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Leung LL, Myles T, Morser J. Thrombin Cleavage of Osteopontin and the Host Anti-Tumor Immune Response. Cancers (Basel) 2023; 15:3480. [PMID: 37444590 DOI: 10.3390/cancers15133480] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Osteopontin (OPN) is a multi-functional protein that is involved in various cellular processes such as cell adhesion, migration, and signaling. There is a single conserved thrombin cleavage site in OPN that, when cleaved, yields two fragments with different properties from full-length OPN. In cancer, OPN has tumor-promoting activity and plays a role in tumor growth and metastasis. High levels of OPN expression in cancer cells and tumor tissue are found in various types of cancer, including breast, lung, prostate, ovarian, colorectal, and pancreatic cancer, and are associated with poor prognosis and decreased survival rates. OPN promotes tumor progression and invasion by stimulating cell proliferation and angiogenesis and also facilitates the metastasis of cancer cells to other parts of the body by promoting cell adhesion and migration. Furthermore, OPN contributes to immune evasion by inhibiting the activity of immune cells. Thrombin cleavage of OPN initiates OPN's tumor-promoting activity, and thrombin cleavage fragments of OPN down-regulate the host immune anti-tumor response.
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Affiliation(s)
- Lawrence L Leung
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Timothy Myles
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - John Morser
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
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2
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Structural Constraint of Osteopontin Facilitates Efficient Binding to CD44. Biomolecules 2021; 11:biom11060813. [PMID: 34070790 PMCID: PMC8228714 DOI: 10.3390/biom11060813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Since the original description in 1996, the interaction between the cytokine osteopontin (OPN) and the homing receptor CD44 has been extensively studied in cancer, inflammation, bone remodeling, and various other conditions. Alternative splicing and extensive posttranslational modifications by both binding partners, as well as the possibility for lateral recruitment of additional membrane receptors or soluble co-ligands into a complex have left the exact molecular requirements for high-affinity OPN-CD44 binding unresolved. We now report that there is a moderate engagement between the unmodified molecules, which results in curved double-reciprocal plots for OPN titration, suggesting the existence of two binding sites or two binding conformations. Structural constraint of OPN, by immobilization or by addition of heparin, is required for its strong ligation of CD44. Prior literature provides evidence that heparin binding to OPN prompts the unfolding of a core element in the protein. This conformational adjustment may be essential for efficient CD44 interaction. The integrin α9β1 seems to compete with the OPN-CD44 engagement, while the integrin αVβ3 reflects additive binding, suggesting that the CD44 contact sites on OPN are downstream of the RGD motif but overlap with the SVVYGLR domain. Hyaluronate has no effect, placing the relevant domain on CD44 downstream of the N-terminus.
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3
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Mateos B, Konrat R, Pierattelli R, Felli IC. NMR Characterization of Long-Range Contacts in Intrinsically Disordered Proteins from Paramagnetic Relaxation Enhancement in 13 C Direct-Detection Experiments. Chembiochem 2018; 20:335-339. [PMID: 30407719 DOI: 10.1002/cbic.201800539] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable 3D structure and are able to adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. A widely used experimental NMR spectroscopy approach to study long-range contacts in IDPs exploits paramagnetic effects, and 1 H detection experiments are generally used to determine paramagnetic relaxation enhancement (PRE) for amide protons. However, under physiological conditions, exchange broadening hampers the detection of solvent-exposed amide protons, which reduces the content of information available. Herein, we present an experimental approach based on direct carbon detection of PRE that provides improved resolution, reduced sensitivity to exchange broadening, and complementary information derived from the use of different starting polarization sources.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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4
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Effect of Phosphorylation on a Human-like Osteopontin Peptide. Biophys J 2017; 112:1586-1596. [PMID: 28445750 PMCID: PMC5406370 DOI: 10.1016/j.bpj.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/25/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022] Open
Abstract
The last decade established that the dynamic properties of the phosphoproteome are central to function and its modulation. The temporal dimension of phosphorylation effects remains nonetheless poorly understood, particularly for intrinsically disordered proteins. Osteopontin, selected for this study due to its key role in biomineralization, is expressed in many species and tissues to play a range of distinct roles. A notable property of highly phosphorylated isoforms of osteopontin is their ability to sequester nanoclusters of calcium phosphate to form a core-shell structure, in a fluid that is supersaturated but stable. In Biology, this process enables soft and hard tissues to coexist in the same organism with relative ease. Here, we extend our understanding of the effect of phosphorylation on a disordered protein, the recombinant human-like osteopontin rOPN. The solution structures of the phosphorylated and unphosphorylated rOPN were investigated by small-angle x-ray scattering and no significant changes were detected on the radius of gyration or maximum interatomic distance. The picosecond-to-nanosecond dynamics of the hydrated powders of the two rOPN forms were further compared by elastic and quasi-elastic incoherent neutron scattering. Phosphorylation was found to block some nanosecond side-chain motions while increasing the flexibility of other side chains on the faster timescale. Phosphorylation can thus selectively change the dynamic behavior of even a highly disordered protein such as osteopontin. Through such an effect on rOPN, phosphorylation can direct allosteric mechanisms, interactions with substrates, cofactors and, in this case, amorphous or crystalline biominerals.
