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Targeting of microvillus protein Eps8 by the NleH effector kinases from enteropathogenic E. coli. Proc Natl Acad Sci U S A 2022; 119:e2204332119. [PMID: 35976880 PMCID: PMC9407544 DOI: 10.1073/pnas.2204332119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Attaching and effacing (AE) lesion formation on enterocytes by enteropathogenic Escherichia coli (EPEC) requires the EPEC type III secretion system (T3SS). Two T3SS effectors injected into the host cell during infection are the atypical kinases, NleH1 and NleH2. However, the host targets of NleH1 and NleH2 kinase activity during infection have not been reported. Here phosphoproteomics identified Ser775 in the microvillus protein Eps8 as a bona fide target of NleH1 and NleH2 phosphorylation. Both kinases interacted with Eps8 through previously unrecognized, noncanonical "proline-rich" motifs, PxxDY, that bound the Src Homology 3 (SH3) domain of Eps8. Structural analysis of the Eps8 SH3 domain bound to a peptide containing one of the proline-rich motifs from NleH showed that the N-terminal part of the peptide adopts a type II polyproline helix, and its C-terminal "DY" segment makes multiple contacts with the SH3 domain. Ser775 phosphorylation by NleH1 or NleH2 hindered Eps8 bundling activity and drove dispersal of Eps8 from the AE lesion during EPEC infection. This finding suggested that NleH1 and NleH2 altered the cellular localization of Eps8 and the cytoskeletal composition of AE lesions during EPEC infection.
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2
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Asthana P, Singh D, Pedersen JS, Hynönen MJ, Sulu R, Murthy AV, Laitaoja M, Jänis J, Riley LW, Venkatesan R. Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis. IUCRJ 2021; 8:757-774. [PMID: 34584737 PMCID: PMC8420772 DOI: 10.1107/s2052252521006199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 05/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb), which is responsible for more than a million deaths annually, uses lipids as the source of carbon and energy for its survival in the latent phase of infection. Mtb cannot synthesize all of the lipid molecules required for its growth and pathogenicity. Therefore, it relies on transporters such as the mammalian cell entry (Mce) complexes to import lipids from the host across the cell wall. Despite their importance for the survival and pathogenicity of Mtb, information on the structural properties of these proteins is not yet available. Each of the four Mce complexes in Mtb (Mce1-4) comprises six substrate-binding proteins (SBPs; MceA-F), each of which contains four conserved domains (N-terminal transmembrane, MCE, helical and C-terminal unstructured tail domains). Here, the properties of the various domains of Mtb Mce1A and Mce4A, which are involved in the import of mycolic/fatty acids and cholesterol, respectively, are reported. In the crystal structure of the MCE domain of Mce4A (MtMce4A39-140) a domain-swapped conformation is observed, whereas solution studies, including small-angle X-ray scattering (SAXS), indicate that all Mce1A and Mce4A domains are predominantly monomeric. Further, structural comparisons show interesting differences from the bacterial homologs MlaD, PqiB and LetB, which form homohexamers when assembled as functional transporter complexes. These data, and the fact that there are six SBPs in each Mtb mce operon, suggest that the MceA-F SBPs from Mce1-4 may form heterohexamers. Also, interestingly, the purification and SAXS analysis showed that the helical domains interact with the detergent micelle, suggesting that when assembled the helical domains of MceA-F may form a hydrophobic pore for lipid transport, as observed in EcPqiB. Overall, these data highlight the unique structural properties of the Mtb Mce SBPs.
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Affiliation(s)
- Pooja Asthana
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Dhirendra Singh
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Mikko J. Hynönen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ramita Sulu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Abhinandan V. Murthy
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Lee W. Riley
- School of Public Health, University of California, Berkeley, California, USA
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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3
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EPS8 phosphorylation by Src modulates its oncogenic functions. Br J Cancer 2020; 123:1078-1088. [PMID: 32641864 PMCID: PMC7525440 DOI: 10.1038/s41416-020-0976-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/18/2020] [Accepted: 06/17/2020] [Indexed: 11/15/2022] Open
Abstract
Background EPS8 is a scaffolding protein that regulates proliferation, actin dynamics and receptor trafficking. Its expression is increased in cancer, enhancing mitogenesis, migration and tumorigenesis. Src phosphorylates EPS8 at four tyrosine residues, although the function is unknown. Here we investigated the pro-oncogenic role of EPS8 tyrosine phosphorylation at Src target sites in HNSCC. Methods Plasmids expressing EPS8 Src-mediated phosphorylation site mutants (Y485F, Y525F, Y602F, Y774F and all four combined [FFFF]) were expressed in cells containing a normal endogenous level of EPS8. In addition, cells were treated with dasatinib to inhibit Src activity. EPS8 downstream targets were evaluated by western blotting. Wound closure, proliferation, immunofluorescence and tumorgenicity assays were used to investigate the impact of phenylalanine mutations on EPS8 biological functions. Results FOXM1, AURKA, and AURKB were decreased in cells expressing FFFF- and Y602F-EPS8 mutants, while cells harbouring the Y485F-, Y525F- and Y774F-EPS8 mutants showed no differences compared to controls. Consistent with this, dasatinib decreased the expression of EPS8 targets. Moreover, Y602F- and FFFF-EPS8 mutants reduced mitogenesis and motility. Strikingly though, FFFF- or Y602F-EPS8 mutants actually promoted tumorigenicity compared with control cells. Conclusions Phosphorylation of EPS8 at Y602 is crucial for signalling to the cell cycle and may provide insight to explain reduced efficacy of dasatinib treatment.
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Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG. Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. J Biol Chem 2020; 295:7849-7864. [PMID: 32317279 PMCID: PMC7278359 DOI: 10.1074/jbc.ra120.012788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3ϵ interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3ϵ interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (ζ chain of T cell receptor–associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro. Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3ϵ. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3ϵ, possibly representing an inactive form of Nck in cells.
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Affiliation(s)
- Kirsten Richter
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arne C Rufer
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Magali Muller
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dominique Burger
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Fabio Casagrande
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tabea Grossenbacher
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sylwia Huber
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melanie N Hug
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Philipp Koldewey
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andrea D'Osualdo
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Daniel Schlatter
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Theodor Stoll
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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5
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Ngan AWL, Grace Tsui M, So DHF, Leung WY, Chan DW, Yao KM. Novel Nuclear Partnering Role of EPS8 With FOXM1 in Regulating Cell Proliferation. Front Oncol 2019; 9:154. [PMID: 30941306 PMCID: PMC6433973 DOI: 10.3389/fonc.2019.00154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
One hallmark of cancer cells is sustaining proliferative signaling that leads to uncontrolled cell proliferation. Both the Forkhead box (FOX) M1 transcription factor and the Epidermal Growth Factor (EGF) receptor Pathway Substrate 8 (EPS8) are known to be activated by mitogenic signaling and their levels upregulated in cancer. Well-known to regulate Rac-mediated actin remodeling at the cell cortex, EPS8 carries a nuclear localization signal but its possible nuclear role remains unclear. Here, we demonstrated interaction of FOXM1 with EPS8 in yeast two-hybrid and immunoprecipitation assays. Immunostaining revealed co-localization of the two proteins during G2/M phase of the cell cycle. EPS8 became nuclear localized when CRM1/Exportin 1-dependent nuclear export was inhibited by Leptomycin B, and a functional nuclear export signal could be identified within EPS8 using EGFP-tagging and site-directed mutagenesis. Downregulation of EPS8 using shRNAs suppressed expression of FOXM1 and the FOXM1-target CCNB1, and slowed down G2/M transition in cervical cancer cells. Chromatin immunoprecipitation analysis indicated recruitment of EPS8 to the CCNB1 and CDC25B promoters. Taken together, our findings support a novel partnering role of EPS8 with FOXM1 in the regulation of cancer cell proliferation and provides interesting insight into future design of therapeutic strategy to inhibit cancer cell proliferation.
