1
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Discovery of new molecular entities able to strongly interfere with Hsp90 C-terminal domain. Sci Rep 2018; 8:1709. [PMID: 29374167 PMCID: PMC5786060 DOI: 10.1038/s41598-017-14902-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/19/2017] [Indexed: 01/22/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is an ATP dependent molecular chaperone deeply involved in the complex network of cellular signaling governing some key functions, such as cell proliferation and survival, invasion and angiogenesis. Over the past years the N-terminal protein domain has been fully investigated as attractive strategy against cancer, but despite the many efforts lavished in the field, none of the N-terminal binders (termed "classical inhibitors"), currently in clinical trials, have yet successfully reached the market, because of the detrimental heat shock response (HSR) that showed to induce; thus, recently, the selective inhibition of Hsp90 C-terminal domain has powerfully emerged as a more promising alternative strategy for anti-cancer therapy, not eliciting this cell rescue cascade. However, the structural complexity of the target protein and, mostly, the lack of a co-crystal structure of C-terminal domain-ligand, essential to drive the identification of new hits, represent the largest hurdles in the development of new selective C-terminal inhibitors. Continuing our investigations on the identification of new anticancer drug candidates, by using an orthogonal screening approach, here we describe two new potent C-terminal inhibitors able to induce cancer cell death and a considerable down-regulation of Hsp90 client oncoproteins, without triggering the undesired heat shock response.
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2
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Liu H, Zhang N, Cui M, Liu Z, Liu S. Mass spectrometry based strategy for studies of binding sites and structural changes of cisplatin binding to myoglobin. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2433-2441. [PMID: 27580490 DOI: 10.1002/rcm.7729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/15/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE It is of great significance to investigate the interaction of the metallodrug cisplatin (cis-[PtCl2 (NH3 )2 ]) with myoglobin for understanding of the mechanism of action of cisplatin and the overexpression of myoglobin in tumor cells. METHODS The reactions of cisplatin and myoglobin were incubated under different conditions. A mass spectrometry (MS)-based strategy combining full proteolysis and limited proteolysis was developed for comprehensive studies of cisplatin-myoglobin interaction. RESULTS The binding sites of cisplatin on myoglobin were identified as Trp14, His64, His81, His113 and His116 using electrospray ionization multiple-stage tandem mass spectrometry (ESI-MSn ) without liquid chromatography (LC) separation. The relative abundances of digested peptides from platinated myoglobin were obviously higher than those from native samples by limited proteolysis. CONCLUSIONS An alternative and simple approach was developed to successfully monitor conformational changes of myoglobin induced by cisplatin binding using an ESI-MS-based quantification method combined with limited proteolysis. Meanwhile, His64 was firstly found to coordinate to platinum, which was likely to affect hydrogen bonds with the oxygen in the heme group. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Huan Liu
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ningbo Zhang
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meng Cui
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China.
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China.
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Shuying Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
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3
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Protein Structural Analysis via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:397-431. [PMID: 27975228 DOI: 10.1007/978-3-319-41448-5_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.
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4
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Rimmer MA, Artigues A, Nadeau OW, Villar MT, Vasquez-Montes V, Carlson GM. Mass Spectrometric Analysis of Surface-Exposed Regions in the Hexadecameric Phosphorylase Kinase Complex. Biochemistry 2015; 54:6887-95. [PMID: 26551836 DOI: 10.1021/acs.biochem.5b00682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphorylase kinase (PhK) is a 1.3 MDa (αβγδ)4 enzyme complex, in which αβγδ protomers associate in D2 symmetry to form two large octameric lobes that are interconnected by four bridges. The approximate locations of the subunits have been mapped in low-resolution cryo-electron microscopy structures of the complex; however, the disposition of the subunits within the complex remains largely unknown. We have used partial proteolysis and chemical footprinting in combination with high-resolution mass spectrometry to identify surface-exposed regions of the intact nonactivated and phospho-activated conformers. In addition to the known interaction of the γ subunit's C-terminal regulatory domain with the δ subunit (calmodulin), our exposure results indicate that the catalytic core of γ may also anchor to the PhK complex at the bottom backside of its C-terminal lobe facing away from the active site cleft. Exposed loops on the α and β regulatory subunits within the complex occur at regions overlapping with tissue-specific alternative RNA splice sites and regulatory phosphorylatable domains. Their phosphorylation alters the surface exposure of α and β, corroborating previous biophysical and biochemical studies that detected phosphorylation-dependent conformational changes in these subunits; however, for the first time, specific affected regions have been identified.
