1
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Doran RC, Yu B, Wright M, O'Rourke SM, Yin L, Richardson JM, Byrne G, Mesa KA, Berman PW. Development of a Stable MGAT1 - CHO Cell Line to Produce Clade C gp120 With Improved Binding to Broadly Neutralizing Antibodies. Front Immunol 2018; 9:2313. [PMID: 30344523 PMCID: PMC6182045 DOI: 10.3389/fimmu.2018.02313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
The high rate of new HIV infections, particularly in Sub-Saharan Africa, emphasizes the need for a safe and effective vaccine to prevent acquired immunodeficiency syndrome (AIDS). To date, the only HIV vaccine trial that has exhibited protective efficacy in humans was the RV144 study completed in Thailand. The finding that protection correlated with antibodies to gp120 suggested that increasing the quality or magnitude of the antibody response that recognize gp120 might improve the modest yet significant protection (31.2%) achieved with this immunization regimen. However, the large-scale production of rgp120 suitable for clinical trials has been challenging due, in part, to low productivity and difficulties in purification. Moreover, the antigens that are currently available were produced largely by the same technology used in the early 1990s and fail to incorporate unique carbohydrates presented on HIV virions required for the binding of several major families of broadly neutralizing antibodies (bNAbs). Here we describe the development of a high-yielding CHO cell line expressing rgp120 from a clade C isolate (TZ97008), representative of the predominant circulating HIV subtype in Southern Africa and Southeast Asia. This cell line, produced using robotic selection, expresses high levels (1.2 g/L) of the TZ97008 rgp120 antigen that incorporates oligomannose glycans required for binding to multiple glycan dependent bNAbs. The resulting rgp120 displays a lower degree of net charge and glycoform heterogeneity as compared to rgp120s produced in normal CHO cells. This homogeneity in net charge facilitates purification by filtration and ion exchange chromatography methods, eliminating the need for expensive custom-made lectin, or immunoaffinity columns. The results described herein document the availability of a novel cell line for the large-scale production of clade C gp120 for clinical trials. Finally, the strategy used to produce a TZ97008 gp120 in the MGAT− CHO cell line can be applied to the production of other candidate HIV vaccines.
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Affiliation(s)
- Rachel C Doran
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Bin Yu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Meredith Wright
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Lu Yin
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jennie M Richardson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Gabriel Byrne
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kathryn A Mesa
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Phillip W Berman
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
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2
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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3
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Leveles I, Németh V, Szabó JE, Harmat V, Nyíri K, Bendes ÁÁ, Papp-Kádár V, Zagyva I, Róna G, Ozohanics O, Vékey K, Tóth J, Vértessy BG. Structure and enzymatic mechanism of a moonlighting dUTPase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2298-308. [PMID: 24311572 DOI: 10.1107/s0907444913021136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/29/2013] [Indexed: 02/08/2023]
Abstract
Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a ϕ11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small β-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of ϕ11 phage dUTPase.