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Affiliation(s)
- Adaline Wan Ling Ngan
- School of Biomedical Sciences, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Michelle Grace Tsui
- School of Biomedical Sciences, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Hon Fai So
- School of Biomedical Sciences, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai Ying Leung
- School of Biomedical Sciences, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - David W Chan
- Department of Obstetrics and Gynaecology, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Ming Yao
- School of Biomedical Sciences, The LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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6
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Rufer AC, Kusznir E, Burger D, Stihle M, Ruf A, Rudolph MG. Domain swap in the C-terminal ubiquitin-like domain of human doublecortin. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:450-462. [PMID: 29717716 DOI: 10.1107/s2059798318004813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/23/2018] [Indexed: 11/10/2022]
Abstract
Doublecortin, a microtubule-associated protein that is only produced during neurogenesis, cooperatively binds to microtubules and stimulates microtubule polymerization and cross-linking by unknown mechanisms. A domain swap is observed in the crystal structure of the C-terminal domain of doublecortin. As determined by analytical ultracentrifugation, an open conformation is also present in solution. At higher concentrations, higher-order oligomers of the domain are formed. The domain swap and additional interfaces observed in the crystal lattice can explain the formation of doublecortin tetramers or multimers, in line with the analytical ultracentrifugation data. Taken together, the domain swap offers a mechanism for the observed cooperative binding of doublecortin to microtubules. Doublecortin-induced cross-linking of microtubules can be explained by the same mechanism. The effect of several mutations leading to lissencephaly and double-cortex syndrome can be traced to the domain swap and the proposed self-association of doublecortin.
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Affiliation(s)
- Arne C Rufer
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Eric Kusznir
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Dominique Burger
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Martine Stihle
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Armin Ruf
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Markus G Rudolph
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
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7
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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8
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Buro C, Burmeister C, Quack T, Grevelding CG. Identification and first characterization of SmEps8, a potential interaction partner of SmTK3 and SER transcribed in the gonads of Schistosoma mansoni. Exp Parasitol 2016; 180:55-63. [PMID: 28017636 DOI: 10.1016/j.exppara.2016.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 10/28/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023]
Abstract
In eukaryotes the roles of protein kinases (PKs) regulating important biological processes such as growth and differentiation are well known. Molecular, biochemical, and physiological analyses trying to unravel principles of schistosome development have substantiated the importance for PKs also in this parasite. Amongst others the role of SmTK3 was studied, one of the first cellular PKs characterized from Schistosoma mansoni. Its function was demonstrated in mitogenic and differentiation processes in the gonads. Furthermore, first insights were obtained for the downstream part of a signal transduction cascade SmTK3 is involved in, which includes the diaphanous homolog SmDia. Here we attempted to further unravel the SmTK3 signaling cascade by searching for upstream interaction partners. Using yeast three-hybrid (Y3H) analyses we detected the epidermal growth factor receptor (EGFR) pathway substrate 8 of S. mansoni (SmEps8) as the most interesting candidate. By detailed interaction analyses we showed a contribution of the Src homology (SH) domains SH2 and SH3 of SmTK3 to binding, with a clear bias towards SH2. Compared to full-length SmEps8, binding was enhanced when only its 5' part including the phosphotyrosine binding domain (PTB) was used for interaction analyses including the SH2 domain of SmTK3, although phosphorylation seemed not to play a decisive role for binding. RT-PCR analyses and in situ hybridization experiments demonstrated similar transcription patterns of SmTK3 and SmEPS8, which co-localize in the reproductive organs. Furthermore, first evidence was obtained for SmEps8 interaction and colocalization with SER, one of the epidermal growth factor receptor (EGFR) homologs detected in S. mansoni. The results of this study provide first evidence for a SER-SmEps8-SmTK3-SmDia signal transduction pathway controlling differentiation processes in the gonads of S. mansoni.
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Affiliation(s)
- C Buro
- BFS, Institute of Parasitology, Justus-Liebig-University Giessen, Germany
| | - C Burmeister
- BFS, Institute of Parasitology, Justus-Liebig-University Giessen, Germany
| | - T Quack
- BFS, Institute of Parasitology, Justus-Liebig-University Giessen, Germany
| | - C G Grevelding
- BFS, Institute of Parasitology, Justus-Liebig-University Giessen, Germany.
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9
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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11
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Logue JS, Cartagena-Rivera AX, Baird MA, Davidson MW, Chadwick RS, Waterman CM. Erk regulation of actin capping and bundling by Eps8 promotes cortex tension and leader bleb-based migration. eLife 2015; 4:e08314. [PMID: 26163656 PMCID: PMC4522647 DOI: 10.7554/elife.08314] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/10/2015] [Indexed: 11/17/2022] Open
Abstract
Within the confines of tissues, cancer cells can use blebs to migrate. Eps8 is an actin bundling and capping protein whose capping activity is inhibited by Erk, a key MAP kinase that is activated by oncogenic signaling. We tested the hypothesis that Eps8 acts as an Erk effector to modulate actin cortex mechanics and thereby mediate bleb-based migration of cancer cells. Cells confined in a non-adhesive environment migrate in the direction of a very large ‘leader bleb.’ Eps8 bundling activity promotes cortex tension and intracellular pressure to drive leader bleb formation. Eps8 capping and bundling activities act antagonistically to organize actin within leader blebs, and Erk mediates this effect. An Erk biosensor reveals concentrated kinase activity within leader blebs. Bleb contents are trapped by the narrow neck that separates the leader bleb from the cell body. Thus, Erk activity promotes actin bundling by Eps8 to enhance cortex tension and drive the bleb-based migration of cancer cells under non-adhesive confinement. DOI:http://dx.doi.org/10.7554/eLife.08314.001 Cells within an animal have to be able to move both during development and later stages of life. For example, white blood cells have to move around the body and into tissues to fight off infections. Normally, cell movement is heavily controlled and will only happen when it is necessary to keep an animal healthy. However, cancer cells can bypass these controls and ‘metastasize’, or spread to new sites in the body. Cells can move in several different ways: on the one hand, cells can use ‘mesenchymal’ movement, in which the skeleton-like scaffolding of molecules within a cell rearranges to push the cell forward. On the other hand, cells can employ ‘amoeboid’ movement, in which they squeeze their way forward by building up pressure in the cell. Although these different types of movement are only used by some healthy cells and not others, cancer cells can switch between the two. How they do this is still unclear, but now Logue et al. have studied this question using several microscopy techniques. Logue et al. watched skin cancer (or melanoma) cells migrating between a glass plate and a slab of agar, which mimics the confined spaces that cancer cells have to move through within the body. The images showed that the cancer cells formed so-called ‘leader blebs’, finger-like projections that put cells on the right track. The experiments revealed that a protein called Eps8 was responsible for making the skin cancer cells move in this amoeboid fashion. The ‘blebbing’ caused by Eps8 is turned on by another protein called Erk that is often overactive in melanoma cells. Furthermore, Erk can accumulate near and within the cell blebs and this leads to the increased movement of the skin cancer cells. Studying cell movement in melanoma is particularly important because it is the metastatic tumors that kill patients. Therefore, increasing our basic understanding of how cells migrate could eventually lead to better treatment options that stop cancer cells from spreading. DOI:http://dx.doi.org/10.7554/eLife.08314.002
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Affiliation(s)
- Jeremy S Logue
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Alexander X Cartagena-Rivera
- National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, United States
| | - Michelle A Baird
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Michael W Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, Florida State University, Tallahassee, United States
| | - Richard S Chadwick
- National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, United States
| | - Clare M Waterman
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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12
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Flexibility and small pockets at protein-protein interfaces: New insights into druggability. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:2-9. [PMID: 25662442 PMCID: PMC4726663 DOI: 10.1016/j.pbiomolbio.2015.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/06/2015] [Accepted: 01/28/2015] [Indexed: 01/04/2023]
Abstract
The transient assembly of multiprotein complexes mediates many aspects of cell regulation and signalling in living organisms. Modulation of the formation of these complexes through targeting protein-protein interfaces can offer greater selectivity than the inhibition of protein kinases, proteases or other post-translational regulatory enzymes using substrate, co-factor or transition state mimetics. However, capitalising on protein-protein interaction interfaces as drug targets has been hindered by the nature of interfaces that tend to offer binding sites lacking the well-defined large cavities of classical drug targets. In this review we posit that interfaces formed by concerted folding and binding (disorder-to-order transitions on binding) of one partner and other examples of interfaces where a protein partner is bound through a continuous epitope from a surface-exposed helix, flexible loop or chain extension may be more tractable for the development of "orthosteric", competitive chemical modulators; these interfaces tend to offer small-volume but deep pockets and/or larger grooves that may be bound tightly by small chemical entities. We discuss examples of such protein-protein interaction interfaces for which successful chemical modulators are being developed.
