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Lim LZ, Song J. NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na 2SO 4 and NaH 2PO 4. Int J Mol Sci 2024; 25:9091. [PMID: 39201778 PMCID: PMC11354479 DOI: 10.3390/ijms25169091] [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: 07/19/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
The Hofmeister series categorizes ions based on their effects on protein stability, yet the microscopic mechanism remains a mystery. In this series, NaCl is neutral, Na2SO4 and Na2HPO4 are kosmotropic, while GdmCl and NaSCN are chaotropic. This study employs CD and NMR to investigate the effects of NaCl, Na2SO4, and Na2HPO4 on the conformation, stability, binding, and backbone dynamics (ps-ns and µs-ms time scales) of the WW4 domain with a high stability and accessible side chains at concentrations ≤ 200 mM. The results indicated that none of the three salts altered the conformation of WW4 or showed significant binding to the four aliphatic hydrophobic side chains. NaCl had no effect on its thermal stability, while Na2SO4 and Na2HPO4 enhanced the stability by ~5 °C. Interestingly, NaCl only weakly interacted with the Arg27 amide proton, whereas Na2SO4 bound to Arg27 and Phe31 amide protons with Kd of 32.7 and 41.6 mM, respectively. Na2HPO4, however, bound in a non-saturable manner to Trp9, His24, and Asn36 amide protons. While the three salts had negligible effects on ps-ns backbone dynamics, NaCl and Na2SO4 displayed no effect while Na2HPO4 significantly increased the µs-ms backbone dynamics. These findings, combined with our recent results with GdmCl and NaSCN, suggest a microscopic mechanism for the Hofmeister series. Additionally, the data revealed a lack of simple correlation between thermodynamic stability and backbone dynamics, most likely due to enthalpy-entropy compensation. Our study rationalizes the selection of chloride and phosphate as the primary anions in extracellular and intracellular spaces, as well as polyphosphate as a primitive chaperone in certain single-cell organisms.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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2
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Lim LZ, Song J. NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN. Int J Mol Sci 2024; 25:7344. [PMID: 39000450 PMCID: PMC11242413 DOI: 10.3390/ijms25137344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
GdmCl and NaSCN are two strong chaotropic salts commonly used in protein folding and stability studies, but their microscopic mechanisms remain enigmatic. Here, by CD and NMR, we investigated their effects on conformations, stability, binding and backbone dynamics on ps-ns and µs-ms time scales of a 39-residue but well-folded WW4 domain at salt concentrations ≤200 mM. Up to 200 mM, both denaturants did not alter the tertiary packing of WW4, but GdmCl exerted more severe destabilization than NaSCN. Intriguingly, GdmCl had only weak binding to amide protons, while NaSCN showed extensive binding to both hydrophobic side chains and amide protons. Neither denaturant significantly affected the overall ps-ns backbone dynamics, but they distinctively altered µs-ms backbone dynamics. This study unveils that GdmCl and NaSCN destabilize a protein before the global unfolding occurs with differential binding properties and µs-ms backbone dynamics, implying the absence of a simple correlation between thermodynamic stability and backbone dynamics of WW4 at both ps-ns and µs-ms time scales.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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3
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Ganguly D, Thomas JA, Ali A, Kumar R. Mechanistic and therapeutic implications of EphA-4 receptor tyrosine kinase in the pathogenesis of Alzheimer's disease. Eur J Neurosci 2022; 56:5532-5546. [PMID: 34989046 DOI: 10.1111/ejn.15591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors belong to a family of tyrosine kinase receptors that plays a pivotal role in the development of the brain. Eph can be divided broadly into two groups, namely, EphA and EphB, comprising nine and five members, respectively. In recent years, the role of EphA-4 has become increasingly apparent in the onset of Alzheimer's disease (AD). Emerging evidence suggests that EphA-4 results in synaptic dysfunction, which in turn promotes the progression of AD. Moreover, pharmacological or genetic ablation of EphA-4 in the murine model of AD can alleviate the symptoms. The current review summarizes different pathways by which EphA-4 can influence pathogenesis. Since, majority of the studies had reported the protective effect of EphA-4 inhibition during AD, designing therapeutics based on decreasing its enzymatic activity might be necessary for introducing the novel interventions. Therefore, the review described peptide and nanobodies inhibitors of EphA-4 that exhibit the potential to modulate EphA-4 and could be used as lead molecules for the targeted therapy of AD.
