1
|
Tang X, Munske GR, Siems WF, Bruce JE. Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactions. Anal Chem 2007; 77:311-8. [PMID: 15623310 DOI: 10.1021/ac0488762] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
A new mass spectrometry identifiable cross-linking strategy has been developed to study protein-protein interactions. The new cross-linker was designed to have two low-energy MS/MS-cleavable bonds in the spacer chain to provide three primary benefits: First, a reporter tag can be released from cross-link due to cleavage of the two labile bonds in the spacer chain. Second, a relatively simple MS/MS spectrum can be generated owing to favorable cleavage of labile bonds. And finally, the cross-linked peptide chains are dissociated from each other, and each then can be fragmented separately to get sequence information. Therefore, this novel type of cross-linker was named protein interaction reporter (PIR). To this end, two RINK groups were utilized to make our first-generation cross-linker using solid-phase peptide synthesis chemistry. The RINK group contains a bond more labile than peptide bonds during low-energy activation. The new cross-linker was applied to cross-link ribonuclease S (RNase S), a noncovalent complex of S-peptide and S-protein. The results demonstrated that the new cross-linker effectively reacted with RNase S to generate various types of cross-linked products. More importantly, the cross-linked peptides successfully released reporter ions during selective MS/MS conditions, and the dissociated peptide chains remained intact during MS(2), thus enabling MS(3) to be performed subsequently. In addition, dead-end, intra-, and inter-cross-linked peptides can be distinguished by analyzing MS/MS spectra.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
18 |
163 |
2
|
Zhang H, Tang X, Munske GR, Tolic N, Anderson GA, Bruce JE. Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry. Mol Cell Proteomics 2008; 8:409-20. [PMID: 18936057 DOI: 10.1074/mcp.m800232-mcp200] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/26/2023] Open
Abstract
We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. The strategy consists of (i) a chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by two-dimensional LC/MSMS and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; and (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to Shewanella oneidensis bacterial cells, and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore most identified interactions involved membrane proteins, suggesting that the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely used approaches.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
17 |
126 |
3
|
Zhang H, Tang X, Munske GR, Zakharova N, Yang L, Zheng C, Wolff MA, Tolic N, Anderson GA, Shi L, Marshall MJ, Fredrickson JK, Bruce JE. In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers. J Proteome Res 2008; 7:1712-20. [PMID: 18303833 DOI: 10.1021/pr7007658] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/29/2022]
Abstract
Outer membrane (OM) cytochromes OmcA (SO1779) and MtrC (SO1778) are the integral components of electron transfer used by Shewanella oneidensis for anaerobic respiration of metal (hydr)oxides. Here the OmcA-MtrC interaction was identified in vivo using a novel hydrophobic chemical cross-linker (MRN) combined with immunoprecipitation techniques. In addition, identification of other OM proteins from the cross-linked complexes allows first visualization of the OmcA-MtrC interaction network. Further experiments on omcA and mtrC mutant cells showed OmcA plays a central role in the network interaction. For comparison, two commercial cross-linkers were also used in parallel, and both resulted in fewer OM protein identifications, indicating the superior properties of MRN for identification of membrane protein interactions. Finally, comparison experiments of in vivo cross-linking and cell lysate cross-linking resulted in significantly different protein interaction data, demonstrating the importance of in vivo cross-linking for study of protein-protein interactions in cells.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
17 |
58 |
4
|
Tang X, Yi W, Munske GR, Adhikari DP, Zakharova NL, Bruce JE. Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes. J Proteome Res 2007; 6:724-34. [PMID: 17269728 PMCID: PMC2527595 DOI: 10.1021/pr060480e] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/18/2023]
Abstract
