1
|
Probing the Structure of the HIV-1 Envelope Trimer Using Aspartate Scanning Mutagenesis. J Virol 2020; 94:JVI.01426-20. [PMID: 32817217 DOI: 10.1128/jvi.01426-20] [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: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
HIV-1 envelope (Env) glycoprotein gp160 exists as a trimer of heterodimers on the viral surface. In most structures of the soluble ectodomain of trimeric HIV-1 envelope glycoprotein, the regions from 512 to 517 of the fusion peptide and from 547 to 568 of the N-heptad repeat are disordered. We used aspartate scanning mutagenesis of subtype B strain JRFL Env as an alternate method to probe residue burial in the context of cleaved, cell surface-expressed Env, as buried residues should be intolerant to substitution with Asp. The data are inconsistent with a fully disordered 547 to 568 stretch, as residues 548, 549, 550, 555, 556, 559, 562, and 566 to 569 are all sensitive to Asp substitution. In the fusion peptide region, residues 513 and 515 were also sensitive to Asp substitution, suggesting that the fusion peptide may not be fully exposed in native Env. gp41 is metastable in the context of native trimer. Introduction of Asp at residues that are exposed in the prefusion state but buried in the postfusion state is expected to destabilize the postfusion state and any intermediate states where the residue is buried. We therefore performed soluble CD4 (sCD4)-induced gp120 shedding experiments to identify Asp mutants at residues 551, 554 to 559, 561 to 567, and 569 that could prevent gp120 shedding. We also observed similar mutational effects on shedding for equivalent mutants in the context of clade C Env from isolate 4-2J.41. These substitutions can potentially be used to stabilize native-like trimer derivatives that are used as HIV-1 vaccine immunogens.IMPORTANCE In most crystal structures of the soluble ectodomain of the HIV-1 Env trimer, some residues in the fusion and N-heptad repeat regions are disordered. Whether this is true in the context of native, functional Env on the virion surface is not known. This knowledge may be useful for stabilizing Env in its prefusion conformation and will also help to improve understanding of the viral entry process. Burial of the charged residue Asp in a protein structure is highly destabilizing. We therefore used Asp scanning mutagenesis to probe the burial of apparently disordered residues in native Env and to examine the effect of mutations in these regions on Env stability and conformation as probed by antibody binding to cell surface-expressed Env, CD4-induced shedding of HIV-1 gp120, and viral infectivity studies. Mutations that prevent shedding can potentially be used to stabilize native-like Env constructs for use as vaccine immunogens.
Collapse
|
2
|
Dolle A, Nagati VB, Hunashal Y, Krishnamurthy K, Pasupulati AK, Raghothama S, Gowd KH. Disulfide engineering on temporin-SHf: Stabilizing the bioactive conformation of an ultra-short antimicrobial peptide. Chem Biol Drug Des 2019; 94:1634-1646. [PMID: 30924306 DOI: 10.1111/cbdd.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/07/2019] [Accepted: 03/17/2019] [Indexed: 12/14/2022]
Abstract
In Silico searching for short antimicrobial peptides has revealed temporin-SHf as the short (8AA), hydrophobic, broad spectrum, and natural antimicrobial peptide. Important drawback associated with temporin-SHf is the susceptibility of its bioactive conformation for denaturation and proteolytic degradation. In the current report, disulfide engineering strategy has been adopted to improve the stability of bioactive conformation of temporin-SHf. The functionally non-critical Leu4 and Ile7 residues at i and i + 3 position of helical conformation of temporin-SHf were mutated with cysteine disulfide. Designed [L4C, I7C]temporin-SHf was synthesized, characterized using NMR spectroscopy, and accessed for antimicrobial activity. [L4C, I7C]Temporin-SHf adopts helical conformation from Phe3 to Phe8 in the absence of membrane-mimetic environment and retains broad spectrum antimicrobial activity. The reduction potential of cysteine disulfide of [L4C, I7C]temporin-SHf is -289 mV. Trypsin-induced digestion and serum-induced digestion have confirmed the advantage of cysteine disulfide in imparting proteolytic stability to temporin-SHf. Disulfide-stabilized temporin-SHf may serve as a good model for the rational design of temporin-SHf based antibiotics for treatment of infectious diseases.