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Affiliation(s)
- Devargya Ganguly
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Joshua Abby Thomas
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Abid Ali
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rahul Kumar
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
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Foo CH, Rootes CL, Cowley K, Marsh GA, Gould CM, Deffrasnes C, Cowled CJ, Klein R, Riddell SJ, Middleton D, Simpson KJ, Wang LF, Bean AGD, Stewart CR. Dual microRNA Screens Reveal That the Immune-Responsive miR-181 Promotes Henipavirus Entry and Cell-Cell Fusion. PLoS Pathog 2016; 12:e1005974. [PMID: 27783670 PMCID: PMC5082662 DOI: 10.1371/journal.ppat.1005974] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 10/03/2016] [Indexed: 12/24/2022] Open
Abstract
Hendra and Nipah viruses (family Paramyxoviridae, genus Henipavirus) are bat-borne viruses that cause fatal disease in humans and a range of other mammalian species. Gaining a deeper understanding of host pathways exploited by henipaviruses for infection may identify targets for new anti-viral therapies. Here we have performed genome-wide high-throughput agonist and antagonist screens at biosafety level 4 to identify host-encoded microRNAs (miRNAs) impacting henipavirus infection in human cells. Members of the miR-181 and miR-17~93 families strongly promoted Hendra virus infection. miR-181 also promoted Nipah virus infection, but did not affect infection by paramyxoviruses from other genera, indicating specificity in the virus-host interaction. Infection promotion was primarily mediated via the ability of miR-181 to significantly enhance henipavirus-induced membrane fusion. Cell signalling receptors of ephrins, namely EphA5 and EphA7, were identified as novel negative regulators of henipavirus fusion. The expression of these receptors, as well as EphB4, were suppressed by miR-181 overexpression, suggesting that simultaneous inhibition of several Ephs by the miRNA contributes to enhanced infection and fusion. Immune-responsive miR-181 levels was also up-regulated in the biofluids of ferrets and horses infected with Hendra virus, suggesting that the host innate immune response may promote henipavirus spread and exacerbate disease severity. This study is the first genome-wide screen of miRNAs influencing infection by a clinically significant mononegavirus and nominates select miRNAs as targets for future anti-viral therapy development.
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Affiliation(s)
- Chwan Hong Foo
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Christina L. Rootes
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Karla Cowley
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Glenn A. Marsh
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Cathryn M. Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Celine Deffrasnes
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Christopher J. Cowled
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Reuben Klein
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Sarah J. Riddell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Deborah Middleton
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Kaylene J. Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Andrew G. D. Bean
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Cameron R. Stewart
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- * E-mail:
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5
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Linneberg C, Harboe M, Laursen LS. Axo-Glia Interaction Preceding CNS Myelination Is Regulated by Bidirectional Eph-Ephrin Signaling. ASN Neuro 2015; 7:7/5/1759091415602859. [PMID: 26354550 PMCID: PMC4568937 DOI: 10.1177/1759091415602859] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In the central nervous system, myelination of axons is required to ensure fast saltatory conduction and for survival of neurons. However, not all axons are myelinated, and the molecular mechanisms involved in guiding the oligodendrocyte processes toward the axons to be myelinated are not well understood. Only a few negative or positive guidance clues that are involved in regulating axo-glia interaction prior to myelination have been identified. One example is laminin, known to be required for early axo-glia interaction, which functions through α6β1 integrin. Here, we identify the Eph-ephrin family of guidance receptors as novel regulators of the initial axo-glia interaction, preceding myelination. We demonstrate that so-called forward and reverse signaling, mediated by members of both Eph and ephrin subfamilies, has distinct and opposing effects on processes extension and myelin sheet formation. EphA forward signaling inhibits oligodendrocyte process extension and myelin sheet formation, and blocking of bidirectional signaling through this receptor enhances myelination. Similarly, EphB forward signaling also reduces myelin membrane formation, but in contrast to EphA forward signaling, this occurs in an integrin-dependent manner, which can be reversed by overexpression of a constitutive active β1-integrin. Furthermore, ephrin-B reverse signaling induced by EphA4 or EphB1 enhances myelin sheet formation. Combined, this suggests that the Eph-ephrin receptors are important mediators of bidirectional signaling between axons and oligodendrocytes. It further implies that balancing Eph-ephrin forward and reverse signaling is important in the selection process of axons to be myelinated.