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Vernet E, Popa G, Pozdnyakova I, Rasmussen JE, Grohganz H, Giehm L, Jensen MH, Wang H, Plesner B, Nielsen HM, Jensen KJ, Berthelsen J, Sundström M, van de Weert M. Large-Scale Biophysical Evaluation of Protein PEGylation Effects: In Vitro Properties of 61 Protein Entities. Mol Pharm 2016; 13:1587-98. [DOI: 10.1021/acs.molpharmaceut.6b00049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Erik Vernet
- Novo Nordisk A/S, 2880 Bagsværd, Denmark
- The
Novo Nordisk Foundation Center for Protein Research (NNF CPR), Faculty
of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gina Popa
- The
Novo Nordisk Foundation Center for Protein Research (NNF CPR), Faculty
of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irina Pozdnyakova
- The
Novo Nordisk Foundation Center for Protein Research (NNF CPR), Faculty
of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob E. Rasmussen
- Department
of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Holger Grohganz
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Giehm
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Malene H. Jensen
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Huabing Wang
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bitten Plesner
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hanne M. Nielsen
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Knud J. Jensen
- Department
of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jens Berthelsen
- Costerton
Biofilm center, Department for Immunology and Microbiology, Faculty
of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Sundström
- The
Novo Nordisk Foundation Center for Protein Research (NNF CPR), Faculty
of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marco van de Weert
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Holt C, Carver JA, Ecroyd H, Thorn DC. Invited review: Caseins and the casein micelle: their biological functions, structures, and behavior in foods. J Dairy Sci 2013; 96:6127-46. [PMID: 23958008 DOI: 10.3168/jds.2013-6831] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/09/2013] [Indexed: 12/27/2022]
Abstract
A typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosphorylation and the same type of flexible, unfolded conformation as caseins. The ability to suppress amyloid fibril formation by forming an alternative amorphous aggregate is also not unique to caseins and underlies the action of molecular chaperones such as the small heat-shock proteins. The open structure of the protein matrix of casein micelles is fragile and easily perturbed by changes in its environment. Perturbations can cause the polypeptide chains to segregate into regions of greater and lesser density. As a result, the reliable determination of the native structure of casein micelles continues to be extremely challenging. The biological functions of caseins, such as their chaperone activity, are determined by their composition and flexible conformation and by how the casein polypeptide chains interact with each other. These same properties determine how caseins behave in the manufacture of many dairy products and how they can be used as functional ingredients in other foods.
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Affiliation(s)
- C Holt
- Institute of Molecular, Cell and Systems Biology, School of Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
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Platzer G, Schedlbauer A, Chemelli A, Ozdowy P, Coudevylle N, Auer R, Kontaxis G, Hartl M, Miles AJ, Wallace BA, Glatter O, Bister K, Konrat R. The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites. Biochemistry 2011; 50:6113-24. [PMID: 21609000 DOI: 10.1021/bi200291e] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Osteopontin (OPN) is an acidic hydrophilic glycophosphoprotein that was first identified as a major sialoprotein in bones. It functions as a cell attachment protein displaying a RGD cell adhesion sequence and as a cytokine that signals through integrin and CD44 cell adhesion molecules. OPN is also implicated in human tumor progression and cell invasion. OPN has intrinsic transforming activity, and elevated OPN levels promote metastasis. OPN gene expression is also strongly activated in avian fibroblasts simultaneously transformed by the v-myc and v-mil(raf) oncogenes. Here we have investigated the solution structure of a 220-amino acid recombinant OPN protein by an integrated structural biology approach employing bioinformatic sequence analysis, multidimensional nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism spectroscopy, and small-angle X-ray scattering. These studies suggest that OPN is an intrinsically unstructured protein in solution. Although OPN does not fold into a single defined structure, its conformational flexibility significantly deviates from random coil-like behavior. OPN comprises distinct local secondary structure elements with reduced conformational flexibility and substantially populates a compact subspace displaying distinct tertiary contacts. These compacted regions of OPN encompass the binding sites for α(V)β(III) integrin and heparin. The conformational flexibility combined with the modular architecture of OPN may represent an important structural prerequisite for its functional diversity.