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Affiliation(s)
- Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 29 Karolina Street, 1113 Budapest, Hungary
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5
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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6
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Ishino T, Economou NJ, McFadden K, Zaks-Zilberman M, Jost M, Baxter S, Contarino MR, Harrington AE, Loll PJ, Pasut G, Lievens S, Tavernier J, Chaiken I. A Protein Engineering Approach Differentiates the Functional Importance of Carbohydrate Moieties of Interleukin-5 Receptor α. Biochemistry 2011; 50:7546-56. [DOI: 10.1021/bi2009135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tetsuya Ishino
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Nicoleta J. Economou
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Karyn McFadden
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Meirav Zaks-Zilberman
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Monika Jost
- Department of Radiation Oncology, Drexel University College of Medicine, 11102 New College
Building, 245 North 15th Street, Philadelphia, Pennsylvania 19102,
United States
| | - Sabine Baxter
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Mark R. Contarino
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Adrian E. Harrington
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Patrick J. Loll
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
| | - Gianfranco Pasut
- Department
of Pharmaceutical Sciences, University of Padua, Via F. Marzolo 5, Padua 35131,
Italy
| | - Sam Lievens
- Department of Medical
Protein
Research, Flanders Interuniversity Institute for Biotechnology, VIB09-Faculty
of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- Department of Medical
Protein
Research, Flanders Interuniversity Institute for Biotechnology, VIB09-Faculty
of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Irwin Chaiken
- Department of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 11102 New College Building, 245 North 15th Street, Philadelphia,
Pennsylvania 19102, United States
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7
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Gift SK, McFadden K, Zentner IJ, Rajagopal S, Zhang MY, Dimitrov DS, Chaiken IM. Monoclonal Antibody m18 Paratope Leading to Dual Receptor Antagonism of HIV-1 gp120. Biochemistry 2011; 50:2769-79. [DOI: 10.1021/bi101161j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Mei-Yun Zhang
- AIDS Institute, Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Dimiter S. Dimitrov
- Center for Cancer Research Nanobiology Program, CCR, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
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8
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Gift SK, Zentner IJ, Schön A, McFadden K, Umashankara M, Rajagopal S, Contarino M, Duffy C, Courter JR, Zhang MY, Gershoni JM, Cocklin S, Dimitrov DS, Smith AB, Freire E, Chaiken IM. Conformational and structural features of HIV-1 gp120 underlying the dual receptor antagonism by cross-reactive neutralizing antibody m18. Biochemistry 2011; 50:2756-68. [PMID: 21351734 DOI: 10.1021/bi101160r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the interaction between cross-reactive HIV-1 neutralizing human monoclonal antibody m18 and HIV-1YU-2 gp120 in an effort to understand how this antibody inhibits the entry of virus into cells. m18 binds to gp120 with high affinity (KD≈5 nM) as measured by surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). SPR analysis further showed that m18 inhibits interactions of gp120 with both soluble CD4 and CD4-induced antibodies that have epitopes overlapping the coreceptor binding site. This dual receptor site antagonism, which occurs with equal potency for both inhibition effects, argues that m18 is not functioning as a mimic of CD4, in spite of the presence of a putative CD4-like loop formed by HCDR3 in the antibody. Consistent with this view, m18 was found to interact with gp120 in the presence of saturating concentrations of a CD4-mimicking small molecule gp120 inhibitor, suggesting that m18 does not require unoccupied CD4 Phe43 binding cavity residues of gp120. Thermodynamic analysis of the m18-gp120 interaction suggests that m18 stabilizes a conformation of gp120 that is unique from and less structured than the CD4-stabilized conformation. Conformational mutants of gp120 were studied for their impact on m18 interaction. Mutations known to disrupt the coreceptor binding region and to lead to complete suppression of 17b binding had minimal effects on m18 binding. This argues that energetically important epitopes for m18 binding lie outside the disrupted bridging sheet region used for 17b and coreceptor binding. In contrast, mutations in the CD4 region strongly affected m18 binding. Overall, the results obtained in this work argue that m18, rather than mimicking CD4 directly, suppresses both receptor binding site functions of HIV-1 gp120 by stabilizing a nonproductive conformation of the envelope protein. These results can be related to prior findings about the importance of conformational entrapment as a common mode of action for neutralizing CD4bs antibodies, with differences mainly in epitope utilization and the extent of gp120 structuring.