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Affiliation(s)
- Cecilie Linneberg
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, Aarhus, Denmark
| | - Mette Harboe
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, Aarhus, Denmark
| | - Lisbeth S Laursen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, Aarhus, Denmark
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6
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Qin H, Lim L, Wei Y, Gupta G, Song J. Resolving the paradox for protein aggregation diseases: NMR structure and dynamics of the membrane-embedded P56S-MSP causing ALS imply a common mechanism for aggregation-prone proteins to attack membranes. F1000Res 2013; 2:221. [PMID: 25254094 PMCID: PMC4168755 DOI: 10.12688/f1000research.2-221.v2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2014] [Indexed: 12/12/2022] Open
Abstract
Paradoxically, aggregation of specific proteins is characteristic of many human diseases and aging, yet aggregates have increasingly been found to be unnecessary for initiating pathogenesis. Here we determined the NMR topology and dynamics of a helical mutant in a membrane environment transformed from the 125-residue cytosolic all-β MSP domain of vesicle-associated membrane protein-associated protein B (VAPB) by the ALS-causing P56S mutation. Despite its low hydrophobicity, the P56S major sperm protein (MSP) domain becomes largely embedded in the membrane environment with high backbone rigidity. Furthermore it is composed of five helices with amphiphilicity comparable to those of the partly-soluble membrane toxin mellitin and α-synuclein causing Parkinson's disease. Consequently, the mechanism underlying this chameleon transformation becomes clear: by disrupting the specific tertiary interaction network stabilizing the native all-β MSP fold to release previously-locked amphiphilic segments, the P56S mutation acts to convert the classic MSP fold into a membrane-active protein that is fundamentally indistinguishable from mellitin and α-synuclein which are disordered in aqueous solution but spontaneously partition into membrane interfaces driven by hydrogen-bond energetics gained from forming α-helix in the membrane environments. As segments with high amphiphilicity exist in all proteins, our study successfully resolves the paradox by deciphering that the proteins with a higher tendency to aggregate have a stronger potential to partition into membranes through the same mechanism as α-synuclein to initially attack membranes to trigger pathogenesis without needing aggregates. This might represent the common first step for various kinds of aggregated proteins to trigger familiar, sporadic and aging diseases. Therefore the homeostasis of aggregated proteins in vivo is the central factor responsible for a variety of human diseases including aging. The number and degree of the membrane attacks by aggregated proteins may act as an endogenous clock to count down the aging process. Consequently, a key approach to fight against them is to develop strategies and agents to maintain or even enhance the functions of the degradation machineries.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Yuanyuan Wei
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
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7
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Qin H, Lim L, Wei Y, Gupta G, Song J. Resolving the paradox for protein aggregation diseases: NMR structure and dynamics of the membrane-embedded P56S-MSP causing ALS imply a common mechanism for aggregation-prone proteins to attack membranes. F1000Res 2013. [PMID: 25254094 DOI: 10.12688/f1000research.2-221.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Paradoxically, aggregation of specific proteins is characteristic of many human diseases and aging, yet aggregates have increasingly been found to be unnecessary for initiating pathogenesis. Here we determined the NMR topology and dynamics of a helical mutant in a membrane environment transformed from the 125-residue cytosolic all-β MSP domain of vesicle-associated membrane protein-associated protein B (VAPB) by the ALS-causing P56S mutation. Despite its low hydrophobicity, the P56S major sperm protein (MSP) domain becomes largely embedded in the membrane environment with high backbone rigidity. Furthermore it is composed of five helices with amphiphilicity comparable to those of the partly-soluble membrane toxin mellitin and α-synuclein causing Parkinson's disease. Consequently, the mechanism underlying this chameleon transformation becomes clear: by disrupting the specific tertiary interaction network stabilizing the native all-β MSP fold to release previously-locked amphiphilic segments, the P56S mutation acts to convert the classic MSP fold into a membrane-active protein that is fundamentally indistinguishable from mellitin and α-synuclein