Collapse
Affiliation(s)
- Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Veera Babu Nagati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Yamanappa Hunashal
- NMR Research Centre, Indian Institute of Science, Bangalore, Karnataka, India
| | - Kiran Krishnamurthy
- NMR Research Centre, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anil Kumar Pasupulati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| |
Collapse
|
3
|
Bayse CA, Pollard DB. Conformation dynamics of cyclic disulfides and selenosulfides in CXXC(U) (X = Gly, Ala) tetrapeptide redox motifs. J Pept Sci 2019; 25:e3160. [PMID: 30873692 DOI: 10.1002/psc.3160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 02/01/2023]
Abstract
Thioredoxin fold proteins often contain a Cys-(Xxx)n -Cys(Sec) or CXn C(U) motif, where the active cysteine (C) or selenocysteine (U) is bridged by X residues, which vary with protein function. The effect of the X residues on the conformation space of the oxidized disulfide and selenosulfide forms of the CXXC(U) motif has been investigated using molecular dynamics (MD) and density functional theory. Multi-microsecond-length MD simulations of the CGGC, CGAC, and CAGC cyclic peptides show that CGGC rings readily exchange between several conformations over the course of the simulation, but steric interactions with the methyl group of Ala limit the conformation space available to the cyclic peptide, especially for CGAC. The potential for the motif to be reduced, as measured by the energy of the lowest unoccupied molecular orbitals, is dependent upon the ring conformation. These results suggest that control of available conformations by the bridging residues and the protein tertiary structure may be important for defining the function of the CXXC motif. Theoretical 77 Se chemical shifts of the selenosulfide moiety are dependent upon the conformation and/or intramolecular Se···O interactions with the backbone carbonyl group of the C-terminal U residue.
Collapse
Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
| | - Deanna B Pollard
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
| |
Collapse
|
4
|
Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R. Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. J Biol Chem 2018; 293:15002-15020. [PMID: 30093409 DOI: 10.1074/jbc.ra118.005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein minimization is an attractive approach for designing vaccines against rapidly evolving pathogens such as human immunodeficiency virus, type 1 (HIV-1), because it can help in focusing the immune response toward conserved conformational epitopes present on complex targets. The outer domain (OD) of HIV-1 gp120 contains epitopes for a large number of neutralizing antibodies and therefore is a primary target for structure-based vaccine design. We have previously designed a bacterially expressed outer-domain immunogen (ODEC) that bound CD4-binding site (CD4bs) ligands with 3-12 μm affinity and elicited a modest neutralizing antibody response in rabbits. In this study, we have optimized ODEC using consensus sequence design, cyclic permutation, and structure-guided mutations to generate a number of variants with improved yields, biophysical properties, stabilities, and affinities (KD of 10-50 nm) for various CD4bs targeting broadly neutralizing antibodies, including the germline-reverted version of the broadly neutralizing antibody VRC01. In contrast to ODEC, the optimized immunogens elicited high anti-gp120 titers in rabbits as early as 6 weeks post-immunization, before any gp120 boost was given. Following two gp120 boosts, sera collected at week 22 showed cross-clade neutralization of tier 1 HIV-1 viruses. Using a number of different prime/boost combinations, we have identified a cyclically permuted OD fragment as the best priming immunogen, and a trimeric, cyclically permuted gp120 as the most suitable boosting molecule among the tested immunogens. This study also provides insights into some of the biophysical correlates of improved immunogenicity.