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Affiliation(s)
- Syna Kuriakose Gift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
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9
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Hiss JA, Schneider G. Architecture, function and prediction of long signal peptides. Brief Bioinform 2009; 10:569-78. [DOI: 10.1093/bib/bbp030] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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10
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Gopi H, Cocklin S, Pirrone V, McFadden K, Tuzer F, Zentner I, Ajith S, Baxter S, Jawanda N, Krebs FC, Chaiken IM. Introducing metallocene into a triazole peptide conjugate reduces its off-rate and enhances its affinity and antiviral potency for HIV-1 gp120. J Mol Recognit 2009; 22:169-74. [PMID: 18498083 DOI: 10.1002/jmr.892] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this work, we identified a high affinity and potency metallocene-containing triazole peptide conjugate that suppresses the interactions of HIV-1 envelope gp120 at both its CD4 and co-receptor binding sites. The ferrocene-peptide conjugate, HNG-156, was formed by an on-resin copper-catalysed [2+3] cycloaddition reaction. Surface plasmon resonance interaction analysis revealed that, compared to a previously reported phenyl-containing triazole conjugate HNG-105 (105), peptide 156 had a higher direct binding affinity for several subtypes of HIV-1 gp120 due mainly to the decreased dissociation rate of the conjugate-gp120 complex. The ferrocene triazole conjugate bound to gp120 of both clade A (92UG037-08) and clade B (YU-2 and SF162) virus subtypes with nanomolar KD in direct binding and inhibited the binding of gp120 to soluble CD4 and to antibodies that bind to HIV-1YU-2 gp120 at both the CD4 binding site and CD4-induced binding sites. HNG-156 showed a close-to nanomolar IC50 for inhibiting cell infection by HIV-1BaL whole virus. The dual receptor site antagonist activity and potency of HNG-156 make it a promising viral envelope inhibitor lead for developing anti-HIV-1 treatments.
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Affiliation(s)
- Hosahudya Gopi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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11
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Chen LW, Raghavan V, Chang PJ, Shedd D, Heston L, Delecluse HJ, Miller G. Two phenylalanines in the C-terminus of Epstein-Barr virus Rta protein reciprocally modulate its DNA binding and transactivation function. Virology 2009; 386:448-61. [PMID: 19232420 DOI: 10.1016/j.virol.2009.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 01/08/2009] [Accepted: 01/15/2009] [Indexed: 12/12/2022]
Abstract
The Rta (R transactivator) protein plays an essential role in the Epstein-Barr viral (EBV) lytic cascade. Rta activates viral gene expression by several mechanisms including direct and indirect binding to target viral promoters, synergy with EBV ZEBRA protein, and stimulation of cellular signaling pathways. We previously found that Rta proteins with C-terminal truncations of 30 aa were markedly enhanced in their capacity to bind DNA (Chen, L.W., Chang, P.J., Delecluse, H.J., and Miller, G., (2005). Marked variation in response of consensus binding elements for the Rta protein of Epstein-Barr virus. J. Virol. 79(15), 9635-9650.). Here we show that two phenylalanines (F600 and F605) in the C-terminus of Rta play a crucial role in mediating this DNA binding inhibitory function. Amino acids 555 to 605 of Rta constitute a functional DNA binding inhibitory sequence (DBIS) that markedly decreased DNA binding when transferred to a minimal DNA binding domain of Rta (aa 1-350). Alanine substitution mutants, F600A/F605A, abolished activity of the DBIS. F600 and F605 are located in the transcriptional activation domain of Rta. Alanine substitutions, F600A/F605A, decreased transcriptional activation by Rta protein, whereas aromatic substitutions, such as F600Y/F605Y or F600W/F605W, partially restored transcriptional activation. Full-length Rta protein with F600A/F605A mutations were enhanced in DNA binding compared to wild-type, whereas Rta proteins with F600Y/F605Y or F600W/F605W substitutions were, like wild-type Rta, relatively poor DNA binders. GAL4 (1-147)/Rta (416-605) fusion proteins with F600A/F605A mutations were diminished in transcriptional activation, relative to GAL4/Rta chimeras without such mutations. The results suggest that, in the context of a larger DBIS, F600 and F605 play a role in the reciprocal regulation of DNA binding and transcriptional activation by Rta. Regulation of DNA binding by Rta is likely to be important in controlling its different modes of action.
