1
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Parveen N, Lin YL, Chou RH, Sun CM, Yu C. Synthesis of Novel Suramin Analogs With Anti-Proliferative Activity via FGF1 and FGFRD2 Blockade. Front Chem 2022; 9:764200. [PMID: 35047478 PMCID: PMC8763243 DOI: 10.3389/fchem.2021.764200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
A promising approach in cancer therapy is the inhibition of cell proliferation using small molecules. In this study, we report the synthesis of suramin derivatives and their applications. We used NMR spectroscopy and docking simulations to confirm binding sites and three-dimensional models of the ligand-protein complex. The WST-1 assay was used to assess cell viability and cell proliferation in vitro to evaluate the inhibition of protein-protein interactions and to investigate the anti-proliferative activities in a breast cancer cell line. All the suramin derivatives showed anti-proliferative activity by blocking FGF1 binding to its receptor FGFRD2. The dissociation constant was measured by fluorescence spectroscopy. The suramin compound derivatives synthesized herein show potential as novel therapeutic agents for their anti-proliferative activity via the inhibition of protein-protein interactions. The cytotoxicity of these suramin derivatives was lower than that of the parent suramin compound, which may be considered a significant advancement in this field. Thus, these novel suramin derivatives may be considered superior anti-metastasis molecules than those of suramin.
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Affiliation(s)
- Nuzhat Parveen
- Chemistry Department, National Tsing Hua University, Hsinchu, Taiwan
| | - Yan-Liang Lin
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ruey-Hwang Chou
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Laboratory and Biotechnology, Asia University, Taichung, Taiwan
| | - Chung-Ming Sun
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chin Yu
- Chemistry Department, National Tsing Hua University, Hsinchu, Taiwan
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2
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Agrawal S, Govind Kumar V, Gundampati RK, Moradi M, Kumar TKS. Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor. Sci Rep 2021; 11:15579. [PMID: 34341408 PMCID: PMC8329156 DOI: 10.1038/s41598-021-95050-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.
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Affiliation(s)
- Shilpi Agrawal
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
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3
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Parveen N, Lin YL, Khan MI, Chou RH, Sun CM, Yu C. Suramin derivatives play an important role in blocking the interaction between FGF1 and FGFRD2 to inhibit cell proliferation. Eur J Med Chem 2020; 206:112656. [PMID: 32827875 DOI: 10.1016/j.ejmech.2020.112656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023]
Abstract
The inhibition of protein function by small compounds plays a critical role in controlling cell proliferation. We report on a new class of small molecule (NCTU-Alan-2026) inhibitors for cell proliferation. NCTU-Alan-2026 blocks the interaction between FGF1 and its receptor FGF1R2D2. Extensive NMR studies combined with fluorescence experiments provided the specific mechanism of how NCTU-Alan-2026 could inhibit cell proliferation. We describe an innovative therapeutic approach for anti-proliferation and demonstrate an example of inhibition of small molecules by blocking the protein-protein interaction. We found that the compound NCTU-Alan-2026 blocked the interaction between the two proteins FGF1 and FGF1R2D2 and inhibited cell proliferation. The toxicity of NCTU-Alan-2026 is lower than that of suramin. Thus, NCTU-Alan-2026 could be a better drug than suramin in the treatment of cancer.
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Affiliation(s)
- Nuzhat Parveen
- Chemistry Department, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yan-Liang Lin
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Md Imran Khan
- Department of Physics, University of Central Florida, Orlando, 32816, Florida, USA
| | - Ruey-Hwang Chou
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, 404, Taiwan; Department of Biotechnology, Asia University, Taichung, 40402, Taiwan
| | - Chung-Ming Sun
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Chin Yu
- Chemistry Department, National Tsing Hua University, Hsinchu, 300, Taiwan.