Collapse
Affiliation(s)
- Ujjwal Rathore
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Mansi Purwar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Raksha Das
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Aditya Arun Kumar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Sanchari Bhattacharyya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Heather Arendt
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Joanne DeStefano
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Aaron Wilson
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Christopher Parks
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Celia C La Branche
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - David C Montefiori
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012,
| |
Collapse
|
5
|
Nautiyal A, Rani PS, Sharples GJ, Muniyappa K. Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. Mol Microbiol 2016; 100:656-74. [PMID: 26817626 DOI: 10.1111/mmi.13338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The Mycobacterium tuberculosis genome possesses homologues of the ruvC and yqgF genes that encode putative Holliday junction (HJ) resolvases. However, their gene expression profiles and enzymatic properties have not been experimentally defined. Here we report that expression of ruvC and yqgF is induced in response to DNA damage. Protein-DNA interaction assays with purified M. tuberculosis RuvC (MtRuvC) and YqgF (MtRuvX) revealed that both associate preferentially with HJ DNA, albeit with differing affinities. Although both MtRuvC and MtRuvX cleaved HJ DNA in vitro, the latter displayed robust HJ resolution activity by symmetrically related, paired incisions. MtRuvX showed a higher binding affinity for the HJ structure over other branched recombination and replication intermediates. An MtRuvX(D28N) mutation, eliminating one of the highly conserved catalytic residues in this class of endonucleases, dramatically reduced its ability to cleave HJ DNA. Furthermore, a unique cysteine (C38) fulfils a crucial role in HJ cleavage, consistent with disulfide-bond mediated dimerization being essential for MtRuvX activity. In contrast, E. coli YqgF is monomeric and exhibits no branched DNA binding or cleavage activity. These results fit with a functional modification of YqgF in M. tuberculosis so that it can act as a dimeric HJ resolvase analogous to that of RuvC.
Collapse
Affiliation(s)
- Astha Nautiyal
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - P Sandhya Rani
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Gary J Sharples
- Department of Chemistry, School of Biological and Biomedical Sciences, Biophysical Sciences Institute, University of Durham, DH1 3LE, UK
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| |
Collapse
|
6
|
Botello-Morte L, Pellicer S, Sein-Echaluce VC, Contreras LM, Neira JL, Abián O, Velázquez-Campoy A, Peleato ML, Fillat MF, Bes MT. Cysteine Mutational Studies Provide Insight into a Thiol-Based Redox Switch Mechanism of Metal and DNA Binding in FurA from Anabaena sp. PCC 7120. Antioxid Redox Signal 2016; 24:173-185. [PMID: 26414804 PMCID: PMC4744886 DOI: 10.1089/ars.2014.6175] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS The ferric uptake regulator (Fur) is the main transcriptional regulator of genes involved in iron homeostasis in most prokaryotes. FurA from Anabaena sp. PCC 7120 contains five cysteine residues, four of them arranged in two redox-active CXXC motifs. The protein needs not only metal but also reducing conditions to remain fully active in vitro. Through a mutational study of the cysteine residues present in FurA, we have investigated their involvement in metal and DNA binding. RESULTS Residue C101 that belongs to a conserved CXXC motif plays an essential role in both metal and DNA binding activities in vitro. Substitution of C101 by serine impairs DNA and metal binding abilities of FurA. Isothermal titration calorimetry measurements show that the redox state of C101 is responsible for the protein ability to coordinate the metal corepressor. Moreover, the redox state of C101 varies with the presence or absence of C104 or C133, suggesting that the environments of these cysteines are mutually interdependent. INNOVATION We propose that C101 is part of a thiol/disulfide redox switch that determines FurA ability to bind the metal corepressor. CONCLUSION This mechanism supports a novel feature of a Fur protein that emerges as a regulator, which connects the response to changes in the intracellular redox state and iron management in cyanobacteria. Antioxid. Redox Signal. 00, 000-000.
