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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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2
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Javed Z, Nguyen HH, Harker KK, Mohr CM, Vano P, Wallace SR, Silvers C, Sim C, Turumella S, Flinn A, Moritz A, Carter-O’Connell I. Using TLC-MALDI-TOF to Interrogate In Vitro Peptidyl Proximal Preferences of PARP14 and Glycohydrolase Specificity. Molecules 2023; 28:6061. [PMID: 37630315 PMCID: PMC10459978 DOI: 10.3390/molecules28166061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
The transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human diphtheria toxin-like ADP-ribosyltransferases (ARTDs; previously referred to as poly-ADP-ribose polymerases or PARPs) and the removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about the sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the in vitro analysis of proximal factors that guide ARTD target selection. We identify a minimal 5-mer peptide sequence that is necessary and sufficient to drive glutamate/aspartate targeting using PARP14 while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is pH and temperature dependent, sequence independent, and occurs within hours. Finally, we use the ADPr-peptides to highlight differential activities within the glycohydrolase family and their sequence preferences. Our results highlight (1) the utility of MALDI-TOF in analyzing proximal ARTD-substrate interactions and (2) the importance of peptide sequences in governing ADPr transfer and removal.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ian Carter-O’Connell
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA 95053, USA (C.M.M.); (P.V.)
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3
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Ruhland F, Gabant G, Toussaint T, Nemcic M, Cadène M, Lucas C. Reproductives signature revealed by protein profiling and behavioral bioassays in termite. Sci Rep 2023; 13:7070. [PMID: 37127756 PMCID: PMC10151321 DOI: 10.1038/s41598-023-33252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/10/2023] [Indexed: 05/03/2023] Open
Abstract
Proteins are known to be social interaction signals in many species in the animal kingdom. Common mediators in mammals and aquatic species, they have seldom been identified as such in insects' behaviors. Yet, they could represent an important component to support social signals in social insects, as the numerous physical contacts between individuals would tend to favor the use of contact compounds in their interactions. However, their role in social interactions is largely unexplored: are they rare or simply underestimated? In this preliminary study, we show that, in the termite Reticulitermes flavipes, polar extracts from reproductives trigger body-shaking of workers (a vibratory behavior involved in reproductives recognition) while extracts from workers do not. Molecular profiling of these cuticular extracts using MALDI-TOF mass spectrometry reveals higher protein diversity in reproductives than in workers and a sex-specific composition exclusive to reproductives. While the effects observed with extracts are not as strong as with live termites, these results open up the intriguing possibility that social signaling may not be limited to cuticular hydrocarbons or other non-polar, volatile chemicals as classically accepted. Our results suggest that polar compounds, in particular some of the Cuticular Protein Compounds (CPCs) shown here by MALDI to be specific to reproductives, could play a significant role in insect societies. While this study is preliminary and further comprehensive molecular characterization is needed to correlate the body-shaking triggering effects with a given set of polar compounds, this exploratory study opens new perspectives for understanding the role of polar compounds such as proteins in caste discrimination, fertility signaling, or interspecific insect communication.
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Affiliation(s)
- Fanny Ruhland
- Institut de Recherche sur la Biologie de l'Insecte (UMR7261), CNRS - University of Tours, Tours, France
| | - Guillaume Gabant
- Centre de Biophysique Moléculaire (UPR 4301), CNRS - University of Orléans, Orléans, France
| | - Timothée Toussaint
- Institut de Recherche sur la Biologie de l'Insecte (UMR7261), CNRS - University of Tours, Tours, France
| | - Matej Nemcic
- Centre de Biophysique Moléculaire (UPR 4301), CNRS - University of Orléans, Orléans, France
| | - Martine Cadène
- Centre de Biophysique Moléculaire (UPR 4301), CNRS - University of Orléans, Orléans, France
| | - Christophe Lucas
- Institut de Recherche sur la Biologie de l'Insecte (UMR7261), CNRS - University of Tours, Tours, France.
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4
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Javed Z, Nguyen HH, Harker K, Mohr CM, Vano P, Wallace SR, Silvers C, Sim C, Turumella S, Flinn A, Carter-O’Connell I. Identification of a Novel PARP14 Site Motif and Glycohydrolase Specificity Using TLC-MALDI-TOF. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533863. [PMID: 36993563 PMCID: PMC10055325 DOI: 10.1101/2023.03.22.533863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human poly-ADP-ribose polymerases, PARPs, and removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the discovery and validation of ADPr site motifs. We identify a minimal 5-mer peptide sequence that is sufficient to drive PARP14 specific activity while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is sequence independent and occurs within hours. Finally, we use the ADPr-peptide to highlight differential activities within the glycohydrolase family and their sequence specificities. Our results highlight: 1) the utility of MALDI-TOF in motif discovery and 2) the importance of peptide sequence in governing ADPr transfer and removal.
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Affiliation(s)
- Zeeshan Javed
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Hannah H. Nguyen
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Kiana Harker
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Christian M. Mohr
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Pia Vano
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Sean R. Wallace
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Clarissa Silvers
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Colin Sim
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Soumya Turumella
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Ally Flinn
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Ian Carter-O’Connell
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
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Darie-Ion L, Whitham D, Jayathirtha M, Rai Y, Neagu AN, Darie CC, Petre BA. Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research. Molecules 2022; 27:6196. [PMID: 36234736 PMCID: PMC9570737 DOI: 10.3390/molecules27196196] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein-protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide "molecular pictures", which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.
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Affiliation(s)
- Laura Darie-Ion
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Yashveen Rai
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 22, 700505 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Brînduşa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
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Wallace SR, Chihab LY, Yamasaki M, Yoshinaga BT, Torres YM, Rideaux D, Javed Z, Turumella S, Zhang M, Lawton DR, Fuller AA, Carter-O’Connell I. Rapid Analysis of ADP-Ribosylation Dynamics and Site-Specificity Using TLC-MALDI. ACS Chem Biol 2021; 16:2137-2143. [PMID: 34647721 PMCID: PMC8609518 DOI: 10.1021/acschembio.1c00542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Poly(ADP-ribose)
polymerases, PARPs, transfer ADP-ribose onto target
proteins from nicotinamide adenine dinucleotide (NAD+).
Current mass spectrometric analytical methods require proteolysis
of target proteins, limiting the study of dynamic ADP-ribosylation
on contiguous proteins. Herein, we present a matrix-assisted laser
desorption/ionization time-of-flight (MALDI-TOF) method that facilitates
multisite analysis of ADP-ribosylation. We observe divergent ADP-ribosylation
dynamics for the catalytic domains of PARPs 14 and 15, with PARP15
modifying more sites on itself (+3–4 ADP-ribose) than the closely
related PARP14 protein (+1–2 ADP-ribose)—despite similar
numbers of potential modification sites. We identify, for the first
time, a minimal peptide fragment (18 amino-acids) that is preferentially
modified by PARP14. Finally, we demonstrate through mutagenesis and
chemical treatment with hydroxylamine that PARPs 14/15 prefer acidic
residues. Our results highlight the utility of MALDI-TOF in the analysis
of PARP target modifications and in elucidating the biochemical mechanism
governing PARP target selection.