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4
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Kerr R, Agrawal S, Maity S, Koppolu B, Jayanthi S, Suresh Kumar G, Gundampati RK, McNabb DS, Zaharoff DA, Kumar TKS. Design of a thrombin resistant human acidic fibroblast growth factor (hFGF1) variant that exhibits enhanced cell proliferation activity. Biochem Biophys Res Commun 2019; 518:191-196. [PMID: 31420170 DOI: 10.1016/j.bbrc.2019.08.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
Acidic fibroblast growth factors (FGF1s) are heparin binding proteins that regulate a wide array of key cellular processes and are also candidates for promising biomedical applications. FGF1-based therapeutic applications are currently limited due to their inherent thermal instability and susceptibility to proteases. Using a wide range of biophysical and biochemical techniques, we demonstrate that reversal of charge on a well-conserved positively charged amino acid, R136, in the heparin binding pocket drastically increases the resistance to proteases, thermal stability, and cell proliferation activity of the human acidic fibroblast growth factor (hFGF1). Two-dimensional NMR data suggest that the single point mutations at position-136 (R136G, R136L, R136Q, R136K, and R136E) did not perturb the backbone folding of hFGF1. Results of the differential scanning calorimetry experiments show that of all the designed R136 mutations only the charge reversal mutation, R136E, significantly increases (ΔTm = 7 °C) the thermal stability of the protein. Limited trypsin and thrombin digestion results reveal that the R136E mutation drastically increases the resistance of hFGF1 to the action of the serine proteases. Isothermal titration calorimetry data show that the R136E mutation markedly decreases the heparin binding affinity of hFGF1. Interestingly, despite lower heparin binding affinity, the cell proliferation activity of the R136E variant is more than double of that exhibited by either the wild type or the other R136 variants. The R136E variant due to its increased thermal stability, resistance to proteases, and enhanced cell proliferation activity are expected to provide valuable clues for the development of hFGF1- based therapeutics for the management of chronic diabetic wounds.
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Affiliation(s)
- Rebecca Kerr
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Shilpi Agrawal
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Sanhita Maity
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Bhanuprasanth Koppolu
- Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill & North Carolina State University, Raleigh, NC, 27695, USA
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Gayatri Suresh Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - David S McNabb
- Department of Biological Sciences, University of Arkansas, University of Arkansas, Fayetteville, AR, 72701, USA
| | - David A Zaharoff
- Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill & North Carolina State University, Raleigh, NC, 27695, USA
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5
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Davis JE, Gundampati RK, Jayanthi S, Anderson J, Pickhardt A, Koppolu BP, Zaharoff DA, Kumar TKS. Effect of extension of the heparin binding pocket on the structure, stability, and cell proliferation activity of the human acidic fibroblast growth factor. Biochem Biophys Rep 2018; 13:45-57. [PMID: 29556563 PMCID: PMC5857160 DOI: 10.1016/j.bbrep.2017.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 12/02/2022] Open
Abstract
Acidic human fibroblast growth factor (hFGF1) plays a key role in cell growth and proliferation. Activation of the cell surface FGF receptor is believed to involve the glycosaminoglycan, heparin. However, the exact role of heparin is a subject of considerable debate. In this context, in this study, the correlation between heparin binding affinity and cell proliferation activity of hFGF1 is examined by extending the heparin binding pocket through selective engineering via charge reversal mutations (D82R, D84R and D82R/D84R). Results of biophysical experiments such as intrinsic tryptophan fluorescence and far UV circular dichroism spectroscopy suggest that the gross native structure of hFGF1 is not significantly perturbed by the engineered mutations. However, results of limited trypsin digestion and ANS binding experiments show that the backbone structure of the D82R variant is more flexible than that of the wild type hFGF1. Results of the temperature and urea-induced equilibrium unfolding experiments suggest that the stability of the charge-reversal mutations increases in the presence of heparin. Isothermal titration calorimetry (ITC) data reveal that the heparin binding affinity is significantly increased when the charge on D82 is reversed but not when the negative charge is reversed at both positions D82 and D84 (D82R/D84R). However, despite the increased affinity of D82R for heparin, the cell proliferation activity of the D82R variant is observed to be reduced compared to the wild type hFGF1. The results of this study clearly demonstrate that heparin binding affinity of hFGF1 is not strongly correlated to its cell proliferation activity.