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Affiliation(s)
- Mary Ashley Rimmer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Maria T Villar
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Gerald M Carlson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
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5
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Vassallo A, Vaccaro MC, De Tommasi N, Dal Piaz F, Leone A. Identification of the plant compound geraniin as a novel Hsp90 inhibitor. PLoS One 2013; 8:e74266. [PMID: 24066128 PMCID: PMC3774728 DOI: 10.1371/journal.pone.0074266] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/30/2013] [Indexed: 01/06/2023] Open
Abstract
Besides its function in normal cellular growth, the molecular chaperone heat shock protein 90 (Hsp90) binds to a large number of client proteins required for promoting cancer cell growth and/or survival. In an effort to discover new small molecules able to inhibit the Hsp90 ATPase and chaperoning activities, we screened, by a surface plasmon resonance assay, a small library including different plant polyphenols. The ellagitannin geraniin, was identified as the most promising molecule, showing a binding affinity to Hsp90α similar to that of 17-(allylamino)-17-demethoxygeldanamycin (17AGG). Geraniin was able to inhibit in vitro the Hsp90α ATPase activity in a dose−dependent manner, with an inhibitory efficiency comparable to that measured for 17-AAG. In addition, this compound compromised the chaperone activity of Hsp90α, monitored by the citrate synthase thermal induced aggregation assay. Geraniin decreased the viability of HeLa and Jurkat cell lines and caused an arrest in G2/M phase. We also proved that following exposure to different concentrations of geraniin, the level of expression of the client proteins c-Raf, pAkt, and EGFR was strongly down−regulated in both the cell lines. These results, along with the finding that geraniin did not exert any appreciable cytotoxicity on normal cells, encourage further studies on this compound as a promising chemical scaffold for the design of new Hsp90 inhibitors.
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Affiliation(s)
- Antonio Vassallo
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | | | | | - Fabrizio Dal Piaz
- Dipartimento di Farmacia, Università degli Studi di Salerno, Fisciano, Italy
- * E-mail:
| | - Antonella Leone
- Dipartimento di Farmacia, Università degli Studi di Salerno, Fisciano, Italy
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6
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Severino V, Paiardini A, Pascarella S, Parente A, Chambery A. Structural analysis of toxic volkensin, a type 2 ribosome inactivating protein from Adenia volkensii Harm (kilyambiti plant): molecular modeling and surface analysis by computational methods and limited proteolysis. Int J Biol Macromol 2009; 45:407-13. [PMID: 19591862 DOI: 10.1016/j.ijbiomac.2009.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 06/29/2009] [Accepted: 06/30/2009] [Indexed: 11/24/2022]
Abstract
Volkensin, isolated from Adenia volkensii, is one of the most toxic type 2 ribosome-inactivating protein (RIP), exerting its biological function by inhibiting protein synthesis. Despite the high sequence identity with type 2 RIPs, including ricin, volkensin shows interesting peculiar properties. In this work a computational model building of volkensin was performed. The volkensin electrostatic potential charge distribution, the hydrophobic profile and the surface topology analyses were also carried out to aid the understanding of structure-function relationships of this potent toxin. Volkensin surface topology was probed by applying a limited proteolysis approach with the aim to gain insights into volkensin conformational features.