The membrane proteome plays a critical role in electron transport processes in Shewanella oneidensis MR-1, a bacterial organism that has great potential for bioremediation. Biotinylation of intact cells with subsequent affinity-enrichment has become a useful tool for characterization of the membrane proteome. As opposed to these commonly used, water-soluble commercial reagents, we here introduce a family of hydrophobic, cell-permeable affinity probes for extensive labeling and detection of membrane proteins. When applied to S. oneidensis cells, all three new chemical probes allowed identification of a substantial proportion of membrane proteins from total cell lysate without the use of specific membrane isolation method. From a total of 410 unique proteins identified, approximately 42% are cell envelope proteins that include outer membrane, periplasmic, and inner membrane proteins. This report demonstrates the first application of this intact cell biotinylation method to S. oneidensis and presents the results of many identified proteins that are involved in metal reduction processes. As a general labeling method, all chemical probes we introduced in this study can be extended to other organisms or cell types and will help expedite the characterization of membrane proteomes.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
18 |
53 |
5
|
Chowdhury SM, Munske GR, Tang X, Bruce JE. Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers. Anal Chem 2007; 78:8183-93. [PMID: 17165806 DOI: 10.1021/ac060789h] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
One of the challenges in protein interaction studies with chemical cross-linking stems from the complexity of intra-, inter-, and dead-end cross-linked peptide mixtures. We have developed new cross-linkers to study protein-protein interactions with mass spectrometry to improve the ability to deal with this complexity. Even the accurate mass capabilities of FTICR-MS alone cannot unambiguously identify cross-linked peptides from cell-labeling experiments due to the complexity of these mixtures resultant from the enormous number of possible cross-linked species. We have developed novel cross-linkers that have unique fragmentation features in the gas phase. The characteristics of these cross-linkers combined with the accurate mass capability of FTICR-MS can help distinguish cross-linking reaction products and assign protein identities. These cross-linkers that we call protein interaction reporters (PIRs) have been constructed with two reactive groups attached through two bonds that can be preferentially cleaved by low-energy CID of the respective protonated precursor ions. After cleavage of the labile bonds, the middle part of the linker serves as a reporter ion to aid identification of cross-linked peptides. This report highlights three new PIRs with new features that have been developed to improve the efficiency of release of reporter ions. The new cross-linkers reported here were tuned with the addition of an affinity tag, a hydrophilic group, a photocleavable group, and new low-energy MS/MS cleavable bonds. This report presents our investigation of the MSMS fragmentation behavior of selected protonated ions of the new compounds. The comprehensive fragmentation of these PIRs and PIR-labeled cross-linked peptides with low-energy collisions and an example of electron capture dissociation in FTICR-MS is presented. These new cross-linkers will contribute to current systems biology research by allowing acquisition of global or large-scale data on protein-protein interactions.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
18 |
49 |
6
|
Khisty VJ, Munske GR, Randall LL. Mapping of the binding frame for the chaperone SecB within a natural ligand, galactose-binding protein. J Biol Chem 1995; 270:25920-7. [PMID: 7592780 DOI: 10.1074/jbc.270.43.25920] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/26/2023] Open
Abstract
The chaperone SecB selectively binds polypeptides that are in a non-native state; however, the details of the interaction between SecB and its ligands are unknown. As a step in elucidation of the molecular mechanism of binding, we have mapped the region of a physiologic ligand (galactose-binding protein) that is in contact with SecB. The binding frame comprises approximately 160 aminoacyl residues and is located in the central portion of the primary sequence. Comparison to the binding frame within maltose-binding protein, which is similarly long and positioned around the center of that polypeptide, reveals no similarity in sequence or in folding motif. The results are consistent with the proposal that the selectivity in binding exhibited by SecB is based on the simultaneous occupancy of multiple binding sites, each of which demonstrates low specificity, by flexible stretches of polypeptide that are only accessible in non-native proteins.