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Affiliation(s)
- Julie Eberle Davis
- Department of Chemistry and Biochemistry, University of Arkansas, 1 University of Arkansas, Fayetteville, AR 72701, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, 1 University of Arkansas, Fayetteville, AR 72701, USA
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, 1 University of Arkansas, Fayetteville, AR 72701, USA
| | - Joshua Anderson
- Department of Chemistry and Biochemistry, University of Arkansas, 1 University of Arkansas, Fayetteville, AR 72701, USA
| | - Abigail Pickhardt
- Department of Chemistry and Biochemistry, University of Arkansas, 1 University of Arkansas, Fayetteville, AR 72701, USA
| | - Bhanu prasanth Koppolu
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina‐Chapel Hill, NC 27695, USA
| | - David A. Zaharoff
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina‐Chapel Hill, NC 27695, USA
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6
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Paul S, Ishida H, Nguyen LT, Liu Z, Vogel HJ. Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics. Protein Sci 2017; 26:946-959. [PMID: 28187530 PMCID: PMC5405426 DOI: 10.1002/pro.3138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/08/2022]
Abstract
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Similar to the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme nonribosomal peptide synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding acyl carrier proteins (ACPs), for which the genes are located near to NRPS gene clusters. Here, we report that the solution NMR structure of apo-LipD is very similar to other four-helix bundle forming ACPs from fatty acid synthase (FAS), polyketide synthase, and NRPS systems. By recording NMR dynamics data, we found that the backbone motions in holo-LipD are more restricted than in apo-LipD due to the attachment of phosphopantetheine moiety. This enhanced stability of holo-LipD was also observed in differential scanning calorimetry experiments. Furthermore, we demonstrate that, unlike several other ACPs, the folding of LipD does not depend on the presence of divalent cations, although the presence of Mg2+ or Ca2+ can increase the protein stability. We propose that small structural rearrangements in the tertiary structure of holo-LipD which lead to the enhanced stability are important for the cognate enzyme recognition for the acylation reaction. Our results also highlight the different surface charges of LipD and FAS-ACP from A. friuliensis that would allow the acyl-CoA ligase to interact preferentially with the LipD instead of binding to the FAS-ACP.
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Affiliation(s)
- Subrata Paul
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hiroaki Ishida
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Leonard T. Nguyen
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Zhihong Liu
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hans J. Vogel
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
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7
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Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11). Biochem J 2013; 451:289-300. [PMID: 23356867 DOI: 10.1042/bj20120627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Non-catalytic cellulosomal CBMs (carbohydrate-binding modules) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligo-saccharides) and enzyme into close contact. In the present study we carried out an atomistic rationalization of the molecular determinants of ligand specificity for a family 11 CBM from thermophilic Clostridium thermocellum [CtCBM11 (C. thermocellum CBM11)], based on a NMR and molecular modelling approach. We have determined the NMR solution structure of CtCBM11 at 25°C and 50°C and derived information on the residues of the protein that are involved in ligand recognition and on the influence of the length of the saccharide chain on binding. We obtained models of the CtCBM11-cellohexaose and CtCBM11-cellotetraose complexes by docking in accordance with the NMR experimental data. Specific ligand-protein CH-π and Van der Waals interactions were found to be determinant for the stability of the complexes and for defining specificity. Using the order parameters derived from backbone dynamics analysis in the presence and absence of ligand and at 25°C and 50°C, we determined that the protein's backbone conformational entropy is slightly positive. This data in combination with the negative binding entropy calculated from ITC (isothermal titration calorimetry) studies supports a selection mechanism where a rigid protein selects a defined oligosaccharide conformation.