which are disordered in aqueous solution but spontaneously partition into membrane interfaces driven by hydrogen-bond energetics gained from forming α-helix in the membrane environments. As segments with high amphiphilicity exist in all proteins, our study successfully resolves the paradox by deciphering that the proteins with a higher tendency to aggregate have a stronger potential to partition into membranes through the same mechanism as α-synuclein to initially attack membranes to trigger pathogenesis without needing aggregates. This might represent the common first step for various kinds of aggregated proteins to trigger familiar, sporadic and aging diseases. Therefore the homeostasis of aggregated proteins in vivo is the central factor responsible for a variety of human diseases including aging. The number and degree of the membrane attacks by aggregated proteins may act as an endogenous clock to count down the aging process. Consequently, a key approach to fight against them is to develop strategies and agents to maintain or even enhance the functions of the degradation machineries.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Yuanyuan Wei
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
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8
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Thomas MG, Saldanha M, Mistry RJ, Dexter DT, Ramsden DB, Parsons RB. Nicotinamide N-methyltransferase expression in SH-SY5Y neuroblastoma and N27 mesencephalic neurones induces changes in cell morphology via ephrin-B2 and Akt signalling. Cell Death Dis 2013; 4:e669. [PMID: 23764850 PMCID: PMC3702289 DOI: 10.1038/cddis.2013.200] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 01/12/2023]
Abstract
Nicotinamide N-methyltransferase (NNMT, E.C. 2.1.1.1) N-methylates nicotinamide to produce 1-methylnicotinamide (MeN). We have previously shown that NNMT expression protected against neurotoxin-mediated cell death by increasing Complex I (CxI) activity, resulting in increased ATP synthesis. This was mediated via protection of the NDUFS3 subunit of CxI from degradation by increased MeN production. In the present study, we have investigated the effects of NNMT expression on neurone morphology and differentiation. Expression of NNMT in SH-SY5Y human neuroblastoma and N27 rat mesencephalic dopaminergic neurones increased neurite branching, synaptophysin expression and dopamine accumulation and release. siRNA gene silencing of ephrin B2 (EFNB2), and inhibition of Akt phosphorylation using LY294002, demonstrated that their sequential activation was responsible for the increases observed. Incubation of SH-SY5Y with increasing concentrations of MeN also increased neurite branching, suggesting that the effects of NNMT may be mediated by MeN. NNMT had no significant effect on the expression of phenotypic and post-mitotic markers, suggesting that NNMT is not involved in determining phenotypic fate or differentiation status. These results demonstrate that NNMT expression regulates neurone morphology in vitro via the sequential activation of the EFNB2 and Akt cellular signalling pathways.
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Affiliation(s)
- M G Thomas
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - M Saldanha
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - R J Mistry
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - D T Dexter
- Parkinson's Disease Research Group, Centre for Neuroinflammation and Neurodegeneration, Division of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - D B Ramsden
- Department of Medicine, University of Birmingham, Edgbaston, Birmingham B15 2TH, UK
| | - R B Parsons
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
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Song J. Why do proteins aggregate? "Intrinsically insoluble proteins" and "dark mediators" revealed by studies on "insoluble proteins" solubilized in pure water. F1000Res 2013; 2:94. [PMID: 24555050 PMCID: PMC3869494 DOI: 10.12688/f1000research.2-94.v1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/22/2022] Open
Abstract
In 2008, I reviewed and proposed a model for our discovery in 2005 that unrefoldable and insoluble proteins could in fact be solubilized in unsalted water. Since then, this discovery has offered us and other groups a powerful tool to characterize insoluble proteins, and we have further addressed several fundamental and disease-relevant issues associated with this discovery. Here I review these results, which are conceptualized into several novel scenarios. 1) Unlike 'misfolded proteins', which still retain the capacity to fold into well-defined structures but are misled to 'off-pathway' aggregation, unrefoldable and insoluble proteins completely lack this ability and will unavoidably aggregate in vivo with ~150 mM ions, thus designated as 'intrinsically insoluble proteins (IIPs)' here. IIPs may largely account for the 'wastefully synthesized' DRiPs identified in human cells. 