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Affiliation(s)
- V Severino
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy
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7
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Tosco A, Monti MC, Fontanella B, Rio MC, Gomez-Paloma L, Leone A, Marzullo L. Copper-binding activity of Trefoil factor 1 (TFF1): a new perspective in the study of the multifunctional roles of TFFs. Peptides 2007; 28:1461-9. [PMID: 17610997 DOI: 10.1016/j.peptides.2007.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 05/25/2007] [Accepted: 06/04/2007] [Indexed: 10/23/2022]
Abstract
Trefoil factors (TFFs) are gastrointestinal peptides playing an essential role in the epithelial restitution. Among the three known TFF peptides, TFF1 is characterized by three disulfide bonds producing a compact globular structure and an extended and disordered tail formed by amino- and carboxy-termini. The presence of a cysteine surrounded by several negatively charged residues in this region of the protein, highly conserved in different species, suggests the possible formation of a metal-binding site. Affinity chromatography and mass spectrometric analyses allowed us to demonstrate a selective binding affinity of TFF1 for copper. The binding induces conformational changes in the tertiary structure as demonstrated by circular dichroism experiments, while limited proteolysis revealed an altered access to the cleavage sites in the amino- and carboxy-termini. The results of this study reveal a new property of TFF1 and suggest that copper could influence its biological activities by interfering with the dimerization of the peptide and/or the interaction with mucins or putative TFF receptors.
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Affiliation(s)
- Alessandra Tosco
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Salerno, Via Ponte Don Melillo, 84084 Fisciano, SA, Italy.
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8
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Monti M, Amoresano A, Giorgetti S, Bellotti V, Pucci P. Limited proteolysis in the investigation of beta2-microglobulin amyloidogenic and fibrillar states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1753:44-50. [PMID: 16213198 DOI: 10.1016/j.bbapap.2005.09.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Revised: 08/26/2005] [Accepted: 09/08/2005] [Indexed: 11/16/2022]
Abstract
Amyloid fibrils of patients treated with regular haemodialysis essentially consists of beta2-microglobulin (beta2-m) and its truncated species DeltaN6beta2-m lacking six residues at the amino terminus. The truncated fragment shows a higher propensity to self-aggregate and constitutes an excellent candidate for the analysis of a protein in the amyloidogenic conformation. The surface topology and the conformational analysis of native beta2-m and the truncated DeltaN6beta2-m species both in the soluble and in the fibrillar forms were investigated by the limited proteolysis/mass spectrometry strategy. The conformation in solution of a further truncated mutant DeltaN3beta2-m lacking three residues at the N-terminus was also examined. This approach appeared particularly suited to investigate the regions that are solvent-exposed, or flexible enough to be accessible to protein-protein interactions and to describe the conformation of transient intermediates. Moreover, proteolysis experiments can also be tailored to investigate amyloid fibrils by discriminating the protein regions constituting the unaccessible core of the fibrils and those still flexible and exposed to the solvent. Although native beta2-m and DeltaN3beta2-m shared essentially the same conformation, significative structural differences exist between the native and the DeltaN6beta2-m proteins in solution with major differences located at the end moiety of strand V and subsequent loop with strand VI and at both the N- and C-termini of the proteins. On the contrary, an identical distribution of preferential proteolytic sites was observed in both proteins in the fibrillar state, which was nearly superimposible to that observed for the soluble form of DeltaN6beta2-m. These data revealed that synthetic fibrils essentially consists of an unaccessible core comprising residues 20-87 of the beta2-m protein with exposed and flexible N- and C-terminal ends. Moreover, proteolytic cleavages observed in vitro at Lys 6 and Lys 19 reproduce specific cleavages that have to take place in vivo to generate the truncated forms of beta2-m occurring in natural fibrils. On the basis of these results, a molecular mechanism for fibril formation has been proposed.