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8
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Wang HM, Yu C. Investigating the refolding pathway of human acidic fibroblast growth factor (hFGF-1) from the residual structure(s) obtained by denatured-state hydrogen/deuterium exchange. Biophys J 2011; 100:154-64. [PMID: 21190667 DOI: 10.1016/j.bpj.2010.11.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 11/26/2022] Open
Abstract
Human fibroblast growth factor 1 (hFGF-1) consists of 12 anti-parallel β-strands arranged into a β-trefoil architecture. We directly measured hydrogen/deuterium exchange rates on the urea-denatured hFGF-1 to obtain the information with regard to the persistent residual interaction(s) in the unfolded hFGF-1. Thirty-eight residues whose heteronuclear single quantum coherence cross-peaks can be observed after exchange show higher protections than those predicted for the same residues in a random coil conformation, suggesting the existence of residual structure(s). The urea-denaturation of hFGF-1 tested by both circular dichroism and fluorescence spectroscopy indicated that the unfolding process is a cooperative two-state process and that the residual structures observed did not originate from the existence of a partially structured intermediate. The coincident disappearance of the native heteronuclear single quantum coherence cross-peaks during the urea-denaturation process suggests that the residual structures observed contain no nativelike interactions. The protected residues (fold ons) in the urea-denatured state are mostly those that exchange slowly in the native state H/D exchange. The distribution of these fold ons in the native structure of hFGF-1 suggests that the refolding starts by collisions between the residual structures (microdomains) between the β-strands VI and VII, and between the β-strands II and III, which appear to be two independent refolding coordinates during the refolding process.
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Affiliation(s)
- Han-Min Wang
- Department of Chemistry, National Tsing-Hua University, Hsin-Chu, Taiwan, Republic of China
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9
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Rudd TR, Uniewicz KA, Ori A, Guimond SE, Skidmore MA, Gaudesi D, Xu R, Turnbull JE, Guerrini M, Torri G, Siligardi G, Wilkinson MC, Fernig DG, Yates EA. Comparable stabilisation, structural changes and activities can be induced in FGF by a variety of HS and non-GAG analogues: implications for sequence-activity relationships. Org Biomol Chem 2010; 8:5390-7. [DOI: 10.1039/c0ob00246a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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NMR characterization of copper and lipid interactions of the C2B domain of synaptotagmin I-relevance to the non-classical secretion of the human acidic fibroblast growth factor (hFGF-1). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:297-302. [PMID: 19835837 DOI: 10.1016/j.bbamem.2009.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 09/18/2009] [Accepted: 09/30/2009] [Indexed: 11/21/2022]
Abstract
Human fibroblast growth factor (hFGF-1) is a approximately 17 kDa heparin binding cytokine. It lacks the conventional hydrophobic N-terminal signal sequence and is secreted through non-classical secretion routes. Under stress, hFGF-1 is released as a multiprotein complex consisting of hFGF-1, S100A13 (a calcium binding protein), and p40 synaptotagmin (Syt1). Copper (Cu(2+)) is shown to be required for the formation of the multiprotein hFGF-1 release complex (Landriscina et al. ,2001; Di Serio et al., 2008). Syt1, containing the lipid binding C2B domain, is believed to play an important role in the eventual export of the hFGF-1 across the lipid bilayer. In this study, we characterize Cu(2+) and lipid interactions of the C2B domain of Syt1 using multidimensional NMR spectroscopy. The results highlight how Cu(2+) appears to stabilize the protein bound to pS vesicles. Cu(2+) and lipid binding interface mapped using 2D (1)H-(15)N heteronuclear single quantum coherence experiments reveal that residues in beta-strand I contributes to the unique Cu(2+) binding site in the C2B domain. In the absence of metal ions, residues located in Loop II and beta-strand IV contribute to binding to unilamelar pS vesicles. In the presence of Cu(2+), additional residues located in Loops I and III appear to stabilize the protein-lipid interactions. The results of this study provide valuable information towards understanding the molecular mechanism of the Cu(2+)-induced non-classical secretion of hFGF-1.
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11
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Anbazhagan V, Wang HM, Lu CS, Yu C. A residue-level investigation of the equilibrium unfolding of the C2A domain of synaptotagmin 1. Arch Biochem Biophys 2009; 490:158-62. [DOI: 10.1016/j.abb.2009.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 08/26/2009] [Accepted: 08/26/2009] [Indexed: 10/20/2022]
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12
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Chen M, Dousis AD, Wu Y, Wittung-Stafshede P, Ma J. Predicting protein folding cores by empirical potential functions. Arch Biochem Biophys 2008; 483:16-22. [PMID: 19135974 DOI: 10.1016/j.abb.2008.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 11/29/2022]
Abstract
Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two beta-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.