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Ding X, Yang Z, Zhou F, Hu X, Zhou C, Luo C, He Z, Liu Q, Li H, Yan F, Wang F, Xiang S, Zhang J. Human intersectin 2 (ITSN2) binds to Eps8 protein and enhances its degradation. BMB Rep 2014; 45:183-8. [PMID: 22449706 DOI: 10.5483/bmbrep.2012.45.3.183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Participates in actin remodeling through Rac and receptor endocytosis via Rab5. Here, we used yeast two-hybrid system with Eps8 as bait to screen a human brain cDNA library. ITSN2 was identified as the novel binding factor of Eps8. The interaction between ITSN2 and Eps8 was demonstrated by the in vivo co-immunoprecipitation and colocalization assays and the in vitro GST pull-down assays. Furthermore, we mapped the interaction domains to the region between amino acids 260-306 of Eps8 and the coiled-coil domain of ITSN2. In addition, protein stability assays and immunofluorescence analysis showed ITSN2 overexpression induced the degradation of Eps8 proteins, which was markedly alleviated with the lysosome inhibitor NH4Cl treatment. Taken together, our results suggested ITSN2 interacts with Eps8 and stimulates the degradation of Eps8 proteins.
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Affiliation(s)
- Xiaofeng Ding
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, China
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Electrostatic effects in the folding of the SH3 domain of the c-Src tyrosine kinase: pH-dependence in 3D-domain swapping and amyloid formation. PLoS One 2014; 9:e113224. [PMID: 25490095 PMCID: PMC4260792 DOI: 10.1371/journal.pone.0113224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/20/2014] [Indexed: 11/19/2022] Open
Abstract
The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.
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Cámara-Artigas A, Martínez-Rodríguez S, Ortiz-Salmerón E, Martín-García JM. 3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops. J Struct Biol 2014; 186:195-203. [DOI: 10.1016/j.jsb.2014.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
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16
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Polle L, Rigano L, Julian R, Ireton K, Schubert WD. Structural Details of Human Tuba Recruitment by InlC of Listeria monocytogenes Elucidate Bacterial Cell-Cell Spreading. Structure 2014; 22:304-14. [DOI: 10.1016/j.str.2013.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/24/2013] [Accepted: 10/24/2013] [Indexed: 11/24/2022]
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17
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Katyal P, Puthenveetil R, Vinogradova O. Structural insights into the recognition of β3 integrin cytoplasmic tail by the SH3 domain of Src kinase. Protein Sci 2013; 22:1358-65. [PMID: 23913837 DOI: 10.1002/pro.2323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/22/2013] [Accepted: 07/22/2013] [Indexed: 01/08/2023]
Abstract
Src kinase plays an important role in integrin signaling by regulating cytoskeletal organization and cell remodeling. Previous in vivo studies have revealed that the SH3 domain of c-Src kinase directly associates with the C-terminus of β3 integrin cytoplasmic tail. Here, we explore this binding interface with a combination of different spectroscopic and computational methods. Chemical shift mapping, PRE, transferred NOE and CD data were used to obtain a docked model of the complex. This model suggests a different binding mode from the one proposed through previous studies wherein, the C-terminal end of β3 spans the region in between the RT and n-Src loops of SH3 domain. Furthermore, we show that tyrosine phosphorylation of β3 prevents this interaction, supporting the notion of a constitutive interaction between β3 integrin and Src kinase.
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Affiliation(s)
- Priya Katyal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
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18
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MacKinnon SS, Malevanets A, Wodak S. Intertwined Associations in Structures of Homooligomeric Proteins. Structure 2013; 21:638-49. [DOI: 10.1016/j.str.2013.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
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19
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Martin-Garcia JM, Luque I, Ruiz-Sanz J, Camara-Artigas A. The promiscuous binding of the Fyn SH3 domain to a peptide from the NS5A protein. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1030-40. [PMID: 22868769 DOI: 10.1107/s0907444912019798] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/02/2012] [Indexed: 12/27/2022]
Abstract
The hepatitis C virus nonstructural 5A (NS5A) protein is a large zinc-binding phosphoprotein that plays an important role in viral RNA replication and is involved in altering signal transduction pathways in the host cell. This protein interacts with Fyn tyrosine kinase in vivo and regulates its kinase activity. The 1.5 Å resolution crystal structure of a complex between the SH3 domain of the Fyn tyrosine kinase and the C-terminal proline-rich motif of the NS5A-derived peptide APPIPPPRRKR has been solved. Crystals were obtained in the presence of ZnCl(2) and belonged to the tetragonal space group P4(1)2(1)2. The asymmetric unit is composed of four SH3 domains and two NS5A peptide molecules; only three of the domain molecules contain a bound peptide, while the fourth molecule seems to correspond to a free form of the domain. Additionally, two of the SH3 domains are bound to the same peptide chain and form a ternary complex. The proline-rich motif present in the NS5A protein seems to be important for RNA replication and virus assembly, and the promiscuous interaction of the Fyn SH3 domain with the NS5A C-terminal proline-rich peptide found in this crystallographic structure may be important in the virus infection cycle.
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Affiliation(s)
- Jose Manuel Martin-Garcia
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almería, Spain
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20
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Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT. Divergence of multimodular polyketide synthases revealed by a didomain structure. Nat Chem Biol 2012; 8:615-21. [PMID: 22634636 PMCID: PMC3477503 DOI: 10.1038/nchembio.964] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 03/30/2012] [Indexed: 01/15/2023]
Abstract
The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues.