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Affiliation(s)
- Gerald Platzer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
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8
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Beich-Frandsen M, Vecerek B, Konarev PV, Sjöblom B, Kloiber K, Hämmerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA, Svergun DI, Konrat R, Bläsi U, Djinovic-Carugo K. Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res 2011; 39:4900-15. [PMID: 21330354 PMCID: PMC3113564 DOI: 10.1093/nar/gkq1346] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of Hfq(Ec). These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of Hfq(Ec).
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Affiliation(s)
- Mads Beich-Frandsen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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9
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Yamaguchi Y, Hanashima S, Yagi H, Takahashi Y, Sasakawa H, Kurimoto E, Iguchi T, Kon S, Uede T, Kato K. NMR characterization of intramolecular interaction of osteopontin, an intrinsically disordered protein with cryptic integrin-binding motifs. Biochem Biophys Res Commun 2010; 393:487-91. [DOI: 10.1016/j.bbrc.2010.02.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 02/08/2010] [Indexed: 11/16/2022]
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Konrat R. The protein meta-structure: a novel concept for chemical and molecular biology. Cell Mol Life Sci 2009; 66:3625-39. [PMID: 19690801 PMCID: PMC11115628 DOI: 10.1007/s00018-009-0117-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 07/20/2009] [Accepted: 07/21/2009] [Indexed: 12/01/2022]
Abstract
The ultimate goal of bioinformatics or computational chemical biology is the sequence-based prediction of protein functionality. However, due to the degeneracy of the primary sequence code there is no unambiguous relationship. The degeneracy can be partly lifted by going to higher levels of abstraction and, for example, incorporating 3D structural information. However, sometimes even at this conceptual level functional ambiguities often remain. Here a novel conceptual framework is described (the protein meta-structure). At this level of abstraction, the protein structure is viewed as an intricate network of interacting residues. This novel conception offers unique possibilities for chemical (molecular) biology, structural genomics and drug discovery. In this review some prototypical applications will be presented that serve to illustrate the potential of the methodology.
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Affiliation(s)
- Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria.
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Schedlbauer A, Coudevylle N, Auer R, Kloiber K, Tollinger M, Konrat R. Autocorrelation analysis of NOESY data provides residue compactness for folded and unfolded proteins. J Am Chem Soc 2009; 131:6038-9. [PMID: 19364097 DOI: 10.1021/ja8074067] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel spectral entropy interpretation for protein NOESY data is presented for the investigation of the spatial distribution of residues in protein structures without the requirement of NOE cross peak assignments. In this approach individual traces S(i)(omega) from a 3D (15)N NOESY-HSQC taken at frequency positions corresponding to different amide groups (residue position i) are subjected to a self-convolution procedure thus leading to the autocorrelation function C(i)(omega) of the NOESY-trace for a particular backbone residue position. The characteristic spatial surrounding of a particular residue position is reflected in the corresponding autocorrelation function and can be quantified by taking the (spectral) entropy S(nu) as an information measure. The feasibility of this novel approach is demonstrated with applications to the proteins Cyclophilin D and Osteopontin and the protein complex between the lipocalin Q83 and the bacterial siderophore Enterobactin. Typically, large entropy values were found for residues located in structurally loosely defined regions, whereas small entropy values were found for residues in hydrophobic core regions of the protein with tightly interacting side chains and distinct chemical shift patterns. The applications to the unfolded Osteopontin and the Q83/Enterobactin protein complex indicated that both local compaction of the polypeptide chain due to transiently formed structural elements and subtle changes in side-chain packing can be efficiently probed by this novel approach.
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Affiliation(s)
- Andreas Schedlbauer
- Institute of Biomolecular Structural Chemistry, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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