesis and virus maturation in Alphavirus infection.
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Affiliation(s)
- Ryan M Schuchman
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Ricardo Vancini
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Amanda Piper
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Denitra Breuer
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Mariana Ribeiro
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Davis Ferreira
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.,Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Joseph Magliocca
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Veronica Emmerich
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Raquel Hernandez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Dennis T Brown
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
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Du R, Wang M, Hu Z, Wang H, Deng F. An in vitro recombination-based reverse genetic system for rapid mutagenesis of structural genes of the Japanese encephalitis virus. Virol Sin 2015; 30:354-62. [PMID: 26463213 DOI: 10.1007/s12250-015-3623-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/22/2015] [Indexed: 01/12/2023] Open
Abstract
Japanese encephalitis virus (JEV) is one of the most common pathogens of severe viral encephalitis, which is a severe threat to human health. Despite instability of the JEV genome in bacteria, many strategies have been developed to establish molecular clone systems of JEV, providing convenient tools for studying the virus life cycle and virus-host interactions. In this study, we adapted an In-Fusion enzyme-based in vitro recombination method to construct a reverse genetic system of JEV, thereby providing a rapid approach to introduce mutations into the structural genes. A truncated genome without the structural genes was constructed as the backbone, and the complementary segment containing the structural genes was recombined in vitro, which was then transfected directly into virus-permissive cells. The progeny of the infectious virus was successfully detected in the supernatant of the transfected cells, and showed an identical phenotype to its parental virus. To provide a proof-of-principle, the 12 conserved cysteine residues in the envelope (E) protein of JEV were respectively mutated using this approach, and all mutations resulted in a complete failure to generate infectious virus. However, a leucine-tophenylanine mutation at amino acid 107 of the E protein did not interfere with the production of the infectious virus. These results suggested that all 12 cysteines in the E protein are essential for the JEV life cycle. In summary, a novel reverse genetic system of JEV was established for rapidly introducing mutations into structural genes, which will serve as a useful tool for functional studies.
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Affiliation(s)
- Ruikun Du
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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Structural differences observed in arboviruses of the alphavirus and flavivirus genera. Adv Virol 2014; 2014:259382. [PMID: 25309597 PMCID: PMC4182009 DOI: 10.1155/2014/259382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/28/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022] Open
Abstract
Arthropod borne viruses have developed a complex life cycle adapted to alternate between insect and vertebrate hosts. These arthropod-borne viruses belong mainly to the families Togaviridae, Flaviviridae, and Bunyaviridae. This group of viruses contains many pathogens that cause febrile, hemorrhagic, and encephalitic disease or arthritic symptoms which can be persistent. It has been appreciated for many years that these viruses were evolutionarily adapted to function in the highly divergent cellular environments of both insect and mammalian phyla. These viruses are hybrid in nature, containing viral-encoded RNA and proteins which are glycosylated by the host and encapsulate viral nucleocapsids in the context of a host-derived membrane. From a structural perspective, these virus particles are macromolecular machines adapted in design to assemble into a packaging and delivery system for the virus genome and, only when associated with the conditions appropriate for a productive infection, to disassemble and deliver the RNA cargo. It was initially assumed that the structures of the virus from both hosts were equivalent. New evidence that alphaviruses and flaviviruses can exist in more than one conformation postenvelopment will be discussed in this review. The data are limited but should refocus the field of structural biology on the metastable nature of these viruses.
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High production of recombinant Norwegian salmonid alphavirus E1 and E2 proteins in Escherichia coli by fusion to secretion signal sequences and removal of hydrophobic domains. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0085-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Disulfide bond formation contributes to herpes simplex virus capsid stability and retention of pentons. J Virol 2011; 85:8625-34. [PMID: 21697480 DOI: 10.1128/jvi.00214-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Disulfide bonds reportedly stabilize the capsids of several viruses, including papillomavirus, polyomavirus, and simian virus 40, and have been detected in herpes simplex virus (HSV) capsids. In this study, we show that in mature HSV-1 virions, capsid proteins VP5, VP23, VP19C, UL17, and UL25 participate in covalent cross-links, and that these are susceptible to dithiothreitol (DTT). In addition, several tegument proteins were found in high-molecular-weight complexes, including VP22, UL36, and UL37. Cross-linked capsid complexes can be detected in virions isolated in the presence and absence of N-ethylmaleimide (NEM), a chemical that reacts irreversibly with free cysteines to block disulfide formation. Intracellular capsids isolated in the absence of NEM contain disulfide cross-linked species; however, intracellular capsids isolated from cells pretreated with NEM did not. Thus, the free cysteines in intracellular capsids appear to be positioned such that disulfide bond formation can occur readily if they are exposed to an oxidizing environment. These results indicate that disulfide cross-links are normally present in extracellular virions but not in intracellular capsids. Interestingly, intracellular capsids isolated in the presence of NEM are unstable; B and C capsids are converted to a novel form that resembles A capsids, indicating that scaffold and DNA are lost. Furthermore, these capsids also have lost pentons and peripentonal triplexes as visualized by cryoelectron microscopy. These data indicate that capsid stability, and especially the retention of pentons, is regulated by the formation of disulfide bonds in the capsid.