Collapse
|
Comparative Study |
30 |
47 |
7
|
Yang L, Tang X, Weisbrod CR, Munske GR, Eng JK, von Haller PD, Kaiser NK, Bruce JE. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies. Anal Chem 2010; 82:3556-66. [PMID: 20373789 DOI: 10.1021/ac902615g] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/30/2022]
Abstract
In this paper, we present the results of proof-of-concept experiments using a novel photocleavable and mass spectrometry identifiable cross-linker pcPIR (photocleavable protein interaction reporter). pcPIR can be dissociated under UV irradiation either off- or online before the introduction to the mass spectrometers. Photo dissociation of cross-linkers is different from either the gas phase or the chemical cleavage of cross-linkers. Different types of cross-links can be identified using the pcPIR mass relationships, where the mass of cross-linked precursor equals the sum of the masses of the released products and reporter. Since pcPIR is cleaved prior to the entrance to the mass spectrometer, the released peptides are available to be sequenced with routine collision-induced dissociation (CID) MS/MS experiments and database search algorithms. In this report, the pcPIR strategy of identifying the cross-linked peptides with on- and off-line photocleavage coupled with novel targeted data dependent LC-MS/MS is demonstrated with the use of standard peptides, bovine serum albumin (BSA), and human hemoglobin tetramer protein complex.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
15 |
44 |
8
|
Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE. In vivo application of photocleavable protein interaction reporter technology. J Proteome Res 2012; 11:1027-41. [PMID: 22168182 DOI: 10.1021/pr200775j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/29/2022]
Abstract
In vivo protein structures and protein-protein interactions are critical to the function of proteins in biological systems. As a complementary approach to traditional protein interaction identification methods, cross-linking strategies are beginning to provide additional data on protein and protein complex topological features. Previously, photocleavable protein interaction reporter (pcPIR) technology was demonstrated by cross-linking pure proteins and protein complexes and the use of ultraviolet light to cleave or release cross-linked peptides to enable identification. In the present report, the pcPIR strategy is applied to Escherichia coli cells, and in vivo protein interactions and topologies are measured. More than 1600 labeled peptides from E. coli were identified, indicating that many protein sites react with pcPIR in vivo. From those labeled sites, 53 in vivo intercross-linked peptide pairs were identified and manually validated. Approximately half of the interactions have been reported using other techniques, although detailed structures exist for very few. Three proteins or protein complexes with detailed crystallography structures are compared to the cross-linking results obtained from in vivo application of pcPIR technology.
Collapse
|
Research Support, Non-U.S. Gov't |
13 |
28 |
9
|
Chakrabarty JK, Naik AG, Fessler MB, Munske GR, Chowdhury SM. Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking. Anal Chem 2016; 88:10215-10222. [PMID: 27649375 DOI: 10.1021/acs.analchem.6b02886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 02/06/2023]
Abstract
Chemical cross-linking and mass spectrometry are now widely used to analyze large-scale protein-protein interactions. The major challenge in cross-linking approaches is the complexity of the mass spectrometric data. New approaches are required that can identify cross-linked peptides with high-confidence and establish a user-friendly analysis protocol for the biomedical scientific community. Here, we introduce a novel cross-linker that can be selectively cleaved in the gas phase using two differential tandem mass-spectrometric fragmentation methods, such as collision-induced or electron transfer dissociation (CID and ETD). This technique produces two signature mass spectra of the same cross-linked peptide, thereby producing high confidence in identifying the sites of interaction. Further tandem mass spectrometry can also give additional confidence on the peptide sequences. We demonstrate a proof-of-concept for this method using standard peptides and proteins. Peptides and proteins were cross-linked and their fragmentation characteristics were analyzed using CID and ETD tandem mass spectrometry. Two sequential cleavages unambiguously identified cross-linked peptides. In addition, the labeling efficiency of the new cross-linker was evaluated in macrophage immune cells after stimulation with the microbial ligand lipopolysaccharide and subsequent pulldown experiments with biotin-avidin affinity chromatography. We believe this strategy will help advance insights into the structural biology and systems biology of cell signaling.
Collapse
|
Research Support, Non-U.S. Gov't |
9 |
22 |
10
|
Christie DJ, Munske GR, Magnuson JA. Activation of saccharide binding in demetalized concanavalin A by transition metal ions. Biochemistry 1979; 18:4638-44. [PMID: 497156 DOI: 10.1021/bi00588a026] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/15/2022]
|
|
46 |
21 |
11
|
Sanchez EJ, Munske GR, Criswell A, Milting H, Dunker AK, Kang C. Phosphorylation of human calsequestrin: implications for calcium regulation. Mol Cell Biochem 2011; 353:195-204. [PMID: 21416293 DOI: 10.1007/s11010-011-0787-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/11/2011] [Accepted: 03/07/2011] [Indexed: 10/18/2022]
Abstract
Both cardiac and skeletal calsequestrin (CASQ2 and CASQ1) serve as a major Ca(2+) storage/buffer protein in the sarcoplasmic reticulum (SR) by sequestering and releasing large numbers of Ca(2+) ions during each muscular contraction and relaxation cycle. CASQ isolated from various species often exists in a phosphorylated form, but phosphorylation's role is not yet understood. Here, the authors identified two phosphorylation sites, Ser(385) and Ser(393), for the first time, in human CASQ2 (hCASQ2) by mass-spectroscopy and evaluated the consequences of such phosphorylation. Substitution of these two serines with phosphoserine-mimicking aspartic-acid residues results in a significant increase in helical content, solubility and Ca(2+)-binding capacity above 6 mM [Ca(2+)]. However, neither substitution of Ser(385) nor Ser(393) alone produce any significant changes. Based on the crystal structures of hCASQ2, Ca(2+) binding capacity data, turbidity, and light scattering profiles, it was propose that phosphorylation at these two positions produces a disorder-to-order or coil-to-helix transition of the C-terminus, which in turn provides a more stable network of polyanions. Therefore, considering all the previous reports and the new data, the observed dynamic in vivo phosphorylation of CASQ could provide the basis not only for effective regulation of Ca(2+) buffering capacity, but also for the junctional SR trafficking mechanism.