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Affiliation(s)
- M Monti
- CEINGE Biotecnologie Avanzate, scarl, Università di Napoli Federico II, Via Comunale Margherita 482, 80145 Napoli, Italy
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9
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Russo G, Cuccurese M, Monti G, Russo A, Amoresano A, Pucci P, Pietropaolo C. Ribosomal protein L7a binds RNA through two distinct RNA-binding domains. Biochem J 2005; 385:289-99. [PMID: 15361074 PMCID: PMC1134697 DOI: 10.1042/bj20040371] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human ribosomal protein L7a is a component of the major ribosomal subunit. We previously identified three nuclear-localization-competent domains within L7a, and demonstrated that the domain defined by aa (amino acids) 52-100 is necessary, although not sufficient, to target the L7a protein to the nucleoli. We now demonstrate that L7a interacts in vitro with a presumably G-rich RNA structure, which has yet to be defined. We also demonstrate that the L7a protein contains two RNA-binding domains: one encompassing aa 52-100 (RNAB1) and the other encompassing aa 101-161 (RNAB2). RNAB1 does not contain any known nucleic-acid-binding motif, and may thus represent a new class of such motifs. On the other hand, a specific region of RNAB2 is highly conserved in several other protein components of the ribonucleoprotein complex. We have investigated the topology of the L7a-RNA complex using a recombinant form of the protein domain that encompasses residues 101-161 and a 30mer poly(G) oligonucleotide. Limited proteolysis and cross-linking experiments, and mass spectral analyses of the recombinant protein domain and its complex with poly(G) revealed the RNA-binding region.
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Affiliation(s)
- Giulia Russo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Monica Cuccurese
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Gianluca Monti
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
| | - Annapina Russo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Angela Amoresano
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
| | - Pietro Pucci
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
- ‡CEINGE Biotecnologie Avanzate S.C.a.r.l., Via Comunale Margherita 482 Napoli, I-80145 Italy
| | - Concetta Pietropaolo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
- To whom correspondence should be addressed (email )
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10
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Casbarra A, Birolo L, Infusini G, Dal Piaz F, Svensson M, Pucci P, Svanborg C, Marino G. Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis. Protein Sci 2004; 13:1322-30. [PMID: 15075403 PMCID: PMC2286754 DOI: 10.1110/ps.03474704] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Revised: 01/12/2004] [Accepted: 01/15/2004] [Indexed: 10/26/2022]
Abstract
A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.
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Affiliation(s)
- Annarita Casbarra
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, I-80126 Napoli, Italy
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11
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Monti M, Garolla di Bard BL, Calloni G, Chiti F, Amoresano A, Ramponi G, Pucci P. The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process. J Mol Biol 2004; 336:253-62. [PMID: 14741220 DOI: 10.1016/j.jmb.2003.10.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Formation of misfolded aggregates is an essential part of what proteins can do. The process of protein aggregation is central to many human diseases and any aggregating event needs to be prevented within a cell and in protein design. In order to aggregate, a protein needs to unfold its native state, at least partially. The conformational state that is prone to aggregate is difficult to study, due to its aggregating potential and heterogeneous nature. Here, we use a systematic approach of limited proteolysis, in combination with electrospray ionisation mass spectrometry, to investigate the regions that are most flexible and solvent-exposed within the native, ligand-bound and amyloidogenic states of muscle acylphosphatase (AcP), a protein previously shown to form amyloid fibrils in the presence of trifluoroethanol. Seven proteases with different degrees of specificity have been used for this purpose. Following exposure to the aggregating conditions, a number of sites along the sequence of AcP become susceptible to proteolytic digestion. The pattern of proteolytic cleavages obtained under these conditions is considerably different from that of the native and ligand-bound conformations and includes a portion within the N-terminal tail of the protein (residues 6-7), the region of the sequence 18-23 and the position 94 near the C terminus. There is a significant overlap between the regions of the sequence found to be solvent-exposed from the present study and those previously identified to be critical in the rate-determining steps of aggregation from protein engineering approaches. This indicates that a considerable degree of solvent exposure is a feature of the portions of a protein that initiate the process of aggregation.