2) The fact that IIPs including membrane proteins are all soluble in unsalted water, but get aggregated upon being exposed to ions, logically suggests that ions existing in the background play a central role in mediating protein aggregation, thus acting as 'dark mediators'. Our study with 14 salts confirms that IIPs lack the capacity to fold into any well-defined structures. We uncover that salts modulate protein dynamics and anions bind proteins with high selectivity and affinity, which is surprisingly masked by pre-existing ions. Accordingly, I modified my previous model. 3) Insoluble proteins interact with lipids to different degrees. Remarkably, an ALS-causing P56S mutation transforms the β-sandwich MSP domain into a helical integral membrane protein. Consequently, the number of membrane-interacting proteins might be much larger than currently recognized. To attack biological membranes may represent a common mechanism by which aggregated proteins initiate human diseases. 4) Our discovery also implies a solution to the 'chicken-and-egg paradox' for the origin of primitive membranes embedded with integral membrane proteins, if proteins originally emerged in unsalted prebiotic media.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119260, Singapore
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Qin H, Lim L, Song J. Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations. BMC BIOPHYSICS 2012; 5:2. [PMID: 22277260 PMCID: PMC3274464 DOI: 10.1186/2046-1682-5-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 01/25/2012] [Indexed: 12/21/2022]
Abstract
Background The role of dynamics in protein functions including signal transduction is just starting to be deciphered. Eph receptors with 16 members divided into A- and B- subclasses are respectively activated by 9 A- and B-ephrin ligands. EphA4 is the only receptor capable of binding to all 9 ephrins and small molecules with overlapped interfaces. Results We first determined the structures of the EphA4 ligand binding domain (LBD) in two crystals of P1 space group. Noticeably, 8 EphA4 molecules were found in one asymmetric unit and consequently from two crystals we obtained 16 structures, which show significant conformational variations over the functionally critical A-C, D-E, G-H and J-K loops. The 16 new structures, together with previous 9 ones, can be categorized into two groups: closed and open forms which resemble the uncomplexed and complexed structures of the EphA4 LBD respectively. To assess whether the conformational diversity over the loops primarily results from the intrinsic dynamics, we initiated 30-ns molecular dynamics (MD) simulations for both closed and open forms. The results indicate that the loops do have much higher intrinsic dynamics, which is further unravelled by NMR H/D exchange experiments. During simulations, the open form has the RMS deviations slightly larger than those of the closed one, suggesting the open form may be less stable in the absence of external contacts. Furthermore, no obvious exchange between two forms is observed within 30 ns, implying that they are dynamically separated. Conclusions Our study provides the first experimental and computational result revealing that the intrinsic dynamics are most likely underlying the conformational diversity observed for the EphA4 LBD loops mediating the binding affinity and specificity. Interestingly, the open conformation of the EphA4 LBD is slightly unstable in the absence of it natural ligand ephrins, implying that the conformational transition from the closed to open has to be driven by the high-affinity interaction with ephrins because the weak interaction with small molecule was found to be insufficient to trigger the transition. Our results therefore highlight the key role of protein dynamics in Eph-ephrin signalling and would benefit future design of agonists/antagonists targeting Eph receptors.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Republic of Singapore
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Lua S, Qin H, Lim L, Shi J, Gupta G, Song J. Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations. PLoS One 2011; 6:e27072. [PMID: 22069488 PMCID: PMC3206076 DOI: 10.1371/journal.pone.0027072] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/09/2011] [Indexed: 12/31/2022] Open
Abstract
T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS). Here using CD, NMR and molecular dynamics (MD) simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1) unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2) Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3) T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4) EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5) As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.