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Affiliation(s)
- Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin
| | - Darren C. Gay
- Department of Chemistry and Biochemistry, The University of Texas at Austin
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio
| | - Mark A. White
- Sealy Center for Structural and Molecular Biophysics, UTMB Galveston
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21
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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22
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Molecular basis for the dual function of Eps8 on actin dynamics: bundling and capping. PLoS Biol 2010; 8:e1000387. [PMID: 20532239 PMCID: PMC2879411 DOI: 10.1371/journal.pbio.1000387] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 04/22/2010] [Indexed: 11/20/2022] Open
Abstract
Actin capping and cross-linking proteins regulate the dynamics and architectures of different cellular protrusions. Eps8 is the founding member of a unique family of capping proteins capable of side-binding and bundling actin filaments. However, the structural basis through which Eps8 exerts these functions remains elusive. Here, we combined biochemical, molecular, and genetic approaches with electron microscopy and image analysis to dissect the molecular mechanism responsible for the distinct activities of Eps8. We propose that bundling activity of Eps8 is mainly mediated by a compact four helix bundle, which is contacting three actin subunits along the filament. The capping activity is mainly mediated by a amphipathic helix that binds within the hydrophobic pocket at the barbed ends of actin blocking further addition of actin monomers. Single-point mutagenesis validated these modes of binding, permitting us to dissect Eps8 capping from bundling activity in vitro. We further showed that the capping and bundling activities of Eps8 can be fully dissected in vivo, demonstrating the physiological relevance of the identified Eps8 structural/functional modules. Eps8 controls actin-based motility through its capping activity, while, as a bundler, is essential for proper intestinal morphogenesis of developing Caenorhabditis elegans.
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Wang H, Teh MT, Ji Y, Patel V, Firouzabadian S, Patel AA, Gutkind JS, Yeudall WA. EPS8 upregulates FOXM1 expression, enhancing cell growth and motility. Carcinogenesis 2010; 31:1132-41. [PMID: 20351091 DOI: 10.1093/carcin/bgq058] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Previous studies from our laboratory have indicated that overexpression of the epidermal growth factor receptor pathway substrate 8 (EPS8) enhances cell proliferation, migration and tumorigenicity in vivo, although the mechanisms involved remain unexplored. A microarray screen to search for potential mediators of EPS8 identified upregulation of multiple cell cycle-related targets such as the transcription factor FOXM1 and several of its reported downstream mediators, including cdc20, cyclin B1, cyclin A, aurora-B kinase and cdc25C in cells with elevated EPS8, as well as matrix metalloproteinase-9, which we reported previously to be upregulated by EPS8-dependent mechanisms. Cells engineered to overexpress FOXM1 showed increased proliferation, similar to EPS8-overexpressing cells. Conversely, targeted knockdown of FOXM1 in EPS8-overexpressing cells reduced proliferation. Cotransfection of EPS8 with a FOXM1-luciferase reporter plasmid into 293-T- or SVpgC2a-immortalized buccal keratinocytes demonstrated that EPS8 enhances FOXM1 promoter activity, whereas chromatin immunoprecipitation assays revealed elevated levels of acetylated histone H3 associated with the FOXM1 promoter in cells expressing high levels of EPS8. Treatment of EPS8-overexpressing cells with inhibitors of phosphoinositide 3-OH kinase or AKT reduced expression of FOXM1 and aurora-B kinase, a transcriptional target of FOXM1. Overexpression of EPS8 induced expression of the chemokine ligands CXCL5 and CXCL12 in a FOXM1-dependent manner, which was blocked by LY294002 or a dominant-negative form of AKT. Additionally, overexpression of FOXM1 enhanced cell migration, whereas targeted knockdown of CXCL5 or inhibition of AKT reduced migration of EPS8-expressing cells. These data suggest that EPS8 enhances cell proliferation and migration in part by deregulating FOXM1 activity and inducing CXC-chemokine expression, mediated by PI3K- and AKT-dependent mechanisms.
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Affiliation(s)
- Huixin Wang
- Philips Institute of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University, 521 N. 11th Street, Richmond, VA 23298-0566, USA
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Yan Z, Wang J, Zhang Y, Qin M, Wang W. Nucleation process in the folding of a domain-swapped dimer. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021910. [PMID: 20365598 DOI: 10.1103/physreve.81.021910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Revised: 12/07/2009] [Indexed: 05/29/2023]
Abstract
Nucleation processes are important for the understanding in protein dynamics. To evaluate the effect of nucleation mechanism in dimerization process, a domain-swapped dimer (Esp8) is simulated with the symmetrized Gō model and the classical Gō model. The pathways of the dimerization are analyzed with computational phi -analysis method. It is found out that some nuclei are observed in the kinetic steps of the dimeric association though the whole pathway is a process with multiple intermediate states. The key residues in the nuclei are rather similar to those observed in the monomeric folding. The differences with the monomeric cases are also discussed. These differences illustrate the effects of dimeric feature on the nucleation process. Besides, manual mutations are carried out to illustrate the importance of the interactions related to the nuclei. It is observed that the mutations in the nuclei-related interactions apparently change the dynamics while other mutations have little effect on the kinetics. All of these results outline a picture that the nucleation processes act as the fundamental steps of high-order organization of protein systems.
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Affiliation(s)
- Zhiqiang Yan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
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25
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Intertwined dimeric structure for the SH3 domain of the c-Src tyrosine kinase induced by polyethylene glycol binding. FEBS Lett 2009; 583:749-53. [PMID: 19185573 DOI: 10.1016/j.febslet.2009.01.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/21/2022]
Abstract
Here we report the first crystal structure of the SH3 domain of the cellular Src tyrosine kinase (c-Src-SH3) domain on its own. In the crystal two molecules of c-Src-SH3 exchange their -RT loops generating an intertwined dimer, in which the two SH3 units, preserving the binding site configuration, are oriented to allow simultaneous binding of two ligand molecules. The dimerization of c-Src-SH3 is induced, both in the crystal and in solution, by the binding of a PEG molecule at the dimer interface, indicating that this type of conformations are energetically close to the native structure. These results have important implications respect to in vivo oligomerization and amyloid aggregation.
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An unrecognized extracellular function for an intracellular adapter protein released from the cytoplasm into the tumor microenvironment. Proc Natl Acad Sci U S A 2009; 106:2182-7. [PMID: 19168626 DOI: 10.1073/pnas.0807543105] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian cell membranes provide an interface between the intracellular and extracellular compartments. It is currently thought that cytoplasmic signaling adapter proteins play no functional role within the extracellular tumor environment. Here, by selecting combinatorial random peptide libraries in tumor-bearing mice, we uncovered a direct, specific, and functional interaction between CRKL, an adapter protein [with Src homology 2 (SH2)- and SH3-containing domains], and the plexin-semaphorin-integrin domain of beta(1) integrin in the extracellular milieu. Through assays in vitro, in cellulo, and in vivo, we show that this unconventional and as yet unrecognized protein-protein interaction between a regulatory integrin domain (rather than a ligand-binding one) and an intracellular adapter (acting outside of the cells) triggers an alternative integrin-mediated cascade for cell growth and survival. Based on these data, here we propose that a secreted form of the SH3/SH2 adaptor protein CRKL may act as a growth-promoting factor driving tumorigenesis and may lead to the development of cancer therapeutics targeting secreted CRKL.