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Affiliation(s)
- Maria Monti
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cinthia 6, 80126 Naples, Italy
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12
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Cheng J, Liu Y, Hong Y, Wang JJ, Yang Q. Screening and identification of genes trans-regulated by hepatitis C virus NC3 protein with microarray assay. Shijie Huaren Xiaohua Zazhi 2003; 11:930-934. [DOI: 10.11569/wcjd.v11.i7.930] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To understand the target genes up-regulated or down-regulated by NS3 protein, we compared the differentially expressed genes between the hepatoblastoma cell line HepG2 transfected by pcDNA3.1(-) and pcDNA3.1-NS3, respectively by cDNA microarray technique.
METHODS The NS3 coding DNA fragment was amplified with polymerase chain reaction (PCR) technique by using pBRTM3011 containing the full length of HCV-H cDNA as the template. The expressive vector of pcDNA3.1-NS3 was constructed by routine molecular biological methods. The HepG2 cells were transfected by pcDNA3.1(-) and pcDNA3.1-NS3, respectively using lipofectamine. The total RNA was isolated and reverse transcribed. The cDNAs were subjected for microarray screening with 1 152 cDNA probes.
RESULTS The expressive vector has been constructed and confirmed by restriction enzyme digestion and DNA sequencing analysis. The expression of NS3 protein has been confirmed by Western blot with single chain variable region (scFv) antibody. High quality mRNA and cDNA had been prepared and successful microarray screening had been conducted. From the scanning results, it was found 34 genes were up-regulated and 37 genes were down-regulated by NS3 protein of HCV.
CONCLUSION NS3 protein is a transactivator. The expression of NS3 protein affected the expression spectrum of HCV infected hepatocyte. The microarray is an important technique for the study of transactivating effects for viral proteins.
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Affiliation(s)
- Jun Cheng
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Yan Liu
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Yuan Hong
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Jian-Jun Wang
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Qian Yang
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
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13
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Monti M, Principe S, Giorgetti S, Mangione P, Merlini G, Clark A, Bellotti V, Amoresano A, Pucci P. Topological investigation of amyloid fibrils obtained from beta2-microglobulin. Protein Sci 2002; 11:2362-9. [PMID: 12237458 PMCID: PMC2373708 DOI: 10.1110/ps.0206902] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Amyloid fibrils of patients treated with regular hemodialysis essentially consists of beta2-microglobulin (beta2-m) and its truncated species DeltaN6beta2-m lacking six residues at the amino terminus. The truncated fragment has a more flexible three-dimensional structure and constitutes an excellent candidate for the analysis of a protein in the amyloidogenic conformation. The surface topology of synthetic fibrils obtained from intact beta2-m and truncated DeltaN6beta2-m was investigated by the limited proteolysis/mass spectrometry approach that appeared particularly suited to gain insights into the structure of beta2-m within the fibrillar polymer. The distribution of prefential proteolytic sites observed in both fibrils revealed that the central region of the protein, which had been easily cleaved in the full-length globular beta2-m, was fully protected in the fibrillar form. In addition, the amino- and carboxy-terminal regions of beta2-m became exposed to the solvent in the fibrils, whereas they were masked completely in the native protein. These data indicate that beta2-m molecules in the fibrils consist of an unaccessible core comprising residues 20-87 with the strands I and VIII being not constrained in the fibrillar polymer and exposed to the proteases. Moreover, proteolytic cleavages observed in vitro at Lys 6 and Lys 19 reproduce specific cleavages that have to occur in vivo to generate the truncated forms of beta2-m occurring in natural fibrils. On the basis of these data, a possible mechanism for fibril formation from native beta2-m is discussed and an explanation for the occurrence of truncated protein species in natural fibrils is given.