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Affiliation(s)
- Sean R. Wallace
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Leila Y. Chihab
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Miles Yamasaki
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Braden T. Yoshinaga
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Yazmin M. Torres
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Damon Rideaux
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Zeeshan Javed
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Soumya Turumella
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Michelle Zhang
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Dylan R. Lawton
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Amelia A. Fuller
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Ian Carter-O’Connell
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
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7
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Schroder RV, Cohen LS, Wang P, Arizala JD, Poget SF. Expression, Purification and Refolding of a Human Na V1.7 Voltage Sensing Domain with Native-like Toxin Binding Properties. Toxins (Basel) 2021; 13:toxins13100722. [PMID: 34679015 PMCID: PMC8541342 DOI: 10.3390/toxins13100722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 01/28/2023] Open
Abstract
The voltage-gated sodium channel NaV1.7 is an important target for drug development due to its role in pain perception. Recombinant expression of full-length channels and their use for biophysical characterization of interactions with potential drug candidates is challenging due to the protein size and complexity. To overcome this issue, we developed a protocol for the recombinant expression in E. coli and refolding into lipids of the isolated voltage sensing domain (VSD) of repeat II of NaV1.7, obtaining yields of about 2 mg of refolded VSD from 1 L bacterial cell culture. This VSD is known to be involved in the binding of a number of gating-modifier toxins, including the tarantula toxins ProTx-II and GpTx-I. Binding studies using microscale thermophoresis showed that recombinant refolded VSD binds both of these toxins with dissociation constants in the high nM range, and their relative binding affinities reflect the relative IC50 values of these toxins for full-channel inhibition. Additionally, we expressed mutant VSDs incorporating single amino acid substitutions that had previously been shown to affect the activity of ProTx-II on full channel. We found decreases in GpTx-I binding affinity for these mutants, consistent with a similar binding mechanism for GpTx-I as compared to that of ProTx-II. Therefore, this recombinant VSD captures many of the native interactions between NaV1.7 and tarantula gating-modifier toxins and represents a valuable tool for elucidating details of toxin binding and specificity that could help in the design of non-addictive pain medication acting through NaV1.7 inhibition.
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Affiliation(s)
- Ryan V. Schroder
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Leah S. Cohen
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
| | - Ping Wang
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
| | - Joekeem D. Arizala
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sébastien F. Poget
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Correspondence:
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8
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Espinosa J, Lin TY, Estrella Y, Kim B, Molina H, Hang HC. Enterococcus NlpC/p60 Peptidoglycan Hydrolase SagA Localizes to Sites of Cell Division and Requires Only a Catalytic Dyad for Protease Activity. Biochemistry 2020; 59:4470-4480. [PMID: 33136372 DOI: 10.1021/acs.biochem.0c00755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptidoglycan is a vital component of the bacterial cell wall, and its dynamic remodeling by NlpC/p60 hydrolases is crucial for proper cell division and survival. Beyond these essential functions, we previously discovered that Enterococcus species express and secrete the NlpC/p60 hydrolase-secreted antigen A (SagA), whose catalytic activity can modulate host immune responses in animal models. However, the localization and peptidoglycan hydrolase activity of SagA in Enterococcus was still unclear. In this study, we show that SagA contributes to a triseptal structure in dividing cells of enterococci and localizes to sites of cell division through its N-terminal coiled-coil domain. Using molecular modeling and site-directed mutagenesis, we identify amino acid residues within the SagA-NlpC/p60 domain that are crucial for catalytic activity and potential substrate binding. Notably, these studies revealed that SagA may function via a catalytic Cys-His dyad instead of the predicted Cys-His-His triad, which is conserved in SagA orthologs from other Enterococcus species. Our results provide key additional insight into peptidoglycan remodeling in Enterococcus by SagA NlpC/p60 hydrolases.
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Affiliation(s)
- Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Ti-Yu Lin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Yadyvic Estrella
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Byungchul Kim
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States.,Departments of Immunology & Microbiology and Chemistry, Scripps Research, La Jolla, California 92037, United States
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9
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Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N. Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Nat Commun 2020; 11:3014. [PMID: 32541820 PMCID: PMC7296003 DOI: 10.1038/s41467-020-16566-1] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/01/2020] [Indexed: 12/20/2022] Open
Abstract
Formation of amyloid-beta (Aβ) oligomer pores in the membrane of neurons has been proposed to explain neurotoxicity in Alzheimer's disease (AD). Here, we present the three-dimensional structure of an Aβ oligomer formed in a membrane mimicking environment, namely an Aβ(1-42) tetramer, which comprises a six stranded β-sheet core. The two faces of the β-sheet core are hydrophobic and surrounded by the membrane-mimicking environment while the edges are hydrophilic and solvent-exposed. By increasing the concentration of Aβ(1-42) in the sample, Aβ(1-42) octamers are also formed, made by two Aβ(1-42) tetramers facing each other forming a β-sandwich structure. Notably, Aβ(1-42) tetramers and octamers inserted into lipid bilayers as well-defined pores. To establish oligomer structure-membrane activity relationships, molecular dynamics simulations were carried out. These studies revealed a mechanism of membrane disruption in which water permeation occurred through lipid-stabilized pores mediated by the hydrophilic residues located on the core β-sheets edges of the oligomers.
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Affiliation(s)
- Sonia Ciudad
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Eduard Puig
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franqués 1, 08028, Barcelona, Spain
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR7178, IPHC, Strasbourg, France
| | - Moeen Meigooni
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andres S Arango
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jimmy Do
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maxim Mayzel
- Swedish NMR Centre, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
| | - Mariam Bayoumi
- Biochemistry, Molecular and Structural Biology Section, University of Leuven, Celestijnenlaan 200G, 3001, Leuven, Belgium
| | - Stéphane Chaignepain
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR7178, IPHC, Strasbourg, France
| | - Vladislav Orekhov
- Swedish NMR Centre, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France
| | - Natàlia Carulla
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.
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10
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N'Guessan K, Grzywa R, Seren S, Gabant G, Juliano MA, Moniatte M, van Dorsselaer A, Bieth JG, Kellenberger C, Gauthier F, Wysocka M, Lesner A, Sienczyk M, Cadene M, Korkmaz B. Human proteinase 3 resistance to inhibition extends to alpha-2 macroglobulin. FEBS J 2020; 287:4068-4081. [PMID: 31995266 DOI: 10.1111/febs.15229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 11/29/2022]
Abstract
Polymorphonuclear neutrophils contain at least four serine endopeptidases, namely neutrophil elastase (NE), proteinase 3 (PR3), cathepsin G (CatG), and NSP4, which contribute to the regulation of infection and of inflammatory processes. In physiological conditions, endogenous inhibitors including α2-macroglobulin (α2-M), serpins [α1-proteinase inhibitor (α1-PI)], monocyte neutrophil elastase inhibitor (MNEI), α1-antichymotrypsin, and locally produced chelonianins (elafin, SLPI) control excessive proteolytic activity of neutrophilic serine proteinases. In contrast to human NE (hNE), hPR3 is weakly inhibited by α1-PI and MNEI but not by SLPI. α2-M is a large spectrum inhibitor that traps a variety of proteinases in response to cleavage(s) in its bait region. We report here that α2-M was more rapidly processed by hNE than hPR3 or hCatG. This was confirmed by the observation that the association between α2-M and hPR3 is governed by a kass in the ≤ 105 m-1 ·s-1 range. Since α2-M-trapped proteinases retain peptidase activity, we first predicted the putative cleavage sites within the α2-M bait region (residues 690-728) using kinetic and molecular modeling approaches. We then identified by mass spectrum analysis the cleavage sites of hPR3 in a synthetic peptide spanning the 39-residue bait region of α2-M (39pep-α2-M). Since the 39pep-α2-M peptide and the corresponding bait area in the whole protein do not contain sequences with a high probability of specific cleavage by hPR3 and were indeed only slowly cleaved by hPR3, it can be concluded that α2-M is a poor inhibitor of hPR3. The resistance of hPR3 to inhibition by endogenous inhibitors explains at least in part its role in tissue injury during chronic inflammatory diseases and its well-recognized function of major target autoantigen in granulomatosis with polyangiitis.