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Abstract
The study of alphavirus entry has been complicated by an inability to clearly identify a receptor and by experiments which only tangentially and indirectly examine the process, producing results that are difficult to interpret. The mechanism of entry has been widely accepted to be by endocytosis followed by acidification of the endosome resulting in virus membrane-endosome membrane fusion. This mechanism has come under scrutiny as better purification protocols and improved methods of analysis have been brought to the study. Results have been obtained that suggest alphaviruses infect cells directly at the plasma membrane without the involvement of endocytosis, exposure to acid pH, or membrane fusion. In this review we compare the data which support the two models and make the case for an alternative pathway of entry by alphaviruses.
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Lundström JO, Pfeffer M. Phylogeographic Structure and Evolutionary History of Sindbis Virus. Vector Borne Zoonotic Dis 2010; 10:889-907. [DOI: 10.1089/vbz.2009.0069] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jan O. Lundström
- Department of Ecology and Evolution/Population Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Swedish Biological Mosquito Control Project, Nedre Dalälven Utvecklings AB, Gysinge, Sweden
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He L, Piper A, Meilleur F, Myles DAA, Hernandez R, Brown DT, Heller WT. The structure of Sindbis virus produced from vertebrate and invertebrate hosts as determined by small-angle neutron scattering. J Virol 2010; 84:5270-6. [PMID: 20219936 PMCID: PMC2863847 DOI: 10.1128/jvi.00044-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 02/25/2010] [Indexed: 01/14/2023] Open
Abstract
The complex natural cycle of vectored viruses that transition between host species, such as between insects and mammals, makes understanding the full life cycle of the virus an incredibly complex problem. Sindbis virus, an arbovirus and prototypic alphavirus having an inner protein shell and an outer glycoprotein coat separated by a lipid membrane, is one example of a vectored virus that transitions between vertebrate and insect hosts. While evidence of host-specific differences in Sindbis virus has been observed, no work has been performed to characterize the impact of the host species on the structure of the virus. Here, we report the first study of the structural differences between Sindbis viruses grown in mammalian and insect cells, which were determined by small-angle neutron scattering (SANS), a nondestructive technique that did not decrease the infectivity of the Sindbis virus particles studied. The scattering data and modeling showed that, while the radial position of the lipid bilayer did not change significantly, it was possible to conclude that it did have significantly more cholesterol when the virus was grown in mammalian cells. Additionally, the outer protein coat was found to be more extended in the mammalian Sindbis virus. The SANS data also demonstrated that the RNA and nucleocapsid protein share a closer interaction in the mammalian-cell-grown virus than in the virus from insect cells.
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Affiliation(s)
- Lilin He
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Amanda Piper
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Flora Meilleur
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dean A. A. Myles
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Raquel Hernandez
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dennis T. Brown
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - William T. Heller
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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Hafer A, Whittlesey R, Brown DT, Hernandez R. Differential incorporation of cholesterol by Sindbis virus grown in mammalian or insect cells. J Virol 2009; 83:9113-21. [PMID: 19587056 PMCID: PMC2738221 DOI: 10.1128/jvi.00755-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 06/26/2009] [Indexed: 01/09/2023] Open
Abstract
Cholesterol has been shown to be essential for the fusion of alphaviruses with artificial membranes (liposomes). Cholesterol has also been implicated as playing an essential and critical role in the processes of entry and egress of alphaviruses in living cells. Paradoxically, insects, the alternate host for alphaviruses, are cholesterol auxotrophs and contain very low levels of this sterol. To further evaluate the role of cholesterol in the life cycle of alphaviruses, the cholesterol levels of the alphavirus Sindbis produced from three different mosquito (Aedes albopictus) cell lines; one other insect cell line, Sf21 from Spodoptera frugiperda; and BHK (mammalian) cells were measured. Sindbis virus was grown in insect cells under normal culture conditions and in cells depleted of cholesterol by growth in serum delipidated by using Cab-O-sil, medium treated with methyl-beta-cyclodextrin, or serum-free medium. The levels of cholesterol incorporated into the membranes of the cells and into the virus produced from these cells were determined. Virus produced from these treated and untreated cells was compared to virus grown in BHK cells under standard conditions. The ability of insect cells to produce Sindbis virus after delipidation was found to be highly cell specific and not dependent on the level of cholesterol in the cell membrane. A very low level of cholesterol was required for the generation of wild-type levels of infectious Sindbis virus from delipidated cells. The data show that one role of the virus membrane is structural, providing the stability required for infectivity that may not be provided by the delipidated membranes in some cells. These data show that the amount of cholesterol in the host cell membrane in and of itself has no effect on the process of virus assembly or on the ability of virus to infect cells. Rather, these data suggest that the cholesterol dependence reported for infectivity and assembly of Sindbis virus is a reflection of differences in the insect cell lines used and the methods of delipidation.
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Affiliation(s)
- Amanda Hafer
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608
| | - Rebecca Whittlesey
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608
| | - Dennis T. Brown
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608
| | - Raquel Hernandez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608
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Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. MASS SPECTROMETRY REVIEWS 2009; 28:785-815. [PMID: 19016300 PMCID: PMC2768138 DOI: 10.1002/mas.20203] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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Hernandez R, Paredes A. Sindbis virus as a model for studies of conformational changes in a metastable virus and the role of conformational changes in in vitro antibody neutralisation. Rev Med Virol 2009; 19:257-72. [DOI: 10.1002/rmv.619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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