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Affiliation(s)
- Maria Monti
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cinthia 6, Italy
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14
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Monzani E, Curto M, Galliano M, Minchiotti L, Aime S, Baroni S, Fasano M, Amoresano A, Salzano AM, Pucci P, Casella L. Binding and relaxometric properties of heme complexes with cyanogen bromide fragments of human serum albumin. Biophys J 2002; 83:2248-58. [PMID: 12324442 PMCID: PMC1302313 DOI: 10.1016/s0006-3495(02)73985-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The spectroscopic and reactivity properties of hemin complexes formed with cyanogen bromide fragments B (residues 1-123), C (124-298), A (299-585), and D (1-298) of human serum albumin (HSA) have been investigated. The complex hemin-D exhibits binding, spectral, circular dichroism, and reactivity characteristics very similar to those of hemin-HSA, indicating that fragment D contains the entire HSA domain involved in heme binding. The characteristics of the other hemin complexes are different, and a detailed investigation of the properties of hemin-C has been carried out because this fragment contains the HSA binding region of several important drugs. Hemin-C contains a low-spin Fe(III) center, with two imidazole ligands, but the complex undergoes a reversible structural transition at basic pH leading to a high-spin, five-coordinated Fe(III) species. This change determines a marked increase in the relaxation rate of water protons. Limited proteolysis experiments and mass spectral analysis carried out on fragment C and hemin-C show that the region encompassing residues Glu-208 to Trp-214 is protected from activity of proteases in the complex and, therefore, is involved in the interaction with hemin. A structural model of fragment C enables us to propose that His-242 and His-288 are the axial ligands for the Fe(III) center.
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Affiliation(s)
- Enrico Monzani
- Dipartimento di Chimica Generale, Università di Pavia, Italy
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15
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Casbarra A, Piaz FD, Ingallinella P, Orrù S, Pucci P, Pessi A, Bianchi E. The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure. Protein Sci 2002; 11:2102-12. [PMID: 12192066 PMCID: PMC2373603 DOI: 10.1110/ps.0206602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We recently reported a new class of inhibitors of the chymotrypsin-like serine protease NS3 of the hepatitis C virus. These inhibitors exploit the binding potential of the S' site of the protease, which is not generally used by the natural substrates. The effect of prime-site occupancy was analyzed by circular dichroism spectroscopy and limited proteolysis-mass spectrometry. Generally, nonprime inhibitors cause a structural change in NS3. Binding in the S' site produces additional conformational changes with different binding modes, even in the case of the NS3/4A cofactor complex. Notably, inhibitor binding either in the S or S' site also has profound effects on the stabilization of the protease. In addition, the stabilization propagates to regions not in direct contact with the inhibitor. In particular, the N-terminal region, which according to structural studies is endowed with low structural stability and is not stabilized by nonprime inhibitors, was now fully protected from proteolytic degradation. From the perspective of drug design, P-P' inhibitors take advantage of binding pockets, which are not exploited by the natural HCV substrates; hence, they are an entry point for a novel class of NS3/4A inhibitors. Here we show that binding of each inhibitor is associated with a specific structural rearrangement. The development of a range of inhibitors belonging to different classes and an understanding of their interactions with the protease are required to address the issue of the most likely outcome of viral protease inhibitor therapy, that is, viral resistance.
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Affiliation(s)
- Annarita Casbarra
- Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte Santangelo, Via Cinthia, 80126 Napoli, Italy
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16
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Birolo L, Dal Piaz F, Pucci P, Marino G. Structural characterization of the M* partly folded intermediate of wild type and P138A aspartate aminotransferase from Escherichia coli. J Biol Chem 2002; 277:17428-37. [PMID: 11875074 DOI: 10.1074/jbc.m200650200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A combination of spectroscopic techniques, hydrogen/deuterium exchange, and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the topology of the monomeric M* partly folded intermediate of aspartate aminotransferase from Escherichia coli in wild type (WT) as well as in a mutant form in which the highly conserved cis-proline at position 138 was replaced by a trans-alanine (P138A). Fluorescence analysis indicates that, although M* is an off-pathway intermediate in the folding of WT aspartate aminotransferase from E. coli, it seems to coincide with an on-pathway folding intermediate for the P138A mutant. Spectroscopic data, hydrogen/deuterium exchange, and limited proteolysis experiments demonstrated the occurrence of conformational differences between the two M* intermediates, with P138A-M* being conceivably more compact than WT-M*. Limited proteolysis data suggested that these conformational differences might be related to a different relative orientation of the small and large domains of the protein induced by the presence of the cis-proline residue at position 138. These differences between the two M* species indicated that in WT-M* Pro138 is in the cis conformation at this stage of the folding process. Moreover, hydrogen/deuterium exchange results showed the occurrence of few differences in the native N(2) forms of WT and P138A, the spectroscopic features and crystallographic structures of which are almost superimposable.