Collapse
Affiliation(s)
- Laura Botello-Morte
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| | - Silvia Pellicer
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| | - Violeta C Sein-Echaluce
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| | - Lellys M Contreras
- 3 Institut of Molecular and Cellular Biology, Miguel Hernández University of Elche , Elche, Spain
| | - José Luis Neira
- 2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain .,3 Institut of Molecular and Cellular Biology, Miguel Hernández University of Elche , Elche, Spain
| | - Olga Abián
- 2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain .,4 IIS Aragon-Aragon Health Science Institute (IACS) and Networked Biomedical Research Center of Hepatic and Digestive Diseases (CIBERehd) , Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain .,5 ARAID Foundation , Government of Aragón, Zaragoza, Spain
| | - María Luisa Peleato
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| | - María F Fillat
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| | - María Teresa Bes
- 1 Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza , Zaragoza, Spain .,2 Institute for Biocomputation and Physics of Complex Systems (BIFI)-Associated Unit to IQRS-CSIC, University of Zaragoza , Zaragoza, Spain
| |
Collapse
|
7
|
Brazin KN, Mallis RJ, Das DK, Feng Y, Hwang W, Wang JH, Wagner G, Lang MJ, Reinherz EL. Structural Features of the αβTCR Mechanotransduction Apparatus That Promote pMHC Discrimination. Front Immunol 2015; 6:441. [PMID: 26388869 PMCID: PMC4558533 DOI: 10.3389/fimmu.2015.00441] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/14/2015] [Indexed: 12/20/2022] Open
Abstract
The αβTCR was recently revealed to function as a mechanoreceptor. That is, it leverages mechanical energy generated during immune surveillance and at the immunological synapse to drive biochemical signaling following ligation by a specific foreign peptide-MHC complex (pMHC). Here, we review the structural features that optimize this transmembrane (TM) receptor for mechanotransduction. Specialized adaptations include (1) the CβFG loop region positioned between Vβ and Cβ domains that allosterically gates both dynamic T cell receptor (TCR)-pMHC bond formation and lifetime; (2) the rigid super β-sheet amalgams of heterodimeric CD3εγ and CD3εδ ectodomain components of the αβTCR complex; (3) the αβTCR subunit connecting peptides linking the extracellular and TM segments, particularly the oxidized CxxC motif in each CD3 heterodimeric subunit that facilitates force transfer through the TM segments and surrounding lipid, impacting cytoplasmic tail conformation; and (4) quaternary changes in the αβTCR complex that accompany pMHC ligation under load. How bioforces foster specific αβTCR-based pMHC discrimination and why dynamic bond formation is a primary basis for kinetic proofreading are discussed. We suggest that the details of the molecular rearrangements of individual αβTCR subunit components can be analyzed utilizing a combination of structural biology, single-molecule FRET, optical tweezers, and nanobiology, guided by insightful atomistic molecular dynamic studies. Finally, we review very recent data showing that the pre-TCR complex employs a similar mechanobiology to that of the αβTCR to interact with self-pMHC ligands, impacting early thymic repertoire selection prior to the CD4(+)CD8(+) double positive thymocyte stage of development.
Collapse
Affiliation(s)
- Kristine N. Brazin
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert J. Mallis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dibyendu Kumar Das
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yinnian Feng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea
| | - Jia-huai Wang
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Matthew J. Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ellis L. Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
8
|
Sharma IM, Prakash S, Dhanaraman T, Chatterji D. Characterization of a dual-active enzyme, DcpA, involved in cyclic diguanosine monophosphate turnover in Mycobacterium smegmatis. MICROBIOLOGY-SGM 2014; 160:2304-2318. [PMID: 25037163 DOI: 10.1099/mic.0.080200-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have reported previously that the long-term survival of Mycobacterium smegmatis is facilitated by a dual-active enzyme MSDGC-1 (renamed DcpA), which controls the cellular turnover of cyclic diguanosine monophosphate (c-di-GMP). Most mycobacterial species possess at least a single copy of a DcpA orthologue that is highly conserved in terms of sequence similarity and domain architecture. Here, we show that DcpA exists in monomeric and dimeric forms. The dimerization of DcpA is due to non-covalent interactions between two protomers that are arranged in a parallel orientation. The dimer shows both synthesis and hydrolysis activities, whereas the monomer shows only hydrolysis activity. In addition, we have shown that DcpA is associated with the cytoplasmic membrane and exhibits heterogeneous cellular localization with a predominance at the cell poles. Finally, we have also shown that DcpA is involved in the change in cell length and colony morphology of M. smegmatis. Taken together, our study provides additional evidence about the role of the bifunctional protein involved in c-di-GMP signalling in M. smegmatis.