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Affiliation(s)
- Mingzhi Chen
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, USA
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13
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Rajalingam D, Graziani I, Prudovsky I, Yu C, Kumar TKS. Relevance of partially structured states in the non-classical secretion of acidic fibroblast growth factor. Biochemistry 2007; 46:9225-38. [PMID: 17636870 PMCID: PMC3656169 DOI: 10.1021/bi7002586] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acidic fibroblast growth factor (aFGF) is a signal peptide-less protein that is secreted into the extracellular compartment as part of a multiprotein release complex, consisting of aFGF, S100A13 (a calcium binding protein), and a 40 kDa (p40) form of synaptotagmin (Syt1), a protein that participates in the docking of a variety of secretory vesicles. p40 Syt1, and specifically its C2A domain, is believed to play a major role in the non-classical secretion of the aFGF release complex mediated by the interaction of aFGF and p40 Syt1with the phospholipids of the cell membrane inner leaflet. In the present study, we investigate the structural characteristics of aFGF and the C2A domain of p40 Syt1 under acidic conditions, using a variety of biophysical techniques including multidimensional NMR spectroscopy. Urea-induced equilibrium unfolding (at pH 3.4) of both aFGF and the C2A domain are non-cooperative and proceed with the accumulation of stable intermediate states. 1-Anilino-8-napthalene sulfonate (ANS) binding and size-exclusion chromatography results suggest that both aFGF and the C2A domain exist as partially structured states under acidic conditions (pH 3.4). Limited trypsin digestion analysis and 1H-15N chemical shift perturbation data reveal that the flexibility of certain portions of the protein backbone is increased in the partially structured state(s) of aFGF. The residues that are perturbed in the partially structured state(s) in aFGF are mostly located at the N- and C-terminal ends of the protein. In marked contrast, most of the interactions stabilizing the native secondary structure are preserved in the partially structured state of the C2A domain. Isothermal titration calorimetry data indicate that the binding affinity between aFGF and the C2A domain is significantly enhanced at pH 3.4. In addition, both aFGF and the C2A domain exhibit much higher lipid binding affinity in their partially structured states. The translocation of the multiprotein FGF release complex across the membrane appears to be facilitated by the formation of partially structured states of aFGF and the C2A domain of p40 Syt1.
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Affiliation(s)
| | - Irene Graziani
- Department of Chemistry and Biochemistry, Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine 04074
| | - Igor Prudovsky
- Department of Chemistry and Biochemistry, Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine 04074
| | - Chin Yu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan
- To whom correspondence should be addressed. Phone: 479-575-5646. Fax: 479-575-4049. (T.K.S.K.). Phone: 886-35-711082. Fax: 886-35-721524. cyu@ mx.nthu.edu.tw (C.Y.)
| | - Thallapuranam Krishnaswamy S. Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
- To whom correspondence should be addressed. Phone: 479-575-5646. Fax: 479-575-4049. (T.K.S.K.). Phone: 886-35-711082. Fax: 886-35-721524. cyu@ mx.nthu.edu.tw (C.Y.)
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14
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Canales A, Lozano R, López-Méndez B, Angulo J, Ojeda R, Nieto PM, Martín-Lomas M, Giménez-Gallego G, Jiménez-Barbero J. Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue. FEBS J 2006; 273:4716-27. [PMID: 16995857 DOI: 10.1111/j.1742-4658.2006.05474.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 3D structure of a complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed synthetic heparin hexasaccharide has been determined by NMR spectroscopy. This hexasaccharide can substitute natural heparins in FGF-1 mitogenesis assays, in spite of not inducing any apparent dimerization of the growth factor. The use of this well defined synthetic heparin analogue has allowed us to perform a detailed NMR structural analysis of the heparin-FGF interaction, overcoming the limitations of NMR to deal with the high molecular mass and heterogeneity of the FGF-1 oligomers formed in the presence of natural heparin fragments. Our results confirm that glycosaminoglycans induced FGF-1 dimerization either in a cis or trans disposition with respect to the heparin chain is not an absolute requirement for biological activity.