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27
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Gushchina LV, Gabdulkhakov AG, Nikonov SV, Mateo PL, Filimonov VV. Structural and thermodynamic studies of Bergerac-SH3 chimeras. Biophys Chem 2008; 139:106-15. [PMID: 19042078 DOI: 10.1016/j.bpc.2008.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 10/24/2008] [Accepted: 10/24/2008] [Indexed: 11/18/2022]
Abstract
Bergerac-type chimeras of spectrin SH3 were designed by extending a beta-hairpin by eight amino acids so that the extension protruded from the domain body like a "nose" being exposed to the solvent. A calorimetric study of several Bergerac-SH3 variants was carried out over a wide range of pH values and protein concentrations and the three-dimensional structure of one of them, SHH, was determined. X-ray studies confirmed that the nose had a well defined beta-structure whilst the chimera formed a stable tetramer within the crystal unit because of four tightly packed noses. In the pH range of 4-7 the heat-induced unfolding of some chimeras was complex and concentration dependent, whilst at pH values below 3.5, low protein concentrations of all the chimeras studied, including SHH, seemed to obey a monomolecular two-state unfolding model. The best set of data was obtained for the SHA variant, the unfolding heat effects of which were systematically higher than those of the WT protein (about 16.4 kJ/mol at 323 K), which may be close to the upper limit of the enthalpy gain due to 10 residue beta-hairpin folding. At the same time, the chimeras with high nose stability, which, like SHH, have a hydrophobic (IVY) cluster on their surface, showed a lower apparent unfolding heat effect, much closer to that of the WT protein. The possible reasons for this difference are discussed.
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Affiliation(s)
- Liubov' V Gushchina
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
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28
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Structural Basis of PxxDY Motif Recognition in SH3 Binding. J Mol Biol 2008; 382:167-78. [DOI: 10.1016/j.jmb.2008.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/20/2008] [Accepted: 07/03/2008] [Indexed: 11/23/2022]
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29
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Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:597-610. [PMID: 17452785 PMCID: PMC2483474 DOI: 10.1107/s0907444907009791] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 02/28/2007] [Indexed: 11/10/2022]
Abstract
Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.
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Harkiolaki M, Gilbert RJC, Jones EY, Feller SM. The C-terminal SH3 domain of CRKL as a dynamic dimerization module transiently exposing a nuclear export signal. Structure 2007; 14:1741-53. [PMID: 17161365 DOI: 10.1016/j.str.2006.09.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 09/26/2006] [Accepted: 09/27/2006] [Indexed: 11/30/2022]
Abstract
CRKL plays essential roles in cell signaling. It consists of an N-terminal SH2 domain followed by two SH3 domains. SH2 and SH3N bind to signaling proteins, but the function of the SH3C domain has remained largely enigmatic. We show here that the SH3C of CRKL forms homodimers in protein crystals and in solution. Evidence for dimer formation of full-length CRKL is also presented. In the SH3C dimer, a nuclear export signal (NES) is mostly buried under the domain surface. The same is true for a monomeric SH3C obtained under different crystallization conditions. Interestingly, partial SH3 unfolding, such as occurs upon dimer/monomer transition, produces a fully-accessible NES through translocation of a single beta strand. Our results document the existence of an SH3 domain dimer formed through exchange of the first SH3 domain beta strand and suggest that partial unfolding of the SH3C is important for the relay of information in vivo.
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Affiliation(s)
- Maria Harkiolaki
- Cancer Research UK Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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31
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Romir J, Lilie H, Egerer-Sieber C, Bauer F, Sticht H, Muller YA. Crystal structure analysis and solution studies of human Lck-SH3; zinc-induced homodimerization competes with the binding of proline-rich motifs. J Mol Biol 2006; 365:1417-28. [PMID: 17118402 DOI: 10.1016/j.jmb.2006.10.058] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/12/2006] [Accepted: 10/16/2006] [Indexed: 01/24/2023]
Abstract
In cytosolic Src-type tyrosine kinases the Src-type homology 3 (SH3) domain binds to an internal proline-rich motif and the presence or the absence of this interaction modulates the kinase enzymatic activity. The Src-type kinase Lck plays an important role during T-cell activation and development, since it phosphorylates the T-cell antigen receptor in an early step of the activation pathway. We have determined the crystal structure of the SH3 domain from Lck kinase at a near-atomic resolution of 1.0 A. Unexpectedly, the Lck-SH3 domain forms a symmetrical homodimer in the crystal and the dimer comprises two identical zinc-binding sites in the interface. The atomic interactions formed across the dimer interface resemble strikingly those observed between SH3 domains and their canonical proline-rich ligands, since almost identical residues participate in both contacts. Ultracentrifugation experiments confirm that in the presence of zinc ions, the Lck-SH3 domain also forms dimers in solution. The Zn(2+) dissociation constant from the Lck-SH3 dimer is estimated to be lower than 100 nM. Moreover, upon addition of a proline-rich peptide with a sequence corresponding to the recognition segment of the herpesviral regulatory protein Tip, competition between zinc-induced homodimerization and binding of the peptide can be detected by both fluorescence spectroscopy and analytical ultracentrifugation. These results suggest that in vivo, too, competition between Lck-SH3 homodimerization and binding of regulatory proline-rich sequence motifs possibly represents a novel mechanism by which kinase activity is modulated. Because the residues that form the zinc-binding site are highly conserved among Lck orthologues but not in other Src-type kinases, the mechanism might be peculiar to Lck and to its role in the initial steps of T-cell activation.
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Affiliation(s)
- Johannes Romir
- Lehrstuhl für Biotechnik, Institut für Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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Zhao J, Parkinson JS. Mutational analysis of the chemoreceptor-coupling domain of the Escherichia coli chemotaxis signaling kinase CheA. J Bacteriol 2006; 188:3299-307. [PMID: 16621823 PMCID: PMC1447439 DOI: 10.1128/jb.188.9.3299-3307.2006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2005] [Accepted: 02/16/2006] [Indexed: 11/20/2022] Open
Abstract
During chemotactic signaling by Escherichia coli, autophosphorylation of the histidine kinase CheA is coupled to chemoreceptor control by the CheW protein, which interacts with the C-terminal P5 domain of CheA. To identify P5 determinants important for CheW binding and receptor coupling control, we isolated and characterized a series of P5 missense mutants. The mutants fell into four phenotypic groups on the basis of in vivo behavioral and protein stability tests and in vitro assays with purified mutant proteins. Group 1 mutants exhibited autophosphorylation and receptor-coupling defects, and their CheA proteins were subject to relatively rapid degradation in vivo. Group 1 mutations were located at hydrophobic residues in P5 subdomain 2 and most likely caused folding defects. Group 2 mutants made stable CheA proteins with normal autophosphorylation ability but with defects in CheW binding and in receptor-mediated activation of CheA autophosphorylation. Their mutations affected residues in P5 subdomain 1 near the interface with the CheA dimerization (P3) and ATP-binding (P4) domains. Mutant proteins of group 3 were normal in all tests yet could not support chemotaxis, suggesting that P5 has one or more important but still unknown signaling functions. Group 4 mutant proteins were specifically defective in receptor-mediated deactivation control. The group 4 mutations were located in P5 subdomain 1 at the P3/P3' interface. We conclude that P5 subdomain 1 is important for CheW binding and for receptor coupling control and that these processes may require substantial motions of the P5 domain relative to the neighboring P3 and P4 domains of CheA.
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Affiliation(s)
- Jinshi Zhao
- Biology Department, 257 South 1400 East, University of Utah, Salt Lake City, Utah 84112, USA
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33
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Schiller MR, Chakrabarti K, King GF, Schiller NI, Eipper BA, Maciejewski MW. Regulation of RhoGEF activity by intramolecular and intermolecular SH3 domain interactions. J Biol Chem 2006; 281:18774-86. [PMID: 16644733 DOI: 10.1074/jbc.m512482200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RhoGEFs are central controllers of small G-proteins in cells and are regulated by several mechanisms. There are at least 22 human RhoGEFs that contain SH3 domains, raising the possibility that, like several other enzymes, SH3 domains control the enzymatic activity of guanine nucleotide exchange factor (GEF) domains through intra- and/or intermolecular interactions. The structure of the N-terminal SH3 domain of Kalirin was solved using NMR spectroscopy, and it folds much like other SH3 domains. However, NMR chemical shift mapping experiments showed that this Kalirin SH3 domain is unique, containing novel cooperative binding site(s) for intramolecular PXXP ligands. Intramolecular Kalirin SH3 domain/ligand interactions, as well as binding of the Kalirin SH3 domain to the adaptor protein Crk, inhibit the GEF activity of Kalirin. This study establishes a novel molecular mechanism whereby intramolecular and intermolecular Kalirin SH3 domain/ligand interactions modulate GEF activity, a regulatory mechanism that is likely used by other RhoGEF family members.