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Affiliation(s)
- Lee-Wen Chen
- Department of Respiratory Care, Chang Gung Institute of Technology, Chaiyi, Taiwan
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12
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Ishino T, Harrington AE, Zaks-Zilberman M, Scibek JJ, Chaiken I. Slow-dissociation effect of common signaling subunit beta c on IL5 and GM-CSF receptor assembly. Cytokine 2008; 42:179-190. [PMID: 18294864 DOI: 10.1016/j.cyto.2007.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 10/25/2007] [Accepted: 12/19/2007] [Indexed: 11/26/2022]
Abstract
Receptor activation by IL5 and GM-CSF is a sequential process that depends on their interaction with a cytokine-specific subunit alpha and recruitment of a common signaling subunit beta (betac). In order to elucidate the assembly dynamics of these receptor subunits, we performed kinetic interaction analysis of the cytokine-receptor complex formation by a surface plasmon resonance biosensor. Using the extracellular domains of receptor fused with C-terminal V5-tag, we developed an assay method to co-anchor alpha and betac subunits on the biosensor surface. We demonstrated that dissociation of the cytokine-receptor complexes was slower when both subunits were co-anchored on the biosensor surface than when alpha subunit alone was anchored. The slow-dissociation effect of betac had a similar impact on GM-CSF receptor stabilization to that of IL5. The effects were abolished by alanine replacement of either Tyr18 or Tyr344 residue in betac, which together constitute key parts of a cytokine binding epitope. The data argue that betac plays an important role in preventing the ligand-receptor complexes from rapidly dissociating. This slow-dissociation effect of betac explains how, when multiple betac cytokine receptor alpha subunits are present on the same cell surface, selective betac usage can be controlled by sequestration in stabilized cytokine-alpha-betac complexes.
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Affiliation(s)
- Tetsuya Ishino
- Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, 245 North, 15th Street, Mail Stop 497, New College Building, Room 11102, Philadelphia, PA 19102-1192, USA
| | - Adrian E Harrington
- Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, 245 North, 15th Street, Mail Stop 497, New College Building, Room 11102, Philadelphia, PA 19102-1192, USA
| | - Meirav Zaks-Zilberman
- Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, 245 North, 15th Street, Mail Stop 497, New College Building, Room 11102, Philadelphia, PA 19102-1192, USA
| | - Jeffery J Scibek
- Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, 245 North, 15th Street, Mail Stop 497, New College Building, Room 11102, Philadelphia, PA 19102-1192, USA
| | - Irwin Chaiken
- Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, 245 North, 15th Street, Mail Stop 497, New College Building, Room 11102, Philadelphia, PA 19102-1192, USA.
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13
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Juncadella IJ, Garg R, Bates TC, Olivera ER, Anguita J. The Ixodes scapularis salivary protein, salp15, prevents the association of HIV-1 gp120 and CD4. Biochem Biophys Res Commun 2007; 367:41-6. [PMID: 18162176 DOI: 10.1016/j.bbrc.2007.12.104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 12/11/2007] [Indexed: 10/22/2022]
Abstract
Ixodes scapularis salivary protein, Salp15, inhibits CD4(+) T cell activation by binding to the most-extracellular domains of the CD4 molecule, potentially overlapping with the gp120-binding region. We now show that Salp15 inhibits the interaction of gp120 and CD4. Furthermore, Salp15 prevents syncytia formation between HL2/3 (a stable HeLa cell line expressing the envelope protein) and CD4-expressing cells. Salp15 prevented gp120-CD4 interaction at least partially through its direct interaction with the envelope glycoprotein. A phage display library screen provided the interacting residues in the C1 domain of gp120. These results provide a potential basis to define exposed gp120 epitopes for the generation of neutralizing vaccines.