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Affiliation(s)
- Shixiong Lua
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jiahai Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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12
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Himanen JP. Ectodomain structures of Eph receptors. Semin Cell Dev Biol 2011; 23:35-42. [PMID: 22044883 DOI: 10.1016/j.semcdb.2011.10.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/17/2011] [Indexed: 11/25/2022]
Abstract
Eph receptors, the largest subfamily of receptor tyrosine kinases (RTKs), and their ephrin ligands are important mediators of cell-cell communication that regulate axon guidance, long-term potentiation, and stem cell development, among others. By now, many Eph receptors and ephrins have also been found to play important roles in the progression of cancer. Since both the receptor and the ligand are membrane-bound, their interaction leads to the multimerization of both molecules to distinct clusters within their respective plasma membranes, resulting in the formation of discrete signaling centers. In addition, and unique to Eph receptors and ephrins, their interaction initiates bi-directional signaling cascades where information is transduced in the direction of both the receptor- and the ligand-bearing cells. The Ephs and the ephrins are divided into two subclasses, A and B, based on their affinities for each other and on sequence conservation. Crystal structures and other biophysical studies have indicated that isolated extracellular Eph and ephrin domains initially form high-affinity heterodimers around a hydrophobic loop of the ligand that is buried in a hydrophobic pocket on the surface of the receptor. The dimers can then further arrange by weaker interactions into higher-order Eph/ephrin clusters observed in vivo at the sites of cell-cell contact. Although the hetero-dimerization is a universal way to initiate signaling, other extracellular domains of Ephs are involved in the formation of higher-order clusters. The structures also show important differences defining the unique partner preferences of the two ligand and receptor subclasses, namely, how subclass specificity is determined both by individual interacting residues and by the precise architectural arrangement of ligands and receptors within the complexes.
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Affiliation(s)
- Juha P Himanen
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Qin H, Noberini R, Huan X, Shi J, Pasquale EB, Song J. Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity. J Biol Chem 2010; 285:644-54. [PMID: 19875447 PMCID: PMC2804212 DOI: 10.1074/jbc.m109.064824] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 10/19/2009] [Indexed: 11/06/2022] Open
Abstract
EphA and EphB receptors preferentially bind ephrin-A and ephrin-B ligands, respectively, but EphA4 is exceptional for its ability to bind all ephrins. Here, we report the crystal structure of the EphA4 ligand-binding domain in complex with ephrin-B2, which represents the first structure of an EphA-ephrin-B interclass complex. A loose fit of the ephrin-B2 G-H loop in the EphA4 ligand-binding channel is consistent with a relatively weak binding affinity. Additional surface contacts also exist between EphA4 residues Gln(12) and Glu(14) and ephrin-B2. Mutation of Gln(12) and Glu(14) does not cause significant structural changes in EphA4 or changes in its affinity for ephrin-A ligands. However, the EphA4 mutant has approximately 10-fold reduced affinity for ephrin-B ligands, indicating that the surface contacts are critical for interclass but not intraclass ephrin binding. Thus, EphA4 uses different strategies to bind ephrin-A or ephrin-B ligands and achieve binding promiscuity. NMR characterization also suggests that the contacts of Gln(12) and Glu(14) with ephrin-B2 induce dynamic changes throughout the whole EphA4 ligand-binding domain. Our findings shed light on the distinctive features that enable the remarkable ligand binding promiscuity of EphA4 and suggest that diverse strategies are needed to effectively disrupt different Eph-ephrin complexes.