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Affiliation(s)
- Martin R Schiller
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06019-4301, USA.
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Bader R, Bamford R, Zurdo J, Luisi BF, Dobson CM. Probing the Mechanism of Amyloidogenesis through a Tandem Repeat of the PI3-SH3 Domain Suggests a Generic Model for Protein Aggregation and Fibril Formation. J Mol Biol 2006; 356:189-208. [PMID: 16364365 DOI: 10.1016/j.jmb.2005.11.034] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 11/07/2005] [Accepted: 11/11/2005] [Indexed: 11/23/2022]
Abstract
Aggregation of the SH3 domain of the PI3 kinase, both as a single domain and as a tandem repeat in which the C terminus of one domain is linked to the N terminus of another by a flexible linker of ten glycine/serine residues, has been studied under a range of conditions in order to investigate the mechanism of protein aggregation and amyloid formation. The tandem repeat was found to form amyloid fibrils much more readily than the single domain under the acidic conditions used here, and the fibrils themselves have higher morphological homogeneity. The folding-unfolding transition of the PI3-SH3 domain shows two-state behaviour and is pH dependent; at pH 3.6, which is near the pH mid-point for folding and only slightly below the isoelectric point of the protein, both the single domain and the tandem repeat spontaneously form broad distributions of soluble oligomers without requirement for nucleation. Under prolonged incubation under these conditions, the oligomers convert into thin, curly fibrils that interact with thioflavin-T, suggesting that they contain an organised beta-sheet structure. Under more acidic conditions (pH 2.0) where the proteins are fully denatured and carry a positive net charge, long, straight fibrils are formed in a process having a pronounced lag phase. The latter was found to be reduced dramatically by the addition of oligomers exceeding a critical size of approximately 20 molecules. The results suggest that the process of aggregation of these SH3 domains can take place by a variety of mechanisms, ranging from downhill formation of relatively amorphous species to nucleated formation of highly organised structures, the relative importance of which varies greatly with solution conditions. Comparison with the behaviour of other amyloidogenic systems suggests that the general mechanistic features outlined here are likely to be common to at least a wide variety of peptides and proteins.
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Affiliation(s)
- Reto Bader
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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35
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Ding F, Prutzman KC, Campbell SL, Dokholyan NV. Topological Determinants of Protein Domain Swapping. Structure 2006; 14:5-14. [PMID: 16407060 DOI: 10.1016/j.str.2005.09.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 09/06/2005] [Accepted: 09/07/2005] [Indexed: 11/20/2022]
Abstract
Protein domain swapping has been repeatedly observed in a variety of proteins and is believed to result from destabilization due to mutations or changes in environment. Based on results from our studies and others, we propose that structures of the domain-swapped proteins are mainly determined by their native topologies. We performed molecular dynamics simulations of seven different proteins, known to undergo domain swapping experimentally, under mildly denaturing conditions and found in all cases that the domain-swapped structures can be recapitulated by using protein topology in a simple protein model. Our studies further indicated that, in many cases, domain swapping occurs at positions around which the protein tends to unfold prior to complete unfolding. This, in turn, enabled prediction of protein structural elements that are responsible for domain swapping. In particular, two distinct domain-swapped dimer conformations of the focal adhesion targeting domain of focal adhesion kinase were predicted computationally and were supported experimentally by data obtained from NMR analyses.
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Affiliation(s)
- Feng Ding
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599, USA
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36
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Roffers-Agarwal J, Xanthos JB, Miller JR. Regulation of actin cytoskeleton architecture by Eps8 and Abi1. BMC Cell Biol 2005; 6:36. [PMID: 16225669 PMCID: PMC1274305 DOI: 10.1186/1471-2121-6-36] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 10/14/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The actin cytoskeleton participates in many fundamental processes including the regulation of cell shape, motility, and adhesion. The remodeling of the actin cytoskeleton is dependent on actin binding proteins, which organize actin filaments into specific structures that allow them to perform various specialized functions. The Eps8 family of proteins is implicated in the regulation of actin cytoskeleton remodeling during cell migration, yet the precise mechanism by which Eps8 regulates actin organization and remodeling remains elusive. RESULTS Here, we show that Eps8 promotes the assembly of actin rich filopodia-like structures and actin cables in cultured mammalian cells and Xenopus embryos, respectively. The morphology of actin structures induced by Eps8 was modulated by interactions with Abi1, which stimulated formation of actin cables in cultured cells and star-like structures in Xenopus. The actin stars observed in Xenopus animal cap cells assembled at the apical surface of epithelial cells in a Rac-independent manner and their formation was accompanied by recruitment of N-WASP, suggesting that the Eps8/Abi1 complex is capable of regulating the localization and/or activity of actin nucleators. We also found that Eps8 recruits Dishevelled to the plasma membrane and actin filaments suggesting that Eps8 might participate in non-canonical Wnt/Polarity signaling. Consistent with this idea, mis-expression of Eps8 in dorsal regions of Xenopus embryos resulted in gastrulation defects. CONCLUSION Together, these results suggest that Eps8 plays multiple roles in modulating actin filament organization, possibly through its interaction with distinct sets of actin regulatory complexes. Furthermore, the finding that Eps8 interacts with Dsh and induced gastrulation defects provides evidence that Eps8 might participate in non-canonical Wnt signaling to control cell movements during vertebrate development.
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Affiliation(s)
- Julaine Roffers-Agarwal
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Jennifer B Xanthos
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Jeffrey R Miller
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
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37
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Yang S, Levine H, Onuchic JN. Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. J Mol Biol 2005; 352:202-11. [PMID: 16061250 DOI: 10.1016/j.jmb.2005.06.062] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 06/22/2005] [Accepted: 06/27/2005] [Indexed: 11/19/2022]
Abstract
Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-based (Gō) model, we demonstrate that in the free-energy landscape of domain swapping, a large free-energy barrier separates monomeric and domain-swapped dimeric configurations. We investigate the effect of finite monomer concentration, by implementing a new semi-analytical method, which involves computing the second virial coefficient, a thermodynamic indicator of inter-molecular interactions. This method, together with the symmetrized structure-based (Gō) model, minimizes the need for expensive many-protein simulations, providing a convenient framework to investigate concentration effect. Finally, we perform direct simulations of domain-swapped trimer formation, showing that this modeling approach can be used for higher-order oligomers.