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Affiliation(s)
- Koffi N'Guessan
- INSERM UMR-1100, CEPR "Centre d'Etude des Pathologies Respiratoires", Tours, France.,Université de Tours, France
| | - Renata Grzywa
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wroclaw University of Science and Technology, Poland
| | - Seda Seren
- INSERM UMR-1100, CEPR "Centre d'Etude des Pathologies Respiratoires", Tours, France.,Université de Tours, France
| | - Guillaume Gabant
- Centre de Biophysique Moléculaire, UPR4301, CNRS, Affiliated with Université d'Orléans, Orléans, France
| | - Maria A Juliano
- Departamento de Biofísica, Escola Paulista Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marc Moniatte
- Proteomics Core Facility, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alain van Dorsselaer
- LSMBO, CNRS UMR-7178 (CNRS-UdS), ECPM, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France
| | - Joseph G Bieth
- Laboratoire d'Enzymologie, INSERM U392, Université Louis Pasteur de Strasbourg, Illkirch, France
| | | | - Francis Gauthier
- INSERM UMR-1100, CEPR "Centre d'Etude des Pathologies Respiratoires", Tours, France.,Université de Tours, France
| | | | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Marcin Sienczyk
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wroclaw University of Science and Technology, Poland
| | - Martine Cadene
- Centre de Biophysique Moléculaire, UPR4301, CNRS, Affiliated with Université d'Orléans, Orléans, France
| | - Brice Korkmaz
- INSERM UMR-1100, CEPR "Centre d'Etude des Pathologies Respiratoires", Tours, France.,Université de Tours, France
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11
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Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
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12
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Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry. Nat Protoc 2017; 12:2391-2410. [DOI: 10.1038/nprot.2017.100] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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13
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Orlova N, Gerding M, Ivashkiv O, Olinares PDB, Chait BT, Waldor MK, Jeruzalmi D. The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators. Nucleic Acids Res 2017; 45:3724-3737. [PMID: 28031373 PMCID: PMC5397143 DOI: 10.1093/nar/gkw1288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/18/2016] [Indexed: 01/23/2023] Open
Abstract
The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a head-to-head dimeric configuration that likely reflects the arrangement in solution. Therefore, major structural reorganization likely accompanies complex formation on the head-to-tail array of binding sites in oriCII. Our findings support the hypothesis that the second Vibrionaceae chromosome arose from an ancestral plasmid, and that RctB may have evolved additional regulatory features.
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Affiliation(s)
- Natalia Orlova
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| | - Matthew Gerding
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Olha Ivashkiv
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
| | - Paul Dominic B Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, NY 10021, USA
| | - Brian T Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, NY 10021, USA
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA.,Ph.D. Program in Biology, The Graduate Center of the City University of New York, NY 10016, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, NY 10016, USA
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14
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Rouck J, Krapf J, Roy J, Huff H, Das A. Recent advances in nanodisc technology for membrane protein studies (2012-2017). FEBS Lett 2017; 591:2057-2088. [PMID: 28581067 PMCID: PMC5751705 DOI: 10.1002/1873-3468.12706] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Historically, the main barrier to membrane protein investigations has been the tendency of membrane proteins to aggregate (due to their hydrophobic nature), in aqueous solution as well as on surfaces. The introduction of biomembrane mimetics has since stimulated momentum in the field. One such mimetic, the nanodisc (ND) system, has proved to be an exceptional system for solubilizing membrane proteins. Herein, we critically evaluate the advantages and imperfections of employing nanodiscs in biophysical and biochemical studies. Specifically, we examine the techniques that have been modified to study membrane proteins in nanodiscs. Techniques discussed here include fluorescence microscopy, solution-state/solid-state nuclear magnetic resonance, electron microscopy, small-angle X-ray scattering, and several mass spectroscopy methods. Newer techniques such as SPR, charge-sensitive optical detection, and scintillation proximity assays are also reviewed. Lastly, we cover how nanodiscs are advancing nanotechnology through nanoplasmonic biosensing, lipoprotein-nanoplatelets, and sortase-mediated labeling of nanodiscs.
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Affiliation(s)
- John Rouck
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - John Krapf
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Jahnabi Roy
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Hannah Huff
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Beckman Institute for Advanced Science, Division of Nutritional Sciences, Neuroscience Program and Department of Bioengineering, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
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15
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Systematic assessment of surfactants for matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Chim Acta 2017; 963:76-82. [DOI: 10.1016/j.aca.2017.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
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16
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Avila CC, Almeida FG, Palmisano G. Direct identification of trypanosomatids by matrix-assisted laser desorption ionization-time of flight mass spectrometry (DIT MALDI-TOF MS). JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:549-557. [PMID: 27659938 DOI: 10.1002/jms.3763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/21/2016] [Accepted: 03/07/2016] [Indexed: 06/06/2023]
Abstract
Accurate and rapid determination of trypanosomatids is essential in epidemiological surveillance and therapeutic studies. Matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) has been shown to be a useful and powerful technique to identify bacteria, fungi, metazoa and human intact cells with applications in clinical settings. Here, we developed and optimized a MALDI-TOF MS method to profile trypanosomatids. trypanosomatid cells were deposited on a MALDI target plate followed by addition of matrix solution. The plate was then subjected to MALDI-TOF MS measurement to create reference mass spectra library and unknown samples were identified by pattern matching using the BioTyper software tool. Several m/z peaks reproducibly and uniquely identified trypanosomatids species showing the potentials of direct identification of trypanosomatids by MALDI-TOF MS. Moreover, this method discriminated different life stages of Trypanosoma cruzi, epimastigote and bloodstream trypomastigote and Trypanosoma brucei, procyclic and bloodstream. T. cruzi Discrete Typing Units (DTUs) were also discriminated in three clades. However, it was not possible to achieve enough resolution and software-assisted identification at the strain level. Overall, this study shows the importance of MALDI-TOF MS for the direct identification of trypanosomatids and opens new avenues for mass spectrometry-based detection of parasites in biofluids. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- C C Avila
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - F G Almeida
- Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - G Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
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17
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Gabant G, Boyer A, Cadene M. SSPaQ: A Subtractive Segmentation Approach for the Exhaustive Parallel Quantification of the Extent of Protein Modification at Every Possible Site. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1328-1343. [PMID: 27245456 DOI: 10.1007/s13361-016-1416-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/19/2016] [Accepted: 04/24/2016] [Indexed: 06/05/2023]
Abstract
Protein modifications, whether chemically induced or post-translational (PTMs), play an essential role for the biological activity of proteins. Understanding biological processes and alterations thereof will rely on the quantification of these modifications on individual residues. Here we present SSPaQ, a subtractive method for the parallel quantification of the extent of modification at each possible site of a protein. The method combines uniform isotopic labeling and proteolysis with MS, followed by a segmentation approach, a powerful tool to refine the quantification of the degree of modification of a peptide to a segment containing a single modifiable amino acid. The strength of this strategy resides in: (1) quantification of all modifiable sites in a protein without prior knowledge of the type(s) of modified residues; (2) insensitivity to changes in the solubility and ionization efficiency of peptides upon modification; and (3) detection of missed cleavages caused by the modification for mitigation. The SSPaQ method was applied to quantify modifications resulting from the interaction of human phosphatidyl ethanolamine binding protein 1 (hPEBP1), a metastasis suppressor gene product, with locostatin, a covalent ligand and antimigratory compound with demonstrated activity towards hPEBP1. Locostatin is shown to react with several residues of the protein. SSPaQ can more generally be applied to induced modification in the context of drugs that covalently bind their target protein. With an alternate front-end protocol, it could also be applied to the quantification of protein PTMs, provided a removal tool is available for that PTM. Graphical Abstract ᅟ.
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Affiliation(s)
- Guillaume Gabant
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France
- University of Orléans, Orléans, France
| | - Alain Boyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Martine Cadene
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France.
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18
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McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M. The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport. Structure 2016; 24:956-64. [PMID: 27161976 PMCID: PMC4899283 DOI: 10.1016/j.str.2016.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/09/2016] [Accepted: 04/14/2016] [Indexed: 01/07/2023]
Abstract
The phosphoenolpyruvate:carbohydrate phosphotransferase systems are found in bacteria, where they play central roles in sugar uptake and regulation of cellular uptake processes. Little is known about how the membrane-embedded components (EIICs) selectively mediate the passage of carbohydrates across the membrane. Here we report the functional characterization and 2.55-Å resolution structure of a maltose transporter, bcMalT, belonging to the glucose superfamily of EIIC transporters. bcMalT crystallized in an outward-facing occluded conformation, in contrast to the structure of another glucose superfamily EIIC, bcChbC, which crystallized in an inward-facing occluded conformation. The structures differ in the position of a structurally conserved substrate-binding domain that is suggested to play a central role in sugar transport. In addition, molecular dynamics simulations suggest a potential pathway for substrate entry from the periplasm into the bcMalT substrate-binding site. These results provide a mechanistic framework for understanding substrate recognition and translocation for the glucose superfamily EIIC transporters.