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Affiliation(s)
- Haina Qin
- From the Department of Biological Sciences, Faculty of Science
| | - Roberta Noberini
- the Burnham Institute for Medical Research, La Jolla, California 92037, and
| | - Xuelu Huan
- National University of Singapore Graduate School for Integrative Sciences and Engineering, and
| | - Jiahai Shi
- From the Department of Biological Sciences, Faculty of Science
| | - Elena B. Pasquale
- the Burnham Institute for Medical Research, La Jolla, California 92037, and
- the Pathology Department, University of California, San Diego, La Jolla, California 92093
| | - Jianxing Song
- From the Department of Biological Sciences, Faculty of Science
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
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Insights into protein aggregation by NMR characterization of insoluble SH3 mutants solubilized in salt-free water. PLoS One 2009; 4:e7805. [PMID: 19956763 PMCID: PMC2776303 DOI: 10.1371/journal.pone.0007805] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/16/2009] [Indexed: 12/02/2022] Open
Abstract
Protein aggregation in vivo has been extensively associated with a large spectrum of human diseases. On the other hand, mechanistic insights into protein aggregation in vitro were incomplete due to the inability in solubilizing insoluble proteins for high-resolution biophysical investigations. However, a new avenue may be opened up by our recent discovery that previously-thought insoluble proteins can in fact be solubilized in salt-free water. Here we use this approach to study the NMR structural and dynamic properties of an insoluble SH3 mutant with a naturally-occurring insertion of Val22 at the tip of the diverging turn. The obtained results reveal: 1) regardless of whether the residue is Val, Ala, Asp or Arg, the insertion will render the first hNck2 SH3 domain to be insoluble in buffers. Nevertheless, all four mutants could be solubilized in salt-free water and appear to be largely unfolded as evident from their CD and NMR HSQC spectra. 2) Comparison of the chemical shift deviations reveals that while in V22-SH3 the second helical region is similarly populated as in the wild-type SH3 at pH 2.0, the first helical region is largely unformed. 3) In V22-SH3, many non-native medium-range NOEs manifest to define non-native helical conformations. In the meanwhile a small group of native-like long-range NOEs still persists, indicating the existence of a rudimentary native-like tertiary topology. 4) Although overall, V22-SH3 has significantly increased backbone motions on the ps-ns time scale, some regions still own restricted backbone motions as revealed by analyzing 15N relaxation data. Our study not only leads to the establishment of the first high-resolution structural and dynamic picture for an insoluble protein, but also shed more light on the molecular events for the nonhierarchical folding mechanism. Furthermore, a general mechanism is also proposed for in vivo protein aggregation triggered by the genetic mutation and posttranslational modification.
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Song J. Insight into "insoluble proteins" with pure water. FEBS Lett 2009; 583:953-9. [PMID: 19233178 DOI: 10.1016/j.febslet.2009.02.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/14/2009] [Accepted: 02/16/2009] [Indexed: 10/21/2022]
Abstract
Many proteins are not refoldable and also insoluble. Previously no general method was available to solubilize them and consequently their structural properties remained unknown. Surprisingly, we recently discovered that all insoluble proteins in our laboratory, which are highly diverse, can be solubilized in pure water. Structural characterization by CD and NMR led to their classification into three groups, all of which appear trapped in the highly disordered or partially-folded states with a substantial exposure of hydrophobic side chains. In this review, I discuss our results in a wide context and subsequently propose a model to rationalize the discovery. The potential applications are also explored in studying protein folding, design and membrane proteins.
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Affiliation(s)
- Jianxing Song
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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17
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Goldgur Y, Paavilainen S, Nikolov D, Himanen JP. Structure of the ligand-binding domain of the EphB2 receptor at 2 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:71-4. [PMID: 19193989 PMCID: PMC2635866 DOI: 10.1107/s1744309108043078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 12/17/2008] [Indexed: 01/03/2023]
Abstract
Eph tyrosine kinase receptors, the largest group of receptor tyrosine kinases, and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, shape and mobility. Recently, several Eph receptors and ephrins have also been found to play important roles in the progression of cancer. Structural and biophysical studies have established detailed information on the binding and recognition of Eph receptors and ephrins. The initial high-affinity binding of Eph receptors to ephrin occurs through the penetration of an extended G-H loop of the ligand into a hydrophobic channel on the surface of the receptor. Consequently, the G-H loop-binding channel of Eph receptors is the main target in the search for Eph antagonists that could be used in the development of anticancer drugs and several peptides have been shown to specifically bind Eph receptors and compete with the cognate ephrin ligands. However, the molecular details of the conformational changes upon Eph/ephrin binding have remained speculative, since two of the loops were unstructured in the original model of the free EphB2 structure and their conformational changes upon ligand binding could consequently not be analyzed in detail. In this study, the X-ray structure of unbound EphB2 is reported at a considerably higher 2 A resolution, the conformational changes that the important receptor loops undergo upon ligand binding are described and the consequences that these findings have for the development of Eph antagonists are discussed.