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Affiliation(s)
- Sichun Yang
- Center for Theoretical Biological Physics and Department of Physics, University of California San Diego, La Jolla, CA 92093-0374, USA
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38
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Khare SD, Wilcox KC, Gong P, Dokholyan NV. Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins 2005; 61:617-32. [PMID: 16152647 DOI: 10.1002/prot.20629] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Diverse point mutations in the enzyme Cu, Zn superoxide dismutase (SOD1) are linked to its aggregation in the familial form of the disease amyotrophic lateral sclerosis. The disease-associated mutations are known to destabilize the protein, but the structural basis of the aggregation of the destabilized protein and the structure of aggregates are not well understood. Here, we investigate in silico the sequence and structural determinants of SOD1 aggregation: (1) We identify sequence fragments in SOD1 that have a high aggregation propensity, using only the sequence of SOD1, and (2) we perform molecular dynamics simulations of the SOD1 dimer folding and misfolding. In both cases, we identify identical regions of the protein as having high propensity to form intermolecular interactions. These regions correspond to the N- and C-termini, and two crossover loops and two beta-strands in the Greek-key native fold of SOD1. Our results suggest that the high aggregation propensity of mutant SOD1 may result from a synergy of two factors: the presence of highly amyloidogenic sequence fragments ("hot spots"), and the presence of these fragments in regions of the protein that are structurally most likely to form intermolecular contacts under destabilizing conditions. Therefore, we postulate that the balance between the self-association of aggregation-prone sequences and the specific structural context of these sequences in the native state determines the aggregation propensity of proteins.
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Affiliation(s)
- Sagar D Khare
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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39
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Abstract
A minimalist representation of protein structures using a Go-like potential for interactions is implemented to investigate the mechanisms of the domain swapping of p13suc1, a protein that exists in two native conformations: a monomer and a domain-swapped dimer formed by the exchange of a beta-strand. Inspired by experimental studies which showed a similarity of the transition states for folding of the monomer and the dimer, in this study we justify this similarity in molecular descriptions. When intermediates are populated in the simulations, formation of a domain-swapped dimer initiates from the ensemble of unfolded monomers, given by the fact that the dimer formation occurs at the folding/unfolding temperature of the monomer (T(f)). It is also shown that transitions, leading to a dimer, involve the presence of two intermediates, one of them has a dimeric form and the other is monomeric; the latter is much more populated than the former. However, at temperatures lower than T(f), the population of intermediates decreases. It is argued that the two folded forms may coexist in absence of intermediates at a temperature much lower than T(f). Computational simulations enable us to find a mechanism, "lock-and-dock", for domain swapping of p13suc1. To explore the route toward dimer formation, the folding of unstructured monomers must be retarded by first locking one of the free ends of each chain. Then, the other free termini could follow and dock at particular regions, where most intrachain contacts are formed, and thus define the transition states of the dimer. The simulations also showed that a decrease in the maximum distance between monomers increased their stability, which is explained based on confinement arguments. Although the simulations are based on models extracted from the native structure of the monomer and the dimer of p13suc1, the mechanism of the domain-swapping process could be general, not only for p13suc1.
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Affiliation(s)
- Jorge Chahine
- Departamento de Física, UNESP-Universidade Estadual Paulista, São José do Rio Preto-SP 15054-000, Brazil.
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40
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Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Recognition of Proline-Rich Motifs by Protein-Protein-Interaction Domains. Angew Chem Int Ed Engl 2005; 44:2852-69. [PMID: 15880548 DOI: 10.1002/anie.200400618] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein-protein interactions are essential in every aspect of cellular activity. Multiprotein complexes form and dissociate constantly in a specifically tuned manner, often by conserved mechanisms. Protein domains that bind proline-rich motifs (PRMs) are frequently involved in signaling events. The unique properties of proline provide a mechanism for highly discriminatory recognition without requiring high affinities. We present herein a detailed, quantitative assessment of the structural features that define the interfaces between PRM-binding domains and their target PRMs, and investigate the specificity of PRM recognition. Together with the analysis of peptide-library screens, this approach has allowed the identification of several highly conserved key interactions found in all complexes of PRM-binding domains. The inhibition of protein-protein interactions by using small-molecule agents is very challenging. Therefore, it is important to first pinpoint the critical interactions that must be considered in the design of inhibitors of PRM-binding domains.
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Affiliation(s)
- Linda J Ball
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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41
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Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Erkennung Prolin-reicher Motive (PRMs) durch Protein-Protein-Wechselwirkungsdomänen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400618] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Wisniewska M, Bossenmaier B, Georges G, Hesse F, Dangl M, Künkele KP, Ioannidis I, Huber R, Engh RA. The 1.1 A resolution crystal structure of the p130cas SH3 domain and ramifications for ligand selectivity. J Mol Biol 2005; 347:1005-14. [PMID: 15784259 DOI: 10.1016/j.jmb.2005.02.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Revised: 02/02/2005] [Accepted: 02/04/2005] [Indexed: 11/26/2022]
Abstract
The Crk-associated tyrosine kinase substrate p130cas (CAS) is a docking protein containing an SH3 domain near its N terminus, followed by a short proline-rich segment, a large central substrate domain composed of 15 repeats of the four amino acid sequence YxxP, a serine-rich region and a carboxy-terminal domain, which possesses consensus binding sites for the SH2 and SH3 domains of Src (YDYV and RPLPSPP, respectively). The SH3 domain of CAS mediates its interaction with several proteins involved in signaling pathways such as focal adhesion kinase (FAK), tyrosine phosphatases PTP1B and PTP-PEST, and the guanine nucleotide exchange factor C3G. As a homolog of the corresponding Src docking domain, the CAS SH3 domain binds to proline-rich sequences (PxxP) of its interacting partners that can adopt a polyproline type II helix. We have determined a high-resolution X-ray structure of the recombinant human CAS SH3 domain. The domain, residues 1-69, crystallized in two related space groups, P2(1) and C222(1), that provided diffraction data to 1.1 A and 2.1 A, respectively. The crystal structure shows, in addition to the conserved SH3 domain architecture, the way in which the CAS characteristic amino acids form an atypically charged ligand-binding surface. This arrangement provides a rationale for the unusual ligand recognition motif exhibited by the CAS SH3 domain. The structure enables modelling of the docking interactions to its ligands, for example from focal adhesion kinase, and supports structure-based drug design of inhibitors of the CAS-FAK interaction.
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Affiliation(s)
- Magdalena Wisniewska
- Max Planck Institut für Biochemie, Strukturforschung, D-82152 Martinsried, Germany
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43
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Abstract
In a recent issue of Nature, van Rossum et al. report binding of a "split" pleckstrin homology (PH) domain from phospholipase C-gamma(1) to the TRPC3 ion channel. Through sequence analyses and in vitro studies, they suggest a novel mode of protein-protein interaction in which two PH domain fragments in distinct proteins associate to form an "intermolecular" PH domain that binds inositol phospholipids and is required for ion channel location and function.
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Affiliation(s)
- Mark A Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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44
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Abstract
Motile bacteria respond to environmental cues to move to more favorable locations. The components of the chemotaxis signal transduction systems that mediate these responses are highly conserved among prokaryotes including both eubacterial and archael species. The best-studied system is that found in Escherichia coli. Attractant and repellant chemicals are sensed through their interactions with transmembrane chemoreceptor proteins that are localized in multimeric assemblies at one or both cell poles together with a histidine protein kinase, CheA, an SH3-like adaptor protein, CheW, and a phosphoprotein phosphatase, CheZ. These multimeric protein assemblies act to control the level of phosphorylation of a response regulator, CheY, which dictates flagellar motion. Bacterial chemotaxis is one of the most-understood signal transduction systems, and many biochemical and structural details of this system have been elucidated. This is an exciting field of study because the depth of knowledge now allows the detailed molecular mechanisms of transmembrane signaling and signal processing to be investigated.