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Affiliation(s)
- Jason G. McCoy
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Zhenning Ren
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Vitali Stanevich
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, KS 66047
| | - Sharmistha Mitra
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Elena J. Levin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Sebastien Poget
- Department of Chemistry, College of Staten Island, Staten Island, NY 10314
| | - Matthias Quick
- Department of Psychiatry and Center for Molecular Recognition, Columbia University and New York State Psychiatric Institute, Division of Molecular Therapeutics, New York, New York 10032
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, KS 66047
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
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19
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Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:952-65. [PMID: 27080007 PMCID: PMC5125627 DOI: 10.1007/s13361-016-1385-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 05/24/2023]
Abstract
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ.
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Affiliation(s)
- Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA.
| | - Martine Cadene
- CBM, CNRS UPR4301, Rue Charles Sadron, CS 80054, 45071, Orleans Cedex 2, France
| | - Paul Dominic Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
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20
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Chen X, Liu Y, Xu Q, Zhu J, Poget SF, Lyons AM. High-Precision Dispensing of Nanoliter Biofluids on Glass Pedestal Arrays for Ultrasensitive Biomolecule Detection. ACS APPLIED MATERIALS & INTERFACES 2016; 8:10788-10799. [PMID: 27070413 DOI: 10.1021/acsami.6b02487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Precise dispensing of nanoliter droplets is necessary for the development of sensitive and accurate assays, especially when the availability of the source solution is limited. Conventional approaches are limited by imprecise positioning, large shear forces, surface tension effects, and high costs. To address the need for precise and economical dispensing of nanoliter volumes, we developed a new approach where the dispensed volume is dependent on the size and shape of defined surface features, thus freeing the dispensing process from pumps and fine-gauge needles requiring accurate positioning. The surface we fabricated, called a nanoliter droplet virtual well microplate (nVWP), achieves high-precision dispensing (better than ±0.5 nL or ±1.6% at 32 nL) of 20-40 nL droplets using a small source drop (3-10 μL) on isolated hydrophilic glass pedestals (500 μm on a side) bonded to arrays of polydimethylsiloxane conical posts. The sharp 90° edge of the glass pedestal pins the solid-liquid-vapor triple contact line (TCL), averting the wetting of the glass sidewalls while the fluid is prevented from receding from the edge. This edge creates a sufficiently large energy barrier such that microliter water droplets can be poised on the glass pedestals, exhibiting contact angles greater >150°. This approach relieves the stringent mechanical alignment tolerances required for conventional dispensing techniques, shifting the control of dispensed volume to the area circumscribed by the glass edge. The effects of glass surface chemistry and dispense velocity on droplet volume were studied using optical microscopy and high-speed video. Functionalization of the glass pedestal surface enabled the selective adsorption of specific peptides and proteins from synthetic and natural biomolecule mixtures, such as venom. We further demonstrate how the nVWP dispensing platform can be used for a variety of assays, including sensitive detection of proteins and peptides by fluorescence microscopy or MALDI-TOF.
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Affiliation(s)
- Xiaoxiao Chen
- ARL Designs LLC, 215 West 125th Street, New York, New York 10027, United States
| | - Yang Liu
- Department of Chemistry, College of Staten Island, City University of New York , 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York , 365 Fifth Avenue, New York, New York 10314, United States
| | - QianFeng Xu
- ARL Designs LLC, 215 West 125th Street, New York, New York 10027, United States
- Department of Chemistry, College of Staten Island, City University of New York , 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Jing Zhu
- Department of Chemistry, College of Staten Island, City University of New York , 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Sébastien F Poget
- Department of Chemistry, College of Staten Island, City University of New York , 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York , 365 Fifth Avenue, New York, New York 10314, United States
| | - Alan M Lyons
- ARL Designs LLC, 215 West 125th Street, New York, New York 10027, United States
- Department of Chemistry, College of Staten Island, City University of New York , 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York , 365 Fifth Avenue, New York, New York 10314, United States
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21
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Lamort AS, Gravier R, Laffitte A, Juliano L, Zani ML, Moreau T. New insights into the substrate specificity of macrophage elastase MMP-12. Biol Chem 2016; 397:469-84. [DOI: 10.1515/hsz-2015-0254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/04/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Macrophage elastase, or MMP-12, is mainly produced by alveolar macrophages and is believed to play a major role in the development of chronic obstructive pulmonary disease (COPD). The catalytic domain of MMP-12 is unique among MMPs in that it is very highly active on numerous substrates including elastin. However, measuring MMP-12 activity in biological fluids has been hampered by the lack of highly selective substrates. We therefore synthesized four series of fluorogenic peptide substrates based on the sequences of MMP-12 cleavage sites in its known substrates. Human MMP-12 efficiently cleaved peptide substrates containing a Pro at P3 in the sequence Pro-X-X↓Leu but lacked selectivity towards these substrates compared to other MMPs, including MMP-2, MMP-7, MMP-9 and MMP-13. On the contrary, the substrate Abz-RNALAVERTAS-EDDnp derived from the CXCR5 chemokine was the most selective substrate for MMP-12 ever reported. All substrates were cleaved more efficiently by full-length MMP-12 than by its catalytic domain alone, indicating that the C-terminal hemopexin domain influences substrate binding and/or catalysis. Docking experiments revealed unexpected interactions between the peptide substrate Abz-RNALAVERTAS-EDDn and MMP-12 residues. Most of our substrates were poorly cleaved by murine MMP-12 suggesting that human and murine MMP-12 have different substrate specificities despite their structural similarity.
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22
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Rivera-Torres IO, Jin TB, Cadene M, Chait BT, Poget SF. Discovery and characterisation of a novel toxin from Dendroaspis angusticeps, named Tx7335, that activates the potassium channel KcsA. Sci Rep 2016; 6:23904. [PMID: 27044983 PMCID: PMC4820689 DOI: 10.1038/srep23904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/16/2016] [Indexed: 02/07/2023] Open
Abstract
Due to their central role in essential physiological processes, potassium channels are common targets for animal toxins. These toxins in turn are of great value as tools for studying channel function and as lead compounds for drug development. Here, we used a direct toxin pull-down assay with immobilised KcsA potassium channel to isolate a novel KcsA-binding toxin (called Tx7335) from eastern green mamba snake (Dendroaspis angusticeps) venom. Sequencing of the toxin by Edman degradation and mass spectrometry revealed a 63 amino acid residue peptide with 4 disulphide bonds that belongs to the three-finger toxin family, but with a unique modification of its disulphide-bridge scaffold. The toxin induces a dose-dependent increase in both open probabilities and mean open times on KcsA in artificial bilayers. Thus, it unexpectedly behaves as a channel activator rather than an inhibitor. A charybdotoxin-sensitive mutant of KcsA exhibits similar susceptibility to Tx7335 as wild-type, indicating that the binding site for Tx7335 is distinct from that of canonical pore-blocker toxins. Based on the extracellular location of the toxin binding site (far away from the intracellular pH gate), we propose that Tx7335 increases potassium flow through KcsA by allosterically reducing inactivation of the channel.
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Affiliation(s)
- Iván O. Rivera-Torres
- LaGuardia Community College, City University of New York, Long Island City, NY 11101, USA
| | - Tony B. Jin
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | | | | | - Sébastien F. Poget
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
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23
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Seibert C, Sanfiz A, Sakmar TP, Veldkamp CT. Preparation and Analysis of N-Terminal Chemokine Receptor Sulfopeptides Using Tyrosylprotein Sulfotransferase Enzymes. Methods Enzymol 2015; 570:357-88. [PMID: 26921955 DOI: 10.1016/bs.mie.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In most chemokine receptors, one or multiple tyrosine residues have been identified within the receptor N-terminal domain that are, at least partially, modified by posttranslational tyrosine sulfation. For example, tyrosine sulfation has been demonstrated for Tyr-3, -10, -14, and -15 of CCR5, for Tyr-3, -14, and -15 of CCR8, and for Tyr-7, -12, and -21 of CXCR4. While there is evidence for several chemokine receptors that tyrosine sulfation is required for optimal interaction with the chemokine ligands, the precise role of tyrosine sulfation for chemokine receptor function remains unclear. Furthermore, the function of the chemokine receptor N-terminal domain in chemokine binding and receptor activation is also not well understood. Sulfotyrosine peptides corresponding to the chemokine receptor N-termini are valuable tools to address these important questions both in structural and functional studies. However, due to the lability of the sulfotyrosine modification, these peptides are difficult to obtain using standard peptide chemistry methods. In this chapter, we provide methods to prepare sulfotyrosine peptides by enzymatic in vitro sulfation of peptides using purified recombinant tyrosylprotein sulfotransferase (TPST) enzymes. In addition, we also discuss alternative approaches for the generation of sulfotyrosine peptides and methods for sulfopeptide analysis.