Collapse
Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Thillaivillalan Dhanaraman
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal H3C 3J7, Québec, Canada
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
9
|
Brazin KN, Mallis RJ, Li C, Keskin DB, Arthanari H, Gao Y, Wu SL, Karger BL, Wagner G, Reinherz EL. Constitutively oxidized CXXC motifs within the CD3 heterodimeric ectodomains of the T cell receptor complex enforce the conformation of juxtaposed segments. J Biol Chem 2014; 289:18880-92. [PMID: 24849600 PMCID: PMC4081929 DOI: 10.1074/jbc.m114.574996] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/19/2014] [Indexed: 11/06/2022] Open
Abstract
The CD3ϵγ and CD3ϵδ heterodimers along with the CD3ζζ homodimer are the signaling components of the T cell receptor (TCR). These invariant dimers are non-covalently associated on the T cell plasma membrane with a clone-specific (i.e. clonotypic) αβ heterodimer that binds its cognate ligand, a complex between a particular antigenic peptide, and an MHC molecule (pMHC). These four TCR dimers exist in a 1:1:1:1 stoichiometry. At the junction between the extracellular and transmembrane domains of each mammalian CD3ϵ, CD3γ, and CD3δ subunit is a highly conserved CXXC motif previously found to be important for thymocyte and T cell activation. The redox state of each CXXC motif is presently unknown. Here we show using LC-MS and a biotin switch assay that these CXXC segments are constitutively oxidized on resting and activated T cells, consistent with their measured reduction potential. NMR chemical shift perturbation experiments comparing a native oxidized CD3δ CXXC-containing segment with that of a mutant SXXS-containing CD3δ segment in LPPG (1-palmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)) micelles show extensive chemical shift differences in residues within the membrane-proximal motif as well as throughout the transmembrane and cytoplasmic domains as a result of the elimination of the native disulfide. Likewise, direct comparison of the native CD3δ segment in oxidizing and reducing conditions reveals numerous spectral differences. The oxidized CXXC maintains the structure within the membrane-proximal stalk region as well as that of its contiguous transmembrane and cytoplasmic domain, inclusive of the ITAM (immunoreceptor tyrosine-based activation motif) involved in signaling. These results suggest that preservation of the CD3 CXXC oxidized state may be essential for TCR mechanotransduction.
Collapse
Affiliation(s)
- Kristine N Brazin
- From the Department of Medical Oncology, Laboratory of Immunobiology, Dana-Farber Cancer Institute and Departments of Medicine and
| | - Robert J Mallis
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School and
| | - Chen Li
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115
| | - Derin B Keskin
- From the Department of Medical Oncology, Laboratory of Immunobiology, Dana-Farber Cancer Institute and
| | - Haribabu Arthanari
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School and
| | - Yuanwei Gao
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115
| | - Shiaw-Lin Wu
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115
| | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115
| | - Gerhard Wagner
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School and
| | - Ellis L Reinherz
- From the Department of Medical Oncology, Laboratory of Immunobiology, Dana-Farber Cancer Institute and Departments of Medicine and
| |
Collapse
|
10
|
In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies. J Comput Aided Mol Des 2013; 27:347-63. [DOI: 10.1007/s10822-013-9650-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
|
11
|
Xie J, Qin M, Cao Y, Wang W. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds. Proteins 2011; 79:2505-16. [PMID: 21661057 DOI: 10.1002/prot.23074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 11/05/2022]
Abstract
Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation.
Collapse
Affiliation(s)
- Jinbing Xie
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | | | | | | |
Collapse
|
12
|
Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Proteins 2011; 79:244-60. [PMID: 21058397 DOI: 10.1002/prot.22878] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity.
Collapse
Affiliation(s)
- S Indu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | | | | | | | | |
Collapse
|