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Affiliation(s)
- Ignacio J Juncadella
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 103 Paige Laboratory, 161 Holdsworth Way, Amherst, MA 01003, USA
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14
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Binz HK, Plückthun A. Engineered proteins as specific binding reagents. Curr Opin Biotechnol 2007; 16:459-69. [PMID: 16005204 DOI: 10.1016/j.copbio.2005.06.005] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 06/10/2005] [Accepted: 06/24/2005] [Indexed: 11/20/2022]
Abstract
Over the past 30 years, monoclonal antibodies have become the standard binding proteins and currently find applications in research, diagnostics and therapy. Yet, monoclonal antibodies now face strong competition from synthetic antibody libraries in combination with powerful library selection technologies. More recently, an increased understanding of other natural binding proteins together with advances in protein engineering, selection and evolution technologies has also triggered the exploration of numerous other protein architectures for the generation of designed binding molecules. Valuable protein-binding scaffolds have been obtained and represent promising alternatives to antibodies for biotechnological and, potentially, clinical applications.
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Affiliation(s)
- H Kaspar Binz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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15
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McFadden K, Cocklin S, Gopi H, Baxter S, Ajith S, Mahmood N, Shattock R, Chaiken I. A recombinant allosteric lectin antagonist of HIV-1 envelope gp120 interactions. Proteins 2007; 67:617-29. [PMID: 17348010 DOI: 10.1002/prot.21295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The first, critical stage of HIV-1 infection is fusion of viral and host cellular membranes initiated by a viral envelope glycoprotein gp120. We evaluated the potential to form a chimeric protein entry inhibitor that combines the action of two gp120-targeting molecules, an allosteric peptide inhibitor 12p1 and a higher affinity carbohydrate-binding protein cyanovirin (CVN). In initial mixing experiments, we demonstrated that the inhibitors do not interfere with each other and instead show functional synergy in inhibiting viral cell infection. Based on this, we created a chimera, termed L5, with 12p1 fused to the C-terminal domain of CVN through a linker of five penta-peptide repeats. L5 revealed the same broad specificity as CVN for gp120 from a variety of clades and tropisms. By comparison to CVN, the L5 chimera exhibited substantially increased inhibition of gp120 binding to receptor CD4, coreceptor surrogate mAb 17b and gp120 antibody F105. These binding inhibition effects by the chimera reflected both the high affinity of the CVN domain and the allosteric action of the 12p1 domain. The results open up the possibility to form high potency chimeras, as well as noncovalent mixtures, as leads for HIV-1 envelope antagonism that can overcome potency limits and potential virus mutational resistance for either 12p1 or CVN alone.
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Affiliation(s)
- Karyn McFadden
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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16
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Schön A, Madani N, Klein JC, Hubicki A, Ng D, Yang X, Smith AB, Sodroski J, Freire E. Thermodynamics of binding of a low-molecular-weight CD4 mimetic to HIV-1 gp120. Biochemistry 2006; 45:10973-80. [PMID: 16953583 PMCID: PMC2504686 DOI: 10.1021/bi061193r] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NBD-556 and the chemically and structurally similar NBD-557 are two low-molecular weight compounds that reportedly block the interaction between the HIV-1 envelope glycoprotein gp120 and its receptor, CD4. NBD-556 binds to gp120 with a binding affinity of 2.7 x 10(5) M(-1) (K(d) = 3.7 muM) in a process characterized by a large favorable change in enthalpy partially compensated by a large unfavorable entropy change, a thermodynamic signature similar to that observed for binding of sCD4 to gp120. NBD-556 binding is associated with a large structuring of the gp120 molecule, as also demonstrated by CD spectroscopy. NBD-556, like CD4, activates the binding of gp120 to the HIV-1 coreceptor, CCR5, and to the 17b monoclonal antibody, which recognizes the coreceptor binding site of gp120. NBD-556 stimulates HIV-1 infection of CD4-negative, CCR5-expressing cells. The thermodynamic signature of the binding of NBD-556 to gp120 is very different from that of another viral entry inhibitor, BMS-378806. Whereas NBD-556 binds gp120 with a large favorable enthalpy and compensating unfavorable entropy changes, BMS-378806 does so with a small binding enthalpy change in a mostly entropy-driven process. NBD-556 is a competitive inhibitor of sCD4 and elicits a similar structuring of the coreceptor binding site, whereas BMS-378806 does not compete with sCD4 and does not induce coreceptor binding. These studies demonstrate that low-molecular-weight compounds can induce conformational changes in the HIV-1 gp120 glycoprotein similar to those observed upon CD4 binding, revealing distinct strategies for inhibiting the function of the HIV-1 gp120 envelope glycoprotein. Furthermore, competitive and noncompetitive compounds have characteristic thermodynamic signatures that can be used to guide the design of more potent and effective viral entry inhibitors.