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Affiliation(s)
- Christoph Seibert
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Anthony Sanfiz
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Christopher T Veldkamp
- Department of Chemistry, University of Wisconsin-Whitewater, Whitewater, Wisconsin, USA.
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24
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Hubin EA, Tabib-Salazar A, Humphrey LJ, Flack JE, Olinares PDB, Darst SA, Campbell EA, Paget MS. Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA. Proc Natl Acad Sci U S A 2015; 112:7171-6. [PMID: 26040003 PMCID: PMC4466734 DOI: 10.1073/pnas.1504942112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential in Mycobacterium tuberculosis (Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that the Mtb RbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of the Mtb RbpA-SID in complex with domain 2 of the housekeeping σ-factor, σ(A). The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σ(A) as well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator.
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Affiliation(s)
- Elizabeth A Hubin
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Aline Tabib-Salazar
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Laurence J Humphrey
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Joshua E Flack
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065;
| | - Mark S Paget
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom;
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25
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Wei JP, Qiao B, Song WJ, Chen T, li F, Li BZ, Wang J, Han Y, Huang YF, Zhou ZJ. Synthesis of magnetic framework composites for the discrimination of Escherichia coli at the strain level. Anal Chim Acta 2015; 868:36-44. [PMID: 25813232 DOI: 10.1016/j.aca.2015.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 11/24/2022]
Abstract
Rapid and efficient characterization and identification of pathogens at the strain level is of key importance for epidemiologic investigations, which still remains a challenge. In this work, solvothermically Fe3O4-COOH@MIL-101 composites were fabricated by in situ crystallization approach. The composites combine the excellent properties of both chromium (III) terephthalate (MIL-101) and carboxylic-functionalized magnetite (Fe3O4-COOH) particles and possess the efficient peptides/proteins enrichment properties and magnetic responsiveness. Fe3O4-COOH@MIL-101 composites as magnetic solid phase extraction materials were used to increase the discriminatory power of MALDI-TOF MS profiles. BSA tryptic peptides at a low concentration of 0.25 fmol μL(-1) could be detected by MALDI-TOF MS. In addition, Fe3O4-COOH@MIL-101 composites were successfully applied in the selective enrichment of the protein biomarkers from bacterial cell lysates and discrimination of Escherichia coli at the strain level. This work provides the possibility for wide applications of magnetic MOFs to discriminate pathogens below the species level.
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Affiliation(s)
- Ji-Ping Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wen-Jun Song
- Tianjin Key Laboratory of Food Biotechnology, Tianjin University of Commerce, Tianjin 300134, China
| | - Tao Chen
- Tianjin Source Environment Technology & Engineering Co., Ltd., Tianjin 300190, China
| | - Fei li
- Tianjin Key Laboratory of Food Biotechnology, Tianjin University of Commerce, Tianjin 300134, China
| | - Bo-Zhi Li
- Tianjin Source Environment Technology & Engineering Co., Ltd., Tianjin 300190, China
| | - Jin Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ye Han
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan-Feng Huang
- State Key Laboratory of Hollow Fiber Membrane Material and Membrane Process, College of Environmental and Chemical Engineering Sciences, Tianjin Polytechnic University, 399 West Binshui Road, Tianjin 300387, China; State Key Laboratory of Medicinal Chemical Biology (Nankai University), Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Zhi-Jiang Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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26
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A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
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27
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Ragni R, Omar OH, Tangorra RR, Milano F, Vona D, Operamolla A, La Gatta S, Agostiano A, Trotta M, Farinola GM. Bursting photosynthesis: designing ad-hoc fluorophores to complement the light harvesting capability of the photosynthetic reaction center. ACTA ACUST UNITED AC 2014. [DOI: 10.1557/opl.2014.617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTThe covalent functionalization of photosynthetic proteins with properly tailored organic molecular antennas represents a powerful approach to build a new generation of hybrid systems capable of exploiting solar energy. In this paper the strategy for the synthesis of the tailored aryleneethynylene organic fluorophore (AE) properly designed to act as light harvesting antenna is presented along with its successful bioconjugation to the photosynthetic reaction center RC from the bacterium Rhodobacter sphaeroides .
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28
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Dutta PK, Lin S, Loskutov A, Levenberg S, Jun D, Saer R, Beatty JT, Liu Y, Yan H, Woodbury NW. Reengineering the Optical Absorption Cross-Section of Photosynthetic Reaction Centers. J Am Chem Soc 2014; 136:4599-604. [DOI: 10.1021/ja411843k] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | | | | | - Daniel Jun
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Rafael Saer
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
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29
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Abstract
Most biophysical experiments require protein samples of high quality and accurately determined concentration. This chapter attempts to compile basic information on the most common methods to assess the purity, dispersity, and stability of protein samples. It also reminds of methods to measure protein concentration and of their limits. The idea is to make aware and remind of the range of methods available and of commonly overlooked pitfalls. The aim is to enable experimenters to fully characterize their preparations of soluble or membrane proteins and gain reliable and reproducible results from their experimental work.
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Affiliation(s)
- Tina Daviter
- ISMB Biophysics Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
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30
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Lajoie L, Congy-Jolivet N, Bolzec A, Gouilleux-Gruart V, Sicard E, Sung HC, Peiretti F, Moreau T, Vié H, Clémenceau B, Thibault G. ADAM17-mediated shedding of FcγRIIIA on human NK cells: identification of the cleavage site and relationship with activation. THE JOURNAL OF IMMUNOLOGY 2013; 192:741-51. [PMID: 24337742 DOI: 10.4049/jimmunol.1301024] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
FcγRIIIA/CD16A, the low-affinity receptor for the IgG Fc portion expressed on human CD56(dim) NK cells and involved in Ab-dependent cell cytotoxicity, is shed upon NK cell activation. We found that recombinant a disintegrin and metalloprotease (ADAM) 17 cleaved the ectodomain of FcγRIIIA/CD16A and a peptide for which the sequence encompasses aa 191-201 of the FcγRIIIA/CD16A stalk region but not ADAM10. MALDI-TOF analysis revealed that the peptide was cleaved between Ala(195) and Val(196) (i.e., 1 aa upstream of the expected position). This location of the cleavage site was confirmed by the finding that ADAM17 failed to cleave a peptide in which Ala and Val were reversed. ADAM17 was found to be expressed on NK cells, and stimulation with PMA or N-ethyl-maleimide resulted in the shedding of FcγRIIIA/CD16A and CD62L, a specific substrate of ADAM17. Selective inhibition of ADAM17 prevented the shedding of both molecules. Moreover, the shedding of FcγRIIIA/CD16A was strongly correlated with degranulation when a wide range of CD56(dim) NK cell activating receptors were stimulated, whereas both ADAM17-dependent shedding and internalization were involved in FcγRIIIA/CD16A downmodulation when the latter was engaged. Finally, the shedding of FcγRIIIA/CD16A was restricted to activated cells, suggesting that ADAM17 acts mainly, if not exclusively, in cis. Taken together, our results demonstrated for the first time, to our knowledge, at the molecular level that ADAM17 cleaves the stalk region of FcγRIIIA/CD16A and identified its cleavage site. The shedding of FcγRIIIA/CD16A was at least partially ADAM17 dependent, and it may be considered as a marker of FcγRIIIA/CD16A-independent NK cell activation highly correlated with degranulation.