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Affiliation(s)
- Leila Birolo
- Dipartimento di Chimica Organica e Biochimica, Università Federico II di Napoli, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
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17
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Fahey E, Chaudhuri JB. Molecular characterisation of size exclusion chromatography refolded urokinase-plasminogen activator. Chem Eng Sci 2001. [DOI: 10.1016/s0009-2509(01)00182-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Scognamiglio R, Notomista E, Barbieri P, Pucci P, Dal Piaz F, Tramontano A, Di Donato A. Conformational analysis of putative regulatory subunit D of the toluene/o-xylene-monooxygenase complex from Pseudomonas stutzeri OX1. Protein Sci 2001; 10:482-90. [PMID: 11344317 PMCID: PMC2374142 DOI: 10.1110/ps.35701] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
A gene cluster isolated from Pseudomonas stutzeri OX1 genomic DNA and containing six ORFs codes for toluene/o-xylene-monooxygenase. The putative regulatory D subunit was expressed in Escherichia coli and purified. Its protein sequence was verified by mass spectrometry mapping and found to be identical to the sequence predicted on the basis of the DNA sequence. The surface topology of subunit D in solution was probed by limited proteolysis carried out under strictly controlled conditions using several proteases as proteolytic probes. The same experiments were carried out on the homologous P2 component of the multicomponent phenol hydroxylase from Pseudomonas putida CF600. The proteolytic fragments released from both proteins in their native state were analyzed by electrospray mass spectrometry, and the preferential cleavage sites were assessed. The results indicated that despite the relatively high similarity between the sequences of the two proteins, some differences in the distribution of preferential proteolytic cleavages were detected, and a much higher conformational flexibility of subunit D was inferred. Moreover, automatic modeling of subunit D was attempted, based on the known three-dimensional structure of P2. Our results indicate that, at least in this case, standard modeling procedures based on automatic alignment on the structure of P2 fail to produce a model consistent with limited proteolysis experimental data. Thus, it is our opinion that reliable techniques such as limited proteolysis can be employed to test three-dimensional models and highlight problems in automatic model building.
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Affiliation(s)
- R Scognamiglio
- Dipartimento di Chimica Organica e Biologica, Universitá di Napoli Federico II, Via Mezzocannone, 16, 80134 Naples, Italy
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19
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Pessi A. A personal account of the role of peptide research in drug discovery: the case of hepatitis C. J Pept Sci 2001; 7:2-14. [PMID: 11245202 DOI: 10.1002/psc.310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although peptides themselves are not usually the end products of a drug discovery effort, peptide research often plays a key role in many aspects of this process. This will be illustrated by reviewing the experience of peptide research carried out at IRBM in the course of our study of hepatitis C virus (HCV). The target of our work is the NS3/4A protease, which is essential for maturation of the viral polyprotein. After a thorough examination of its substrate specificity we fine-tuned several substrate-derived peptides for enzymology studies, high-throughput screening and as fluorescent probes for secondary binding assays. In the course of these studies we made the key observation: that the protease is inhibited by its own cleavage products. Single analog and combinatorial optimization then derived potent peptide inhibitors. The crucial role of the NS4A cofactor was also addressed. NS4A is a small transmembrane protein, whose central domain is the minimal region sufficient for enzyme activation. Structural studies were performed with a peptide corresponding to the minimal activation domain, with a series of product inhibitors and with both. We found that NS3/4A is an induced fit enzyme, requiring both the cofactor and the substrate to acquire its bioactive conformation; this explained some puzzling results of 'serine-trap' type inhibitors. A more complete study on NS3 activation, however, requires the availability of the full-length NS4A protein. This was prepared by native chemical ligation, after sequence engineering to enhance its solubility; structural studies are in progress. Current work is focused on the P' region of the substrate, which, at variance with the P region, is not used for ground state binding to the enzyme and might give rise to inhibitors showing novel interactions with the enzyme.