Collapse
|
Research Support, Non-U.S. Gov't |
14 |
17 |
12
|
Sanchez EJ, Lewis KM, Munske GR, Nissen MS, Kang C. Glycosylation of skeletal calsequestrin: implications for its function. J Biol Chem 2011; 287:3042-50. [PMID: 22170046 DOI: 10.1074/jbc.m111.326363] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/06/2022] Open
Abstract
Calsequestrin (CASQ) serves as a major Ca(2+) storage/buffer protein in the sarcoplasmic reticulum (SR). When purified from skeletal muscle, CASQ1 is obtained in its glycosylated form. Here, we have confirmed the specific site and degree of glycosylation of native rabbit CASQ1 and have investigated its effect on critical properties of CASQ by comparison with the non-glycosylated recombinant form. Based on our comparative approach utilizing crystal structures, Ca(2+) binding capacities, analytical ultracentrifugation, and light-scattering profiles of the native and recombinant rabbit CASQ1, we propose a novel and dynamic role for glycosylation in CASQ. CASQ undergoes a unique degree of mannose trimming as it is trafficked from the proximal endoplasmic reticulum to the SR. The major glycoform of CASQ (GlcNAc(2)Man(9)) found in the proximal endoplasmic reticulum can severely hinder formation of the back-to-back interface, potentially preventing premature Ca(2+)-dependent polymerization of CASQ and ensuring its continuous mobility to the SR. Only trimmed glycans can stabilize both front-to-front and the back-to-back interfaces of CASQ through extensive hydrogen bonding and electrostatic interactions. Therefore, the mature glycoform of CASQ (GlcNAc(2)Man(1-4)) within the SR can be retained upon establishing a functional high capacity Ca(2+) binding polymer. In addition, based on the high resolution structures, we propose a molecular mechanism for the catecholaminergic polymorphic ventricular tachycardia (CPVT2) mutation, K206N.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
14 |
17 |
13
|
Chowdhury SM, Munske GR, Ronald RC, Bruce JE. Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thio-ether bonds in peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:493-501. [PMID: 17126025 PMCID: PMC1864951 DOI: 10.1016/j.jasms.2006.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Received: 06/19/2006] [Revised: 10/11/2006] [Accepted: 10/20/2006] [Indexed: 05/12/2023]
Abstract
Thio-ether bonds in the cysteinyl side chain of peptides, formed with the most commonly used cysteine blocking reagent iodoacetamide, after conversion to sulfoxide, releases a neutral fragment mass in a low-energy MS/MS experiment in the gas phase of the mass spectrometer [6]. In this study, we show that the neutral loss fragments produced from the mono-oxidized thio-ether bonds (sulfoxide) in peptides, formed by alkyl halide or double-bond containing cysteine blocking reagents are different under low-energy MS/MS conditions. We have evaluated the low-energy fragmentation patterns of mono-oxidized modified peptides with different cysteine blocking reagents, such as iodoacetamide, 3-maleimidopropionic acid, and 4-vinylpyridine using FTICR-MS. We propose that the mechanisms of gas-phase fragmentation of mono-oxidized thio-ether bonds in the side chain of peptides, formed by iodoacetamide and double-bond containing cysteine blocking reagents, maleimide and vinylpyridine, are different because of the availability of acidic beta-hydrogens in these compounds. Moreover, we investigated the fragmentation characteristics of mono-oxidized thio-ether bonds within the peptide sequence to develop novel mass-spectrometry identifiable chemical cross-linkers. This methionine type of oxidized thio-ether bond within the peptide sequence did not show anticipated low-energy fragmentation. Electron capture dissociation (ECD) of the side chain thio-ether bond containing oxidized peptides was also studied. ECD spectra of the oxidized peptides showed a greater extent of peptide backbone cleavage, compared with CID spectra. This fragmentation information is critical to researchers for accurate data analysis of this undesired modification in proteomics research, as well as other methods that may utilize sulfoxide derivatives.