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Affiliation(s)
- Laurie Lajoie
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 7292, Génétique, Immunothérapie, Chimie et Cancer, Université François-Rabelais de Tours, 37032 Tours Cedex, France
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31
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Kryza T, Achard C, Parent C, Marchand-Adam S, Guillon-Munos A, Iochmann S, Korkmaz B, Respaud R, Courty Y, Heuzé-Vourc'h N. Angiogenesis stimulated by human kallikrein-related peptidase 12 acting via a platelet-derived growth factor B-dependent paracrine pathway. FASEB J 2013; 28:740-51. [PMID: 24225148 DOI: 10.1096/fj.13-237503] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
KLK12, a kallikrein peptidase, is thought to take part in the control of angiogenesis. Our analysis of the secretome of endothelial cells (ECs) that had been treated with KLK12 showed that KLK12 converts the extracellular matrix- or membrane-bound precursor of platelet-derived growth factor B (PDGF-B) into a soluble form. Both PDGF-B and vascular endothelial growth factor A (VEGF-A) take part in the induction of angiogenesis by KLK12 in a coculture model of angiogenesis that mimics endothelial tubule formation. We used a cellular approach to analyze the interplay between KLK12, PDGF-B, and VEGF-A and showed that release of PDGF-B by KLK12 leads to the fibroblast-mediated secretion of VEGF-A. This then stimulates EC differentiation and the formation of capillary tube-like structures. Thus, KLK12 favors the interaction of ECs and stromal cells. The released PDGF-B acts as a paracrine factor that modulates VEGF-A secretion by stromal cells, which ultimately leads to angiogenesis. Moreover, the genes encoding KLK12 and PDGFB are both expressed in ECs and up-regulated in tumor cells kept under hypoxic conditions, which is consistent with the physiological involvement of KLK12 in PDGF-B maturation.
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Affiliation(s)
- Thomas Kryza
- 2CEPR INSERM U1100/EA 6305, Faculté de Médecine, 10 Blvd. Tonnellé, F-37032 Tours cedex, France.
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32
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Signor L, Boeri Erba E. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa. J Vis Exp 2013. [PMID: 24056304 PMCID: PMC3857990 DOI: 10.3791/50635] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g.13C labelling). Electrospray ionisation (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra. Here we present an accessible approach for analysing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and α-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analysing intact proteins larger than 100 kDa by MALDI-MS.
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Affiliation(s)
- Luca Signor
- Institute of Structural Biology "J.P. Ebel", UMR5075, Commissariat à L'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université J. Fourier
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33
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Wilson C, Ramai D, Serjanov D, Lama N, Levinger L, Chang EJ. Tethered domains and flexible regions in tRNase Z(L), the long form of tRNase Z. PLoS One 2013; 8:e66942. [PMID: 23874404 PMCID: PMC3714273 DOI: 10.1371/journal.pone.0066942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022] Open
Abstract
tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase ZL structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase ZL performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase ZL function.
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Affiliation(s)
- Christopher Wilson
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Daryl Ramai
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Dmitri Serjanov
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Neema Lama
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Louis Levinger
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Emmanuel J. Chang
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
- * E-mail:
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34
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Dana D, Davalos AR, De S, Rathod P, Gamage RK, Huestis J, Afzal N, Zavlanov Y, Paroly SS, Rotenberg SA, Subramaniam G, Mark KJ, Chang EJ, Kumar S. Development of cell-active non-peptidyl inhibitors of cysteine cathepsins. Bioorg Med Chem 2013; 21:2975-87. [PMID: 23623677 DOI: 10.1016/j.bmc.2013.03.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/15/2013] [Accepted: 03/23/2013] [Indexed: 11/26/2022]
Abstract
Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. However, small molecule inhibitors that are cell-permeable and non-peptidyl in nature are scarcely available. Herein the synthesis and development of sulfonyloxiranes as covalent inhibitors of cysteine cathepsins are reported. From a library of compounds, compound 5 is identified as a selective inhibitor of cysteine cathepsins. Live cell imaging and immunocytochemistry of metastatic human breast carcinoma MDA-MB-231 cells document the efficacy of compound 5 in inhibiting cysteine cathepsin activity in living cells. A cell-motility assay demonstrates that compound 5 is effective in mitigating the cell-migratory potential of highly metastatic breast carcinoma MDA-MB-231 cells.
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Affiliation(s)
- Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of The City University of New York, Queens, NY 11367-1597, USA
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35
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Schey KL, Grey AC, Nicklay JJ. Mass spectrometry of membrane proteins: a focus on aquaporins. Biochemistry 2013; 52:3807-17. [PMID: 23394619 DOI: 10.1021/bi301604j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Membrane proteins are abundant, critically important biomolecules that conduct essential functions in all cells and are the targets of a significant number of therapeutic drugs. However, the analysis of their expression, modification, protein-protein interactions, and structure by mass spectrometry has lagged behind similar studies of soluble proteins. Here we review the limitations to analysis of integral membrane and membrane-associated proteins and highlight advances in sample preparation and mass spectrometry methods that have led to the successful analysis of this protein class. Advances in the analysis of membrane protein posttranslational modification, protein-protein interaction, protein structure, and tissue distributions by imaging mass spectrometry are discussed. Furthermore, we focus our discussion on the application of mass spectrometry for the analysis of aquaporins as a prototypical integral membrane protein and how advances in analytical methods have revealed new biological insights into the structure and function of this family of proteins.
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Affiliation(s)
- Kevin L Schey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.
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36
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Chen F, Gerber S, Heuser K, Korkhov VM, Lizak C, Mireku S, Locher KP, Zenobi R. High-mass matrix-assisted laser desorption ionization-mass spectrometry of integral membrane proteins and their complexes. Anal Chem 2013; 85:3483-8. [PMID: 23463947 DOI: 10.1021/ac4000943] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Analyzing purified membrane proteins and membrane protein complexes by mass spectrometry has been notoriously challenging and required highly specialized buffer conditions, sample preparation methods, and apparatus. Here we show that a standard matrix-assisted laser desorption/ionization (MALDI) protocol, if used in combination with a high-mass detector, allows straightforward mass spectrometric measurements of integral membrane proteins and their complexes, directly following purification in detergent solution. Molecular weights can be determined precisely (mass error ≤ 0.1%) such that high-mass MALDI-MS was able to identify the site for N-linked glycosylation of the eukaryotic multidrug ABC transporter Cdr1p without special purification steps, which is impossible by any other current approach. After chemical cross-linking with glutaraldehyde in the presence of detergent micelles, the subunit stoichiometries of a series of integral membrane protein complexes, including the homomeric PglK and the heteromeric BtuCD as well as BtuCDF, were unambiguously resolved. This thus adds a valuable tool for biophysical characterization of integral membrane proteins.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
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37
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Kandiah M, Urban PL. Advances in ultrasensitive mass spectrometry of organic molecules. Chem Soc Rev 2013; 42:5299-322. [DOI: 10.1039/c3cs35389c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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38
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Bechara C, Bolbach G, Bazzaco P, Sharma KS, Durand G, Popot JL, Zito F, Sagan S. MALDI-TOF mass spectrometry analysis of amphipol-trapped membrane proteins. Anal Chem 2012; 84:6128-35. [PMID: 22703540 DOI: 10.1021/ac301035r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphipols (APols) are amphipathic polymers with the ability to substitute detergents to keep membrane proteins (MPs) soluble and functional in aqueous solutions. APols also protect MPs against denaturation. Here, we have examined the ability of APol-trapped MPs to be analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For that purpose, we have used ionic and nonionic APols and as model proteins (i) the transmembrane domain of Escherichia coli outer membrane protein A, a β-barrel, eubacterial MP, (ii) Halobacterium salinarum bacteriorhodopsin, an α-helical archaebacterial MP with a single cofactor, and (iii, iv) two eukaryotic MP complexes comprising multiple subunits and many cofactors, cytochrome b(6)f from the chloroplast of the green alga Chlamydomonas reinhardtii and cytochrome bc(1) from beef heart mitochondria. We show that these MP/APol complexes can be readily analyzed by MALDI-TOF-MS; most of the subunits and some lipids and cofactors were identified. APols alone, even ionic ones, had no deleterious effects on MS signals and were not detected in mass spectra. Thus, the combination of MP stabilization by APols and MS analyses provides an interesting new approach to investigating supramolecular interactions in biological membranes.
