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Yip KT, Zhong X, Seibel N, Arnolds O, Schöpel M, Stoll R. Human melanoma inhibitory protein binds to the FN12-14 Hep II domain of fibronectin. Biointerphases 2017; 12:02D415. [PMID: 28565914 PMCID: PMC5451317 DOI: 10.1116/1.4984008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/03/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
The heparin binding site (Hep II) of fibronectin plays a major role in tumor cell metastasis. Its interaction with heparan sulfate proteoglycans occurs in a variety of physiological processes including focal adhesion and migration. The melanoma inhibitory activity (MIA) is an important protein that is functionally involved in melanoma development, progression, and tumor cell invasion. After its secretion by malignant melanoma cells, MIA interacts with fibronectin and thereby actively facilitates focal cell detachment from surrounding structures and strongly promotes tumor cell invasion and the formation of metastases. In this report, the authors have determined the molecular basis of the interaction of MIA with the Hep II domain of fibronectin based on nuclear magnetic resonance spectroscopic binding assays. The authors have identified the type III modules 12 to 14 of fibronectin's Hep II as the major MIA binding sites. These results now provide a new target protein-protein binding interface for the discovery of novel antimetastatic agents against malignant melanoma in the future.
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Affiliation(s)
- King Tuo Yip
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Xueyin Zhong
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Nadia Seibel
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Oliver Arnolds
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Miriam Schöpel
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Raphael Stoll
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
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Pantoja-Uceda D, Arolas JL, García P, López-Hernández E, Padró D, Aviles FX, Blanco FJ. The NMR Structure and Dynamics of the Two-Domain Tick Carboxypeptidase Inhibitor Reveal Flexibility in Its Free Form and Stiffness upon Binding to Human Carboxypeptidase B. Biochemistry 2008; 47:7066-78. [DOI: 10.1021/bi800403m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Joan L. Arolas
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Pascal García
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Eva López-Hernández
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Daniel Padró
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francesc X. Aviles
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francisco J. Blanco
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
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Kuang Z, Yao S, Keizer DW, Wang CC, Bach LA, Forbes BE, Wallace JC, Norton RS. Structure, dynamics and heparin binding of the C-terminal domain of insulin-like growth factor-binding protein-2 (IGFBP-2). J Mol Biol 2006; 364:690-704. [PMID: 17020769 DOI: 10.1016/j.jmb.2006.09.006] [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: 06/22/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 11/24/2022]
Abstract
Insulin-like growth factor-binding protein-2 (IGFBP-2) is the largest member of a family of six proteins (IGFBP-1 to 6) that bind insulin-like growth factors I and II (IGF-I/II) with high affinity. In addition to regulating IGF actions, IGFBPs have IGF-independent functions. The C-terminal domains of IGFBPs contribute to high-affinity IGF binding, and confer binding specificity and have overlapping but variable interactions with many other molecules. Using nuclear magnetic resonance (NMR) spectroscopy, we have determined the solution structure of the C-terminal domain of IGFBP-2 (C-BP-2) and analysed its backbone dynamics based on 15N relaxation parameters. C-BP-2 has a thyroglobulin type 1 fold consisting of an alpha-helix, a three-stranded anti-parallel beta-sheet and three flexible loops. Compared to C-BP-6 and C-BP-1, structural differences that may affect IGF binding and underlie other functional differences were found. C-BP-2 has a longer disordered loop I, and an extended C-terminal tail, which is unstructured and very mobile. The length of the helix is identical with that of C-BP-6 but shorter than that of C-BP-1. Reduced spectral density mapping analysis showed that C-BP-2 possesses significant rapid motion in the loops and termini, and may undergo slower conformational or chemical exchange in the structured core and loop II. An RGD motif is located in a solvent-exposed turn. A pH-dependent heparin-binding site on C-BP-2 has been identified. Protonation of two histidine residues, His271 and His228, seems to be important for this binding, which occurs at slightly acidic pH (6.0) and is more significant at pH 5.5, but is largely suppressed at pH 7.4. Possible preferential binding of IGFBP-2 and its C- domain fragments to glycosaminoglycans in the acidic extracellular matrix (ECM) of tumours may be related to their roles in cancer.