Collapse
|
research-article |
18 |
15 |
14
|
Ko YH, Vanni P, Munske GR, McFadden BA. Substrate-decreased modification by diethyl pyrocarbonate of two histidines in isocitrate lyase from Escherichia coli. Biochemistry 1991; 30:7451-6. [PMID: 1854747 DOI: 10.1021/bi00244a012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/29/2022]
Abstract
The inactivation of tetrameric 188-kDa isocitrate lyase from Escherichia coli at pH 6.8 (37 degrees C) by diethyl pyrocarbonate, exhibiting saturation kinetics, is accompanied by modification of histidine residues 266 and 306. Substrates isocitrate, glyoxylate, or glyoxylate plus succinate protect the enzyme from inactivation, but succinate alone does not. Removal of the carbethoxy groups from inactivated enzyme by treatment with hydroxylamine restores activity of isocitrate lyase. The present results suggest that the group-specific modifying reagent diethyl pyrocarbonate may be generally useful in determining the position of active site histidine residues in enzymes.
Collapse
|
|
34 |
15 |
15
|
Abstract
Flow microcalorimetry has been used to examine the delta H of binding of two types of saccharides, a series of simple monosaccharides and a series of alpha-(1----4)-linked glucosides, to the lectin Concanavalin A. It has been found that the delta H decreases with any change in the stereochemistry of a hydroxyl group relative to methyl alpha-D-mannopyranoside. The data have allowed the calculation of the relative contribution of two of the hydroxyl groups. The delta H's of binding for the alpha-(1----4)-linked glucosides are approximately 31 kJ/mol, and the apparent association constants vary insignificantly with increasing length. This result indicates that only one glucose residue binds to concanavalin A by hydrogen bonds, and that the additional glucose residues have no interaction either by hydrogen bonds or by nonspecific hydrophobic interactions. This result confirms the absence of an extended binding site for alpha-(1----4)-linked glucopyranosides, in contrast to that proposed for alpha-(1----2)-linked mannopyranosides which show an increase in apparent association constants with increasing length.
Collapse
|
|
41 |
13 |
16
|
Abstract
The transport of chlortetracycline by Streptococcus faecalis is energy dependent. Addition of glucose to energy-depleted cells enhances both the transport rates and accumulation levels. Transport rates can be altered independently of glucose by treating cells with ionophores that increase or decrease the proton gradient. The transport of the antibiotic is linked only to the transmembrane pH difference, delta pH, and not the transmembrane electrical potential, delta psi. This conclusion was verified by quantitative measurements of delta pH, delta psi, and tetracycline accumulation levels. A linear correlation between delta pH and the tetracycline electrochemical potential was observed. Tetracycline most likely accumulates by the symport of protons in which the protons are bound to an anionic form of the antibiotic to form an uncharged molecule.
Collapse
|
research-article |
41 |
11 |
17
|
Chowdhury SM, Munske GR, Siems WF, Bruce JE. A new maleimide-bound acid-cleavable solid-support reagent for profiling phosphorylation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:899-909. [PMID: 15739244 DOI: 10.1002/rcm.1869] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 05/24/2023]
Abstract
A new chemical strategy for phosphopeptide profiling is reported in this study. Phosphorylation represents one of the most important classes of posttranslational modifications of proteins. Here we report a generalized strategy that employs solid-phase capture and mass-encoding steps to selectively enrich phosphopeptides from complex mixtures. This method exploits conversion of phosphates into thiols and reactive compounds to selectively isolate products of phosphorylation. Selective isolation of phosphopeptides is achieved with a simple, novel, acid-cleavable, solid-support-bound maleimide reagent. Our chemistry efforts have focused on minimization of linker size and simplification of reagent production with incorporation of common solid-phase peptide synthesis steps. Relative quantitation was demonstrated by modifying phosphopeptides with incorporation of ethanedithiol and propanedithiol. We observed that appropriate normalization is necessary to utilize mass tag strategies for relative quantitation of posttranslational modifications. The utility of solid-phase capture was determined with model phosphopeptides, and the method was demonstrated with enriching phosphopeptides from beta-casein, alpha-casein and ovalbumin. The solid-phase capture and release methods were also demonstrated with unfractionated whole histone protein mixtures to show this compound applicability in real biological samples. The new chemical strategy will ultimately be utilized for high-throughput profiling of phosphorylation and possibly other posttranslational modifications.