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Affiliation(s)
- A Pessi
- Department of Biotechnology, Istituto di Ricerche di Biologia Molecolare P. Angeletti (IRBM), Rome, Italy.
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20
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Cingolani G, Lashuel HA, Gerace L, Müller CW. Nuclear import factors importin alpha and importin beta undergo mutually induced conformational changes upon association. FEBS Lett 2000; 484:291-8. [PMID: 11078895 DOI: 10.1016/s0014-5793(00)02154-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A heterodimer of importin alpha and importin beta accomplishes the nuclear import of proteins carrying classical nuclear localization signals (NLS). The interaction between the two import factors is mediated by the IBB domain of importin alpha and involves an extended recognition surface as shown by X-ray crystallography. Using a combination of biochemical and biophysical techniques we have investigated the formation of the importin beta:IBB domain complex in solution. Our data suggest that upon binding to the IBB domain, importin beta adopts a compact, proteolytically resistant conformation, while simultaneously the IBB domain folds into an alpha helix. We suggest a model to describe how these dual mutually induced conformational changes may orchestrate the nuclear import of NLS cargo in vivo.
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Affiliation(s)
- G Cingolani
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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21
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Esposito G, Michelutti R, Verdone G, Viglino P, Hernández H, Robinson CV, Amoresano A, Dal Piaz F, Monti M, Pucci P, Mangione P, Stoppini M, Merlini G, Ferri G, Bellotti V. Removal of the N-terminal hexapeptide from human beta2-microglobulin facilitates protein aggregation and fibril formation. Protein Sci 2000; 9:831-45. [PMID: 10850793 PMCID: PMC2144642 DOI: 10.1110/ps.9.5.831] [Citation(s) in RCA: 222] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The solution structure and stability of N-terminally truncated beta2-microglobulin (deltaN6beta2-m), the major modification in ex vivo fibrils, have been investigated by a variety of biophysical techniques. The results show that deltaN6beta2-m has a free energy of stabilization that is reduced by 2.5 kcal/mol compared to the intact protein. Hydrogen exchange of a mixture of the truncated and full-length proteins at microM concentrations at pH 6.5 monitored by electrospray mass spectrometry reveals that deltaN6beta2-m is significantly less protected than its wild-type counterpart. Analysis of deltaN6beta2-m by NMR shows that this loss of protection occurs in beta strands I, III, and part of II. At mM concentration gel filtration analysis shows that deltaN6beta2-m forms a series of oligomers, including trimers and tetramers, and NMR analysis indicates that strand V is involved in intermolecular interactions that stabilize this association. The truncated species of beta2-microglobulin was found to have a higher tendency to self-associate than the intact molecule, and unlike wild-type protein, is able to form amyloid fibrils at physiological pH. Limited proteolysis experiments and analysis by mass spectrometry support the conformational modifications identified by NMR and suggest that deltaN6beta2-m could be a key intermediate of a proteolytic pathway of beta2-microglobulin. Overall, the data suggest that removal of the six residues from the N-terminus of beta2-microglobulin has a major effect on the stability of the overall fold. Part of the tertiary structure is preserved substantially by the disulfide bridge between Cys25 and Cys80, but the pairing between beta-strands far removed from this constrain is greatly perturbed.
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Affiliation(s)
- G Esposito
- Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Italy
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