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Affiliation(s)
- Yehuda Goldgur
- Structural Biology Program, Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, New York 10065, USA
| | - Sari Paavilainen
- JBL Laboratory, University of Turku, BioCity 6A, 20520 Turku, Finland
| | - Dimitar Nikolov
- Structural Biology Program, Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, New York 10065, USA
| | - J. P. Himanen
- Structural Biology Program, Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, New York 10065, USA
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Qin H, Pu HX, Li M, Ahmed S, Song J. Identification and structural mechanism for a novel interaction between a ubiquitin ligase WWP1 and Nogo-A, a key inhibitor for central nervous system regeneration. Biochemistry 2009; 47:13647-58. [PMID: 19035836 DOI: 10.1021/bi8017976] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nogo-A has been extensively demonstrated to play key roles in inhibiting central nervous system regeneration, regulating endoplasmic reticulum formation, and maintaining the integrity of the neuromuscular junction. In this study, an E3 ubiquitin ligase WWP1 was first identified to be a novel interacting partner for Nogo-A both in vitro and in vivo. By using CD, ITC, and NMR, we have further conducted extensive studies on all four WWP1 WW domains and their interactions with a Nogo-A peptide carrying the only PPxY motif. The results lead to several striking findings. (1) Despite containing an unstructured region, the 186-residue WWP1 fragment containing all four WW domains is able to interact with the Nogo-A(650-666) peptide with a high affinity, with a dissociation constant (K(d)) of 1.68 microM. (2) Interestingly, four isolated WW domains show differential structural properties in the free states. WW1 and WW2 are only partially folded, while WW4 is well-folded. Nevertheless, they all become well-folded upon binding to Nogo-A(650-666), with K(d) values ranging from 1.03 to 3.85 microM. (3) The solution structure of the best-folded WW4 domain is determined, and the binding-perturbed residues were derived for both WW4 and Nogo-A(650-666) by NMR HSQC titrations. Moreover, on the basis of the NMR data, the complex model is constructed by HADDOCK 2.0. This study provides rationales as well as a template Nogo-A(650-666) for further design of molecules to intervene in the WWP1-Nogo-A interaction which may regulate the Nogo-A protein level by controlling its ubiquitination.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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Qin H, Shi J, Noberini R, Pasquale EB, Song J. Crystal structure and NMR binding reveal that two small molecule antagonists target the high affinity ephrin-binding channel of the EphA4 receptor. J Biol Chem 2008; 283:29473-84. [PMID: 18708347 DOI: 10.1074/jbc.m804114200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Eph receptor tyrosine kinases regulate a variety of physiological and pathological processes not only during development but also in adult organs, and therefore they represent a promising class of drug targets. The EphA4 receptor plays important roles in the inhibition of the regeneration of injured axons, synaptic plasticity, platelet aggregation, and likely in certain types of cancer. Here we report the first crystal structure of the EphA4 ligand-binding domain, which adopts the same jellyroll beta-sandwich architecture as shown previously for EphB2 and EphB4. The similarity with EphB receptors is high in the core beta-stranded regions, whereas large variations exist in the loops, particularly the D-E and J-K loops, which form the high affinity ephrin binding channel. We also used isothermal titration calorimetry, NMR spectroscopy, and computational docking to characterize the binding to EphA4 of two small molecules, 4- and 5-(2,5 dimethyl-pyrrol-1-yl)-2-hydroxybenzoic acid which antagonize ephrin-induced effects in EphA4-expressing cells. We show that the two molecules bind to the EphA4 ligand-binding domain with K(d) values of 20.4 and 26.4 microm, respectively. NMR heteronuclear single quantum coherence titrations revealed that upon binding, both molecules significantly perturb EphA4 residues Ile(31)-Met(32) in the D-E loop, Gln(43) in the E beta-strand, and Ile(131)-Gly(132) in the J-K loop. Molecular docking shows that they can occupy a cavity in the high affinity ephrin binding channel of EphA4 in a similar manner, by interacting mainly with the EphA4 residues in the E strand and D-E and J-K loops. However, many of the interactions observed in Eph receptor-ephrin complexes are absent, which is consistent with the small size of the two molecules and may account for their relatively weak binding affinity. Thus, our studies provide the first published structure of the ligand-binding domain of an EphA receptor of the A subclass. Furthermore, the results demonstrate that the high affinity ephrin binding channel of the Eph receptors is amenable to targeting with small molecule antagonists and suggest avenues for further optimization.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 11926
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