Collapse
|
|
20 |
10 |
18
|
Martin SE, Ganguly T, Munske GR, Fulton MD, Hopkins MR, Berkman CE, Black ME. Development of inhibitor-directed enzyme prodrug therapy (IDEPT) for prostate cancer. Bioconjug Chem 2014; 25:1752-60. [PMID: 25157916 PMCID: PMC4198102 DOI: 10.1021/bc500362n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/22/2023]
Abstract
![]()
Prostate
cancer (PCa) is the second most common cause of cancer
death among American men after lung cancer. Unfortunately, current
therapies do not provide effective treatments for patients with advanced,
metastatic, or hormone refractory disease. Therefore, we seek to generate
therapeutic agents for a novel PCa treatment strategy by delivering
a suicide enzyme (yCDtriple) to a cell membrane bound biomarker
found on PCa cells (prostate-specific membrane antigen (PSMA)). This
approach has resulted in a new PCa treatment strategy reported here
as inhibitor-directed enzyme prodrug therapy (IDEPT). The therapeutic
agents described were generated using a click chemistry reaction between
the unnatural amino acid (p-azidophenylalanine (pAzF)) incorporated into yCDtriple and the dibenzylcyclooctyne
moiety of our PSMA targeting agent (DBCO-PEG4-AH2-TG97). After characterization of the therapeutic agents, we demonstrate
significant PCa cell killing of PSMA-positive cells. Importantly,
we demonstrate that this click chemistry approach can be used to efficiently
couple a therapeutic protein to a targeting agent and may be applicable
to the ablation of other types of cancers and/or malignancies.
Collapse
|
Research Support, N.I.H., Extramural |
11 |
9 |
19
|
Munske GR, Magnuson JA, Krakauer H. A conformational change in concanavalin A detected by a calorimetric study of the binding of methyl alpha-D-mannopyranoside. Biochem Biophys Res Commun 1978; 84:684-90. [PMID: 718710 DOI: 10.1016/0006-291x(78)90759-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/24/2022]
|
|
47 |
8 |
20
|
Abstract
Tetracycline transport by Streptococcus faecalis occurs by an energy-dependent, carrier-mediated process. The Michaelis constant for transport was unchanged, but the maximal velocity was increased when an energy source, glucose, was present. Accumulation levels, sometimes 25-fold greater than the external concentration, were controlled by the transport system.
Collapse
|
research-article |
41 |
8 |
21
|
Christie DJ, Munske GR, Appel DM, Magnuson JA. Conformational changes following Mn(II) binding to demetalized concanavalin A1. Biochem Biophys Res Commun 1980; 95:1043-8. [PMID: 7417299 DOI: 10.1016/0006-291x(80)91578-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/25/2023]
|
|
45 |
7 |
22
|
Chowdhury SM, Munske GR, Yang J, Zhukova D, Nguen H, Bruce JE. Solid-phase N-terminal peptide enrichment study by optimizing trypsin proteolysis on homoarginine-modified proteins by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:635-644. [PMID: 24519826 PMCID: PMC3969842 DOI: 10.1002/rcm.6820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Received: 08/05/2013] [Revised: 10/21/2013] [Accepted: 12/25/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Proteolytic cleavages generate active precursor proteins by creating new N-termini in the proteins. A number of strategies have recently been published regarding the enrichment of original or newly formed N-terminal peptides using guanidination of lysine residues and amine-reactive reagents. For effective enrichment of N-terminal peptides, the efficiency of trypsin proteolysis on homoarginine (guanidinated) modified proteins must be understood and simple and versatile solid-phase N-terminal capture strategies should be developed. METHODS We present here a mass spectrometry (MS)-based study to evaluate and optimize the trypsin proteolysis on a guanidinated-modified protein. Trypsin proteolysis was studied using different amounts of trypsin to modified protein ratios. To capture the original N-termini, after guanidination of proteins, original N-termini were acetylated and the proteins were digested with trypsin. The newly formed N-terminal tryptic peptides were captured with a new amine reactive acid-cleavable solid-phase reagent. The original N-terminal peptides were then collected from the supernatant of the solution. RESULTS We demonstrated a detailed study of the efficiency of enzyme trypsin on homoarginine-modified proteins. We observed that the rate of hydrolysis of homoarginine residues compared to their lysine/arginine counterparts were slower but generally cleaved after an overnight digestion period depending on the protein to protease concentration ratios. Selectivity of the solid-phase N-terminal reagent was studied by enrichment of original N-terminal peptides from two standard proteins, ubiquitin and RNaseS. CONCLUSIONS We found enzyme trypsin is active in the guanidinated form of the protein depending on the enzyme to protein concentrations, time and the proximity of arginine residues in the sequence. The novel solid-phase capture reagent also successfully enriched N-terminal peptides from the standard protein mixtures. We believe this trypsin proteolysis study on homoarginine-modified proteins and our simple and versatile solid-phase capture strategy could be very useful for enrichment and sequence determination of proteins N-termini by MS.