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Affiliation(s)
- Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Navid Madani
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Jeffrey C. Klein
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Amy Hubicki
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Danny Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Xinzhen Yang
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joseph Sodroski
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
- All correspondence should be addressed to E. Freire, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218; Phone (410) 516−7743; Fax (410) 516−6469; e-mail
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Dunfee RL, Thomas ER, Gorry PR, Wang J, Taylor J, Kunstman K, Wolinsky SM, Gabuzda D. The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia. Proc Natl Acad Sci U S A 2006; 103:15160-5. [PMID: 17015824 PMCID: PMC1586182 DOI: 10.1073/pnas.0605513103] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Indexed: 11/18/2022] Open
Abstract
HIV infects tissue macrophages and brain microglia, which express lower levels of CD4 and CCR5 than CD4+ T cells in peripheral blood. Mechanisms that enhance HIV tropism for macrophages in the CNS and other tissues are not well understood. Here, we identify an HIV envelope glycoprotein (Env) variant in the CD4-binding site of gp120, Asn 283 (N283), that is present at a high frequency in brain tissues from AIDS patients with HIV-associated dementia (HAD). N283 increases gp120 affinity for CD4 by decreasing the gp120-CD4 dissociation rate, enhancing the capacity of HIV Envs to use low levels of CD4 for virus entry and increasing viral replication in macrophages and microglia. Structural modeling suggests that the enhanced ability of Envs with N283 to use low levels of CD4 is due to a hydrogen bond formed with Gln 40 of CD4. N283 is significantly more frequent in brain-derived Envs from HAD patients (41%; n=330) compared with non-HAD patients (8%; n=151; P<0.001). These findings suggest that the macrophage-tropic HIV Env variant N283 is associated with brain infection and dementia in vivo, representing an example of a HIV variant associated with a specific AIDS-related complication.
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Affiliation(s)
- Rebecca L. Dunfee
- *Department of Cancer Immunology and AIDS, Dana–Farber Cancer Institute, Boston, MA 02115
- Departments of Pathology and
| | - Elaine R. Thomas
- *Department of Cancer Immunology and AIDS, Dana–Farber Cancer Institute, Boston, MA 02115
- Departments of Pathology and
| | - Paul R. Gorry
- *Department of Cancer Immunology and AIDS, Dana–Farber Cancer Institute, Boston, MA 02115
- Departments of Pathology and
| | - Jianbin Wang
- *Department of Cancer Immunology and AIDS, Dana–Farber Cancer Institute, Boston, MA 02115
- Departments of Pathology and
| | - Joann Taylor
- Department of Medicine, Northwestern University Medical School, Chicago, IL 60611
| | - Kevin Kunstman
- Department of Medicine, Northwestern University Medical School, Chicago, IL 60611
| | - Steven M. Wolinsky
- Department of Medicine, Northwestern University Medical School, Chicago, IL 60611
| | - Dana Gabuzda
- *Department of Cancer Immunology and AIDS, Dana–Farber Cancer Institute, Boston, MA 02115
- Neurology, Harvard Medical School, Boston, MA 02115; and
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18