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Affiliation(s)
- Zhihe Kuang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia
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7
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Yao S, Headey SJ, Keizer DW, Bach LA, Norton RS. C-terminal domain of insulin-like growth factor (IGF) binding protein 6: conformational exchange and its correlation with IGF-II binding. Biochemistry 2004; 43:11187-95. [PMID: 15366928 DOI: 10.1021/bi049456+] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin-like growth factor binding proteins (IGFBPs) function as carriers and regulators of the insulin-like growth factors (IGF-I and -II). Within the family of six binding proteins, IGFBP-6 is unique in having a 20-100-fold higher affinity for IGF-II over IGF-I and appears to act primarily as an inhibitor of IGF-II actions. We have recently determined the solution structure of the C-terminal domain of IGFBP-6 (C-BP-6), which shows the presence of substantial flexible regions, including three loop regions. In this paper, we report results from (15)N relaxation measurements carried out in both the laboratory and rotating frames. Analysis of conventional (15)N relaxation data (R(1), R(2), and steady-state (15)N-[(1)H] nuclear Overhauser effect) indicated that there was a considerable number of residues involved in conformational/chemical exchange. Measurements of off-resonance (15)N R(1)(rho) in the rotating frame and (15)N relaxation dispersion using an in- and antiphase coherence-averaged Carr-Purcell-Meiboom-Gill sequence were thus carried out to gain further insight into the solution dynamics of C-BP-6. Although the off-resonance (15)N relaxation data showed no clear evidence for residues undergoing microsecond motion, the (15)N relaxation dispersion data allowed us to identify 15 residues that clearly exhibit submilli- to millisecond motion. A good correlation was observed between residues exhibiting motion at submilli- to millisecond time scales and those affected by IGF-II binding, as identified through the perturbation of nuclear magnetic resonance (NMR) spectra of C-BP-6 following IGF-II addition. A complete NMR relaxation study of C-BP-6 dynamics in complex with IGF-II was hampered by peak broadening and disappearance of C-BP-6 in the presence of IGF-II. Nonetheless, current results strongly suggest possible conformation switching or population shifting between pre-existing conformations in C-BP-6 upon binding to IGF-II.
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Affiliation(s)
- Shenggen Yao
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia.
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Stoll R, Renner C, Buettner R, Voelter W, Bosserhoff AK, Holak TA. Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains. Protein Sci 2003; 12:510-9. [PMID: 12592021 PMCID: PMC2312446 DOI: 10.1110/ps.0222603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by (15)N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting beta-sheets, such as the RT-loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT-loop, the n-Src loop, for the loop comprising residues 13 to 19, which we refer to as the"disulfide loop", in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte-derived protein (FDP)/MIA-like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain-like fold in solution with expanded ligand interactions.
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Affiliation(s)
- Raphael Stoll
- Max Planck Institute of Biochemistry, D-82152 München, Germany
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Renner C, Moroder L, Holak TA. Analytical solution to the Lipari-Szabo model based on the reduced spectral density approximation offers a novel protocol for extracting motional parameters. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 151:32-39. [PMID: 11444934 DOI: 10.1006/jmre.2001.2346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An analytical solution to the Lipari-Szabo model is derived for isotropic overall tumbling. The parameters of the original Lipari-Szabo model, the order parameter S2 and the effective internal correlation time tau(e), are calculated from two values of the spectral density function. If additionally the spectral density value J(0) is known, the exchange contribution R(ex) term can also be determined. The overall tumbling time tau(c) must be determined in advance, for example, from T1/T2 ratios. The required spectral density values are obtained by reduced spectral density mapping from T1, T2, and NOE measurements. Our computer simulations show that the reduced spectral density mapping is a very good approximation in almost all cases in which the Lipari-Szabo model is applicable. The robustness of the analytical formula to experimental errors is also investigated by extensive computer simulations and is found to be similar to that of the fitting procedures. The derived formulas were applied to the experimental 15N relaxation data of ubiquitin. Our results agree well with the published parameter values of S2 and tau(e), which were obtained from standard fitting procedures. The analytical approach to extract parameters of molecular motions may be more robust than standard analyses and provides a safeguard against spurious fitting results, especially for determining the exchange contribution R(ex).
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Affiliation(s)
- C Renner
- Max Planck Institute for Biochemistry, Martinsried, 82152, Germany
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