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Affiliation(s)
- Chérine Bechara
- Université Pierre et Marie Curie (UPMC Université Paris 06), Laboratoire des BioMolécules (LBM), Paris, France
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39
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Dana D, Das TK, Kumar I, Davalos AR, Mark KJ, Ramai D, Chang EJ, Talele TT, Kumar S. Design, synthesis, and evaluation of 2-(arylsulfonyl)oxiranes as cell-permeable covalent inhibitors of protein tyrosine phosphatases. Chem Biol Drug Des 2012; 80:489-99. [PMID: 22726577 DOI: 10.1111/j.1747-0285.2012.01437.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potential covalent inhibitors of protein tyrosine phosphatases. A detailed kinetic analysis of inactivation by these covalent inhibitors reveals that this class of compounds inhibits a panel of protein tyrosine phosphatases in a time- and dose-dependent manner, consistent with the covalent modification of the enzyme active site. An inactivation experiment in the presence of sodium arsenate, a known competitive inhibitor of protein tyrosine phosphatase, indicated that these inhibitors were active site bound. This finding is consistent with the mass spectrometric analysis of the covalently modified protein tyrosine phosphatase enzyme. Additional experiments indicated that these compounds remained inert toward other classes of arylphosphate-hydrolyzing enzymes, and alkaline and acid phosphatases. Cell-based experiments with human A549 lung cancer cell lines indicated that 2-(phenylsulfonyl)oxirane (1) caused an increase in intracellular pTyr levels in a dose-dependent manner thereby suggesting its cell-permeable nature. Taken together, the newly identified 2-(arylsulfonyl)oxiranyl moiety could serve as a novel chemotype for the development of activity-based probes and therapeutic agents against protein tyrosine phosphatase superfamily of enzymes.
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Affiliation(s)
- Dibyendu Dana
- Department of Chemistry & Biochemistry, Queens College-CUNY, 65-30 Kissena Blvd., Flushing, NY 11367, USA
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40
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Structural, biochemical, and functional characterization of the cyclic nucleotide binding homology domain from the mouse EAG1 potassium channel. J Mol Biol 2012; 423:34-46. [PMID: 22732247 DOI: 10.1016/j.jmb.2012.06.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/14/2012] [Accepted: 06/16/2012] [Indexed: 11/21/2022]
Abstract
KCNH channels are voltage-gated potassium channels with important physiological functions. In these channels, a C-terminal cytoplasmic region, known as the cyclic nucleotide binding homology (CNB-homology) domain displays strong sequence similarity to cyclic nucleotide binding (CNB) domains. However, the isolated domain does not bind cyclic nucleotides. Here, we report the X-ray structure of the CNB-homology domain from the mouse EAG1 channel. Through comparison with the recently determined structure of the CNB-homology domain from the zebrafish ELK (eag-like K(+)) channel and the CNB domains from the MlotiK1 and HCN (hyperpolarization-activated cyclic nucleotide-gated) potassium channels, we establish the structural features of CNB-homology domains that explain the low affinity for cyclic nucleotides. Our structure establishes that the "self-liganded" conformation, where two residues of the C-terminus of the domain are bound in an equivalent position to cyclic nucleotides in CNB domains, is a conserved feature of CNB-homology domains. Importantly, we provide biochemical evidence that suggests that there is also an unliganded conformation where the C-terminus of the domain peels away from its bound position. A functional characterization of this unliganded conformation reveals a role of the CNB-homology domain in channel gating.
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41
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Gan J, Zhu J, Yan G, Liu Y, Yang P, Liu B. Periodic mesoporous organosilica as a multifunctional nanodevice for large-scale characterization of membrane proteins. Anal Chem 2012; 84:5809-15. [PMID: 22663254 DOI: 10.1021/ac301146a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile protocol has been developed for large-scale characterization of hydrophobic membrane proteins based on the periodic mesoporous organosilica (PMO) acting as both an extractor for hydrophobic substrate capture and a nanoreactor for efficient in situ digestion. With introduction of organic groups in the pore frameworks and the presence of hydrophilic silanol groups on the surface, PMO can be well-dispersed into not only an organic solution to concentrate the dissolved membrane proteins but also an aqueous solution containing enzymes for sequential rapid proteolysis in the nanopores. The unique amphiphilic property of PMO ensures a facile switch in different solutions to realize the processes of substrate dissolution, enrichment, and digestion effectively. Furthermore, this novel PMO-assisted protocol has been successfully applied for identification of complex membrane proteins extracted from mouse liver as proof of general applicability.
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Affiliation(s)
- Jinrui Gan
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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42
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Identification and characterization of a bacterial hydrosulphide ion channel. Nature 2012; 483:494-7. [PMID: 22407320 DOI: 10.1038/nature10881] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 01/20/2012] [Indexed: 01/06/2023]
Abstract
The hydrosulphide ion (HS(-)) and its undissociated form, hydrogen sulphide (H(2)S), which are believed to have been critical to the origin of life on Earth, remain important in physiology and cellular signalling. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H(2)S (ref. 4). The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD(+), which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite. Above a certain concentration threshold, both H(2)S and HS(-) inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase, necessitating a release mechanism for the export of this toxic metabolite from the cell. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS(-) channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate (FocA) and for nitrite (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS(-) ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel's crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.
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Derache C, Meudal H, Aucagne V, Mark KJ, Cadène M, Delmas AF, Lalmanach AC, Landon C. Initial insights into structure-activity relationships of avian defensins. J Biol Chem 2011; 287:7746-55. [PMID: 22205704 DOI: 10.1074/jbc.m111.312108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Numerous β-defensins have been identified in birds, and the potential use of these peptides as alternatives to antibiotics has been proposed, in particular to fight antibiotic-resistant and zoonotic bacterial species. Little is known about the mechanism of antibacterial activity of avian β-defensins, and this study was carried out to obtain initial insights into the involvement of structural features or specific residues in the antimicrobial activity of chicken AvBD2. Chicken AvBD2 and its enantiomeric counterpart were chemically synthesized. Peptide elongation and oxidative folding were both optimized. The similar antimicrobial activity measured for both L- and D-proteins clearly indicates that there is no chiral partner. Therefore, the bacterial membrane is in all likelihood the primary target. Moreover, this work indicates that the three-dimensional fold is required for an optimal antimicrobial activity, in particular for gram-positive bacterial strains. The three-dimensional NMR structure of chicken AvBD2 defensin displays the structural three-stranded antiparallel β-sheet characteristic of β-defensins. The surface of the molecule does not display any amphipathic character. In light of this new structure and of the king penguin AvBD103b defensin structure, the consensus sequence of the avian β-defensin family was analyzed. Well conserved residues were highlighted, and the potential strategic role of the lysine 31 residue of AvBD2 was emphasized. The synthetic AvBD2-K31A variant displayed substantial N-terminal structural modifications and a dramatic decrease in activity. Taken together, these results demonstrate the structural as well as the functional role of the critical lysine 31 residue in antimicrobial activity.