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Ishino T, Pillalamarri U, Panarello D, Bhattacharya M, Urbina C, Horvat S, Sarkhel S, Jameson B, Chaiken I. Asymmetric usage of antagonist charged residues drives interleukin-5 receptor recruitment but is insufficient for receptor activation. Biochemistry 2006; 45:1106-15. [PMID: 16430207 PMCID: PMC2538410 DOI: 10.1021/bi0518038] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cyclic peptide AF17121 (VDECWRIIASHTWFCAEE) is a library-derived antagonist for human Interleukin-5 receptor alpha (IL5Ralpha). We have previously demonstrated that AF17121 mimics Interleukin-5 (IL5) by binding in a region of IL5Ralpha that overlaps the IL5 binding epitope. In the present study, to explore the functional importance of the amino acid residues of AF17121 required for effective binding to, and antagonism of, IL5Ralpha, each charged residue was subjected to site-directed mutagenesis and examined for IL5Ralpha interaction by using a surface plasmon resonance biosensor. One residue, Arg(6), was found to be essential for receptor antagonism; its replacement with either alanine or lysine completely abolished the interaction between AF17121 and IL5Ralpha. Other charged residues play modulatory roles. One class consists of the N-terminal acidic cluster (Asp(2) and Glu(3)) for which alanine replacement decreased the association rate. A second class consists of His(11) and the C-terminal acidic cluster (Glu(17) and Glu(18)) for which alanine replacement increased the dissociation rate. Binding model analysis of the mutants of the latter class of residues indicated the existence of conformational rearrangement during the interaction. On the basis of these results, we propose a model in which Arg(6) and N-terminal acidic residues drive the encounter complex, while Arg(6), His(11), and C-terminal acidic residues are involved in stabilizing the final complex. These data argue that the charged residues of AF17121 are utilized asymmetrically in the pathway of inhibitor-receptor complex formation to deactivate the receptor function. The results also help focus emerging models for the mechanism by which IL5 activates the IL5Ralpha-betac receptor system.
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Affiliation(s)
- Tetsuya Ishino
- Department of Biochemistry and Molecular Biology and A. J. Drexel Institute of Basic and Applied Protein Science, Drexel University College of Medicine Pennsylvania 19102, USA
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19
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Zhao Q, Ma L, Jiang S, Lu H, Liu S, He Y, Strick N, Neamati N, Debnath AK. Identification of N-phenyl-N'-(2,2,6,6-tetramethyl-piperidin-4-yl)-oxalamides as a new class of HIV-1 entry inhibitors that prevent gp120 binding to CD4. Virology 2005; 339:213-25. [PMID: 15996703 DOI: 10.1016/j.virol.2005.06.008] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 05/02/2005] [Accepted: 06/02/2005] [Indexed: 11/19/2022]
Abstract
We have identified two N-phenyl-N'-(2,2,6,6-tetramethyl-piperidin-4-yl)-oxalamide analogs as a novel class of human immunodeficiency virus type 1 (HIV-1) entry inhibitors that block the gp120-CD4 interaction, using database screening techniques. The lead compounds, NBD-556 and NBD-557, are small molecule organic compounds with drug-like properties. These compounds showed potent cell fusion and virus-cell fusion inhibitory activity at low micromolar levels. A systematic study showed that these compounds target viral entry by inhibiting the binding of HIV-1 envelope glycoprotein gp120 to the cellular receptor CD4 but did not inhibit reverse transcriptase, integrase, or protease, indicating that they do not target the later stages of the HIV-1 life cycle to inhibit HIV-1 infection. These compounds were equally potent inhibitors of both X4 and R5 viruses tested in CXCR4 and CCR5 expressing cell lines, respectively, indicating that their anti-HIV-1 activity is not dependent on the coreceptor tropism of the virus. A surface plasmon resonance study, which measures binding affinity, clearly demonstrated that these compounds bind to unliganded HIV-1 gp120 but not to the cellular receptor CD4. NBD-556 and NBD-557 were active against HIV-1 laboratory-adapted strains including an AZT-resistant strain and HIV-1 primary isolates, indicating that these compounds can potentially be further modified to become potent HIV-1 entry inhibitors.