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Affiliation(s)
- Melinda D Baker
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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45
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Lindorff-Larsen K, Røgen P, Paci E, Vendruscolo M, Dobson CM. Protein folding and the organization of the protein topology universe. Trends Biochem Sci 2005; 30:13-9. [PMID: 15653321 DOI: 10.1016/j.tibs.2004.11.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The mechanism by which proteins fold to their native states has been the focus of intense research in recent years. The rate-limiting event in the folding reaction is the formation of a conformation in a set known as the transition-state ensemble. The structural features present within such ensembles have now been analysed for a series of proteins using data from a combination of biochemical and biophysical experiments together with computer-simulation methods. These studies show that the topology of the transition state is determined by a set of interactions involving a small number of key residues and, in addition, that the topology of the transition state is closer to that of the native state than to that of any other fold in the protein universe. Here, we review the evidence for these conclusions and suggest a molecular mechanism that rationalizes these findings by presenting a view of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose an explanation for the overwhelming importance of topology in the transition states for protein folding.
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46
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Abstract
Recent structures of the heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) have revealed two unexpected examples of RNA recognition motif (RRM)-like domains with specialized features for protein recognition. These unusual RRMs, called U2AF homology motifs (UHMs), represent a novel class of protein recognition motifs. Defining a set of rules to distinguish traditional RRMs from UHMs is key to identifying novel UHM family members. Here we review the critical sequence features necessary to mediate protein-UHM interactions, and perform comprehensive database searches to identify new members of the UHM family. The resulting implications for the functional and evolutionary relationships among candidate UHM family members are discussed.
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Affiliation(s)
- Clara L. Kielkopf
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Corresponding author. E-MAIL ; FAX (410) 955-2926
| | - Stephan Lücke
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Michael R. Green
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Corresponding author. E-MAIL ; FAX (508) 856-5473
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47
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Yuzawa S, Ogura K, Horiuchi M, Suzuki NN, Fujioka Y, Kataoka M, Sumimoto H, Inagaki F. Solution Structure of the Tandem Src Homology 3 Domains of p47 in an Autoinhibited Form. J Biol Chem 2004; 279:29752-60. [PMID: 15123602 DOI: 10.1074/jbc.m401457200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phagocyte NADPH oxidase is a multisubunit enzyme responsible for the generation of superoxide anions (O(2).) that kill invading microorganisms. p47(phox) is a cytosolic subunit of the phagocyte NADPH oxidase, which plays a crucial role in the assembly of the activated NADPH oxidase complex. The molecular shapes of the p47(phox) tandem SH3 domains either with or without a polybasic/autoinhibitory region (PBR/AIR) at the C terminus were studied using small angle x-ray scattering. The tandem SH3 domains with PBR/AIR formed a compact globular structure, whereas the tandem SH3 domains lacking the PBR/AIR formed an elongated structure. Alignment anisotropy analysis by NMR based on the residual dipolar couplings revealed that the tandem SH3 domains with PBR/AIR were in good agreement with a globular module corresponding to the split half of the intertwisted dimer in crystalline state. The structure of the globular module was elucidated to represent a solution structure of the tandem SH3 domain in the autoinhibited form, where the PBR/AIR bundled the tandem SH3 domains and the linker forming a closed structure. Once PBR/AIR is released by phosphorylation, rearrangements of the SH3 domains may occur, forming an open structure that binds to the cytoplasmic proline-rich region of membrane-bound p22(phox).
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Affiliation(s)
- Satoru Yuzawa
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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48
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Japelj B, Waltho JP, Jerala R. Comparison of backbone dynamics of monomeric and domain-swapped stefin A. Proteins 2004; 54:500-12. [PMID: 14747998 DOI: 10.1002/prot.10624] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Three-dimensional domain swapping has been observed in increasing number of proteins and has been implicated in the initial stages of protein aggregation, including that of the cystatins. Stefin A folds as a monomer under native conditions, while under some denaturing conditions domain-swapped dimer is formed. We have determined the backbone dynamics of the monomeric and domain-swapped dimeric forms of stefin A by (15)N relaxation using a model-free approach. The overall correlation times of the molecules were determined to be 4.6 +/- 0.1 ns and 9.2 +/- 0.2 ns for the monomer and the dimer, respectively. In the monomer, decreased order parameters indicate an increased mobility for the N-terminal trunk, the first and the second binding loops. At the opposite side of the molecule, the loop connecting the alpha-helix with strand B, the beginning of strand B and the loop connecting strands C and D show increased localized mobility. In the domain-swapped dimer, a distinctive feature of the structure is the concatenation of strands B and C into a single long beta-strand. The newly formed linker region between strands B and C, which substitutes for the first binding loop in the monomer, has order parameters typical for the remainder of the beta-strands. Thus, the interaction between subunits that occurs on domain-swapping has consequences for the dynamics of the protein at long-range from the site of conformational change, where an increased rigidity in the newly formed linker region is accompanied by an increased mobility of loops remote from that site.
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Affiliation(s)
- Bostjan Japelj
- Laboratory of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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49
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Harkiolaki M, Lewitzky M, Gilbert RJC, Jones EY, Bourette RP, Mouchiroud G, Sondermann H, Moarefi I, Feller SM. Structural basis for SH3 domain-mediated high-affinity binding between Mona/Gads and SLP-76. EMBO J 2003; 22:2571-82. [PMID: 12773374 PMCID: PMC156755 DOI: 10.1093/emboj/cdg258] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
SH3 domains are protein recognition modules within many adaptors and enzymes. With more than 500 SH3 domains in the human genome, binding selectivity is a key issue in understanding the molecular basis of SH3 domain interactions. The Grb2-like adaptor protein Mona/Gads associates stably with the T-cell receptor signal transducer SLP-76. The crystal structure of a complex between the C-terminal SH3 domain (SH3C) of Mona/Gads and a SLP-76 peptide has now been solved to 1.7 A. The peptide lacks the canonical SH3 domain binding motif P-x-x-P and does not form a frequently observed poly-proline type II helix. Instead, it adopts a clamp-like shape around the circumfence of the SH3C beta-barrel. The central R-x-x-K motif of the peptide forms a 3(10) helix and inserts into a negatively charged double pocket on the SH3C while several other residues complement binding through hydrophobic interactions, creating a short linear SH3C binding epitope of uniquely high affinity. Interestingly, the SH3C displays ion-dependent dimerization in the crystal and in solution, suggesting a novel mechanism for the regulation of SH3 domain functions.
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Affiliation(s)
- Maria Harkiolaki
- Cancer Research UK Cell Signalling Group and Weatherall Institute of Molecular Medicine, Oxford, UK
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Groemping Y, Lapouge K, Smerdon SJ, Rittinger K. Molecular basis of phosphorylation-induced activation of the NADPH oxidase. Cell 2003; 113:343-55. [PMID: 12732142 DOI: 10.1016/s0092-8674(03)00314-3] [Citation(s) in RCA: 287] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The multi-subunit NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of reactive oxygen species. Activation of the NADPH oxidase requires the targeting of a cytoplasmic p40-p47-p67(phox) complex to the membrane bound heterodimeric p22-gp91(phox) flavocytochrome. This interaction is prevented in the resting state due to an auto-inhibited conformation of p47(phox). The X-ray structure of the auto-inhibited form of p47(phox) reveals that tandem SH3 domains function together to maintain the cytoplasmic complex in an inactive form. Further structural and biochemical data show that phosphorylation of p47(phox) activates a molecular switch that relieves the inhibitory intramolecular interaction. This permits p47(phox) to interact with the cytoplasmic tail of p22(phox) and initiate formation of the active, membrane bound enzyme complex.
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Affiliation(s)
- Yvonne Groemping
- Division of Protein Structure, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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