Collapse
|
Research Support, N.I.H., Extramural |
11 |
7 |
23
|
Munske GR, Magnuson JA, Barbet AF. Trypanosoma brucei: a fluorescence and spin label study of the membranes of the bloodstream form. Exp Parasitol 1986; 62:423-9. [PMID: 3780935 DOI: 10.1016/0014-4894(86)90051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/07/2023]
Abstract
Fluidity of the plasma membrane of Trypanosoma brucei brucei has been examined with fluorescence and electron spin resonance spectroscopy. Fluorescent probes 1,6-diphenyl-1,3,5-hexatriene and 8-anilino-1-naphthalene sulfonate and the spin label probe 5-doxyl stearate have been employed to examine fluidity under a variety of conditions. The temperature dependence of 8-anilino-1-naphthalene sulfonate polarization and of the order parameter S for 5-doxyl stearate reveals phase alterations near 30 C. 1,6-Diphenyl-1,3,5-hexatriene polarization shows that proteolysis of the surface glycoprotein with trypsin increases fluidity but treatment with human serum which is trypanocidal produces no detectable change in membrane fluidity.
Collapse
|
|
39 |
3 |
24
|
Zhang B, Munske GR, Timokhin VI, Ralph J, Davydov DR, Vermerris W, Sattler SE, Kang C. Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition. J Biol Chem 2022; 298:101761. [PMID: 35202651 PMCID: PMC8942828 DOI: 10.1016/j.jbc.2022.101761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 12/07/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Plant NADPH-dependent cytochrome P450 reductase (CPR) is a multidomain enzyme that donates electrons for hydroxylation reactions catalyzed by class II cytochrome P450 monooxygenases involved in the synthesis of many primary and secondary metabolites. These P450 enzymes include trans-cinnamate-4-hydroxylase, p-coumarate-3′-hydroxylase, and ferulate-5-hydroxylase involved in monolignol biosynthesis. Because of its role in monolignol biosynthesis, alterations in CPR activity could change the composition and overall output of lignin. Therefore, to understand the structure and function of three CPR subunits from sorghum, recombinant subunits SbCPR2a, SbCPR2b, and SbCPR2c were subjected to X-ray crystallography and kinetic assays. Steady-state kinetic analyses demonstrated that all three CPR subunits supported the oxidation reactions catalyzed by SbC4H1 (CYP73A33) and SbC3′H (CYP98A1). Furthermore, comparing the SbCPR2b structure with the well-investigated CPRs from mammals enabled us to identify critical residues of functional importance and suggested that the plant flavin mononucleotide–binding domain might be more flexible than mammalian homologs. In addition, the elucidated structure of SbCPR2b included the first observation of NADP+ in a native CPR. Overall, we conclude that the connecting domain of SbCPR2, especially its hinge region, could serve as a target to alter biomass composition in bioenergy and forage sorghums through protein engineering.
Collapse
|
|
3 |
1 |
25
|
Urdea MS, Christie DJ, Munske GR, Magnuson JA, Legg JI. A Co(III) derivative of concanavalin A. Biochem Biophys Res Commun 1979; 91:1045-50. [PMID: 526265 DOI: 10.1016/0006-291x(79)91985-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/23/2022]
|
|
46 |
1 |