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Affiliation(s)
- Qian Zhao
- Laboratory of Molecular Modeling and Drug Design of the Lindsley F. Kimball Research Institute of The New York Blood Center, 310 E 67th Street, New York, NY 10021, USA
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20
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Abstract
The use of so-called protein scaffolds for the generation of novel binding proteins via combinatorial engineering has recently emerged as a powerful alternative to natural or recombinant antibodies. This concept requires an extraordinary stable protein architecture tolerating multiple substitutions or insertions at the primary structural level. With respect to broader applicability it should involve a type of polypeptide fold which is observed in differing natural contexts and with distinct biochemical functions, so that it is likely to be adaptable to novel molecular recognition purposes. The quickly growing number of approaches can be classified into three groups: carrier proteins for the display of single variegated loops, scaffolds providing rigid elements of secondary structure, and protein frameworks supporting a group of conformationally variable loops in a fixed spatial arrangement. Generally, such artificial receptor proteins should be based on monomeric and small polypeptides that are robust, easily engineered, and efficiently produced in inexpensive prokaryotic expression systems. Today, progress in protein library technology allows for the parallel development of immunoglobulin (Ig) as well as scaffold-based affinity reagents. Both biomolecular tools have the potential to complement each other, thus expanding the possibility to find an affinity reagent suitable for a given application. The repertoire of protein scaffolds hitherto recruited for combinatorial protein engineering purposes will probably be further expanded in the future, including both additional natural proteins and de novo designed proteins, contributing to the collection of libraries available at present. In this review both the structural features and the practical use of scaffold proteins will be discussed and exemplified.
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Affiliation(s)
- Per-Ake Nygren
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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22
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Ishino T, Pasut G, Scibek J, Chaiken I. Kinetic interaction analysis of human interleukin 5 receptor alpha mutants reveals a unique binding topology and charge distribution for cytokine recognition. J Biol Chem 2003; 279:9547-56. [PMID: 14662768 DOI: 10.1074/jbc.m309327200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human interleukin 5 receptor alpha (IL5Ralpha) comprises three fibronectin type III domains (D1, D2, and D3) in the extracellular region. Previous results have indicated that residues in the D1D2 domains are crucial for high affinity interaction with human interleukin 5 (IL5). Yet, it is the D2D3 domains that have sequence homology with the classic cytokine recognition motif that is generally assumed to be the minimum cytokine-recognizing unit. In the present study, we used kinetic interaction analysis of alanine-scanning mutational variants of IL5Ralpha to define the residues involved in IL5 recognition. Soluble forms of IL5Ralpha variants were expressed in S2 cells, selectively captured via their C-terminal V5 tag by anti-V5 tag antibody immobilized onto the sensor chip and examined for IL5 interaction by using a sandwich surface plasmon resonance biosensor method. Marked effects on the interaction kinetics were observed not only in D1 (Asp(55), Asp(56), and Glu(58)) and D2 (Lys(186) and Arg(188)) domains, but also in the D3 (Arg(297)) domain. Modeling of the tertiary structure of IL5Ralpha indicated that these binding residues fell into two clusters. The first cluster consists of D1 domain residues that form a negatively charged patch, whereas the second cluster consists of residues that form a positively charged patch at the interface of D2 and D3 domains. These results suggest that the IL5 x IL5Ralpha system adopts a unique binding topology, in which the cytokine is recognized by a D2D3 tandem domain combined with a D1 domain, to form an extended cytokine recognition interface.
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Affiliation(s)
- Tetsuya Ishino
- Biochemistry Department and A. J. Drexel Institute of Basic and Applied Protein Science, College of Medicine, Drexel University, Philadelphia, Pennsylvania 19102, USA
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