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Affiliation(s)
- Chrystelle Derache
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans, France
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Marty MT, Das A, Sligar SG. Ultra-thin layer MALDI mass spectrometry of membrane proteins in nanodiscs. Anal Bioanal Chem 2011; 402:721-9. [PMID: 22057720 DOI: 10.1007/s00216-011-5512-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 10/13/2011] [Accepted: 10/17/2011] [Indexed: 02/02/2023]
Abstract
Nanodiscs have become a leading technology to solubilize membrane proteins for biophysical, enzymatic, and structural investigations. Nanodiscs are nanoscale, discoidal lipid bilayers surrounded by an amphipathic membrane scaffold protein (MSP) belt. A variety of analytical tools has been applied to membrane proteins in nanodiscs, including several recent mass spectrometry studies. Mass spectrometry of full-length proteins is an important technique for analyzing protein modifications, for structural studies, and for identification of proteins present in binding assays. However, traditional matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry methods for analyzing full-length membrane proteins solubilized in nanodiscs are limited by strong signal from the MSP belt and weak signal from the membrane protein inside the nanodisc. Herein, we show that an optimized ultra-thin layer MALDI sample preparation technique dramatically enhances the membrane protein signal and nearly completely eliminates the MSP signal. First-shot MALDI and MALDI imaging are used to characterize the spots formed by the ultra-thin layer method. Furthermore, the membrane protein enhancement and MSP suppression are shown to be independent of the type of membrane protein and are applicable to mixtures of membrane proteins in nanodiscs.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Trimpin S, Ren Y, Wang B, Lietz CB, Richards AL, Marshall DD, Inutan ED. Extending the Laserspray Ionization Concept to Produce Highly Charged Ions at High Vacuum on a Time-of-Flight Mass Analyzer. Anal Chem 2011; 83:5469-75. [DOI: 10.1021/ac2007976] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Yue Ren
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Beixi Wang
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Christopher B. Lietz
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Alicia L. Richards
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Darrell D. Marshall
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Ellen D. Inutan
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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46
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The variable detergent sensitivity of proteases that are utilized for recombinant protein affinity tag removal. Protein Expr Purif 2011; 78:139-42. [PMID: 21539919 DOI: 10.1016/j.pep.2011.04.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/22/2011] [Accepted: 04/18/2011] [Indexed: 11/23/2022]
Abstract
Recombinant proteins typically include one or more affinity tags to facilitate purification and/or detection. Expression constructs with affinity tags often include an engineered protease site for tag removal. Like other enzymes, the activities of proteases can be affected by buffer conditions. The buffers used for integral membrane proteins contain detergents, which are required to maintain protein solubility. We examined the detergent sensitivity of six commonly-used proteases (enterokinase, factor Xa, human rhinovirus 3C protease, SUMOstar, tobacco etch virus protease, and thrombin) by use of a panel of 94 individual detergents. Thrombin activity was insensitive to the entire panel of detergents, thus suggesting it as the optimal choice for use with membrane proteins. Enterokinase and factor Xa were only affected by a small number of detergents, making them good choices as well.
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47
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Berridge G, Chalk R, D’Avanzo N, Dong L, Doyle D, Kim JI, Xia X, Burgess-Brown N, deRiso A, Carpenter EP, Gileadi O. High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins. Anal Biochem 2011; 410:272-80. [PMID: 21093405 PMCID: PMC3041925 DOI: 10.1016/j.ab.2010.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/04/2010] [Accepted: 11/05/2010] [Indexed: 11/17/2022]
Abstract
We have developed a method for intact mass analysis of detergent-solubilized and purified integral membrane proteins using liquid chromatography-mass spectrometry (LC-MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2-5 μg of protein. The method is also compatible with our standard LC-MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
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48
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Mainini V, Angel PM, Magni F, Caprioli RM. Detergent enhancement of on-tissue protein analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:199-204. [PMID: 21157864 PMCID: PMC4160130 DOI: 10.1002/rcm.4850] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Matrix-Assisted Laser Desorption/Ionization (MALDI) Imaging Mass Spectrometry (IMS) is a molecular technology that allows simultaneous investigation of the content and spatial distribution of molecules within tissue. In this work, we examine different classes of detergents, the anionic sodium dodecyl sulfate (SDS), the nonionic detergents Triton X-100, Tween 20 and Tween 80, and the zwitterionic 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) for use in MALDI IMS of analytes above m/z 4000. These detergents were found to be compatible with MALDI MS and did not cause signal suppression relative to non-detergent applications and did not produce interfering background signals. In general, these detergents enhanced signal acquisition within the mass range m/z 4-40 000. Adding detergents into the matrix was comparable with the separate application of detergent and matrix. Evaluation of spectra collected from organ-specific regions of a whole mouse pup section showed that different detergents perform optimally with different organs, indicating that detergent selection should be optimized on the specific tissue for maximum gain. These data show the utility of detergents towards enhancement of protein signals for on-tissue MALDI IMS analysis.
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Affiliation(s)
- Veronica Mainini
- Department of Experimental Medicine, University of Milano-Bicocca, via Cadore 48, 20052, Monza, Milano, Italy
| | - Peggi M. Angel
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, MRB III Suite 9160, Nashville, TN 37232, USA
| | - Fulvio Magni
- Department of Experimental Medicine, University of Milano-Bicocca, via Cadore 48, 20052, Monza, Milano, Italy
| | - Richard M. Caprioli
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, MRB III Suite 9160, Nashville, TN 37232, USA
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49
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Bigler Wang D, Sherman NE, Shannon JD, Leonhardt SA, Mayeenuddin LH, Yeager M, McIntire WE. Binding of β4γ5 by adenosine A1 and A2A receptors determined by stable isotope labeling with amino acids in cell culture and mass spectrometry. Biochemistry 2010; 50:207-20. [PMID: 21128647 DOI: 10.1021/bi101227y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Characterization of G protein βγ dimer isoform expression in different cellular contexts has been impeded by low levels of protein expression, broad isoform heterogeneity, and antibodies of limited specificity, sensitivity, or availability. As a new approach, we used quantitative mass spectrometry to characterize native βγ dimers associated with adenosine A(1):α(i1) and adenosine A(2A):α(S) receptor fusion proteins expressed in HEK-293 cells. Cells expressing A(1):α(i1) were cultured in media containing [(13)C(6)]Arg and [(13)C(6)]Lys and βγ labeled with heavy isotopes purified. Heavy βγ was combined with either recombinant βγ purified from Sf9 cells, βγ purified from the A(2A):α(S) expressed in HEK-293 cells cultured in standard media, or an enriched βγ fraction from HEK-293 cells. Samples were separated by SDS-PAGE, protein bands containing β and γ were excised, digested with trypsin, and separated by HPLC, and isotope ratios were analyzed by mass spectrometry. Three β isoforms, β(1), β(2), and β(4), and seven γ isoforms, γ(2), γ(4), γ(5), γ(7), γ(10), γ(11), and γ(12), were identified in the analysis. β(1) and γ(5) were most abundant in the enriched βγ fraction, and this βγ profile was generally mirrored in the fusion proteins. However, both A(2A):α(S) and A(1):α(i1) bound more β(4) and γ(5) compared to the enriched βγ fraction; also, more β(4) was associated with A(2A):α(S) than A(1):α(i1). Both fusion proteins also contained less γ(2), γ(10), and γ(12) than the enriched βγ fraction. These results suggest that preferences for particular βγ isoforms may be driven in part by structural motifs common to adenosine receptor family members.
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Affiliation(s)
- Dora Bigler Wang
- Department of Pharmacology, University of Virginia Health System, Charlottesville, 22908, United States
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50
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Gheyi T, Rodgers L, Romero R, Sauder JM, Burley SK. Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1795-1801. [PMID: 20685133 PMCID: PMC2963156 DOI: 10.1016/j.jasms.2010.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/21/2010] [Accepted: 06/22/2010] [Indexed: 05/29/2023]
Abstract
A strategy for increasing the efficiency of protein crystallization/structure determination with mass spectrometry has been developed. This approach combines insights from limited proteolysis/mass spectrometry and crystallization via in situ proteolysis. The procedure seeks to identify protease-resistant polypeptide chain segments from purified proteins on the time-scale of crystal formation, and subsequently crystallizing the target protein in the presence of the optimal protease at the right relative concentration. We report our experience with 10 proteins of unknown structure, two of which yielded high-resolution X-ray structures. The advantage of this approach comes from its ability to select only those structure determination candidates that are likely to benefit from application of in situ proteolysis, using conditions most likely to result in formation of a stable proteolytic digestion product suitable for crystallization.
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Affiliation(s)
- Tarun Gheyi
- New York SGX Research Center for Structural Genomics, Structural Biology, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California 92121, USA.
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