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Canales-Mayordomo A, Fayos R, Angulo J, Ojeda R, Martín-Pastor M, Nieto PM, Martín-Lomas M, Lozano R, Giménez-Gallego G, Jiménez-Barbero J. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by 15N NMR relaxation methods. JOURNAL OF BIOMOLECULAR NMR 2006; 35:225-39. [PMID: 16937240 DOI: 10.1007/s10858-006-9024-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 04/26/2006] [Indexed: 05/11/2023]
Abstract
The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR).
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Affiliation(s)
- Angeles Canales-Mayordomo
- Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28006, Madrid, Spain
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16
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Sivaraja V, Kumar TKS, Prudovsky I, Yu C. Three-dimensional solution structure of a unique S100 protein. Biochem Biophys Res Commun 2005; 335:1140-8. [PMID: 16122705 DOI: 10.1016/j.bbrc.2005.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 08/01/2005] [Indexed: 11/30/2022]
Abstract
S100A13 is a homodimeric protein that belongs to the S100 subfamily of EF-hand Ca2+-binding proteins. S100A13 exhibits unique physical and functional properties not observed in other members of the S100 family. S100A13 is crucial for the non-classical export of acidic fibroblast growth factors (FGFs-1), which lack signal peptide at their N-terminal end. In the present study, we report the three-dimensional solution structure of Ca2+-bound S100A13 using a variety of 3D NMR experiments. The structure of S100A13 is globular with four helices and an antiparallel beta-sheet in each subunit. The dimer interface is formed mainly by an antiparallel arrangement of helices H1, H1', H4, and H4'. Isothermal titration calorimetry (ITC) experiments show that S100A13 binds non-cooperatively to four calcium ions. Prominent differences exist between the three-dimensional structures of S100A13 and other S100 proteins. The hydrophobic pocket that largely contributes to protein-protein interactions in other S100 proteins is absent in S100A13. The structure of S100A13 is characterized by a large patch of negatively charged residues flanked by dense cationic clusters contributed largely by the positively charged residues located at the C-terminal end. Results of ITC experiments reveal that S100A13 lacking the C-terminal segment (residues 88-98) fails to bind FGF-1. The three-dimensional structure of S100A13 not only provides useful clues on its role in the non-classical export of signal peptide-less proteins such as FGF-1 but also paves the way for rational design of drugs against FGF-induced tumors.
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Affiliation(s)
- Vaithiyalingam Sivaraja
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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17
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Kathir KM, Kumar TKS, Rajalingam D, Yu C. Time-dependent changes in the denatured state(s) influence the folding mechanism of an all beta-sheet protein. J Biol Chem 2005; 280:29682-8. [PMID: 15941715 DOI: 10.1074/jbc.m504389200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Newt fibroblast growth factor (nFGF-1) is an approximately 15-kDa all beta-sheet protein devoid of disulfide bonds. Urea-induced equilibrium unfolding of nFGF-1, monitored by steady state fluorescence and far-UV circular dichroism spectroscopy, is cooperative with no detectable intermediate(s). Urea-induced unfolding of nFGF-1 is reversible, but the percentage of the protein recovered in the native state depends on the time of incubation of the protein in the denaturant. The yield of the protein in the native state decreases with the increase in time of incubation in the denaturant. The failure of the protein to refold to its native state is not due to trivial chemical reactions that could possibly occur upon prolonged incubation in the denaturant. (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra, limited proteolytic digestion, and fluorescence data suggest that the misfolded state(s) of nFGF-1 has structural features resembling that of the denatured state(s). GroEL, in the presence of ATP, is observed to rescue the protein from being trapped in the misfolded state(s). (1)H-(15)N HSQC data of nFGF-1, acquired in the denatured state(s) (in 8 m urea), suggest that the protein undergoes subtle time-dependent structural changes in the denaturant. To our knowledge, this report for the first time demonstrates that the commitment to adapt unproductive pathways leading to protein misfolding/aggregation occurs in the denatured state ensemble.
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18
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Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, Sakagami N, Terada T, Shirouzu M, Yoshida M, Hirota H, Osanai T, Tanaka A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kinoshita K, Güntert P, Kigawa T, Yokoyama S. Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci 2005; 13:2089-100. [PMID: 15273307 PMCID: PMC2279815 DOI: 10.1110/ps.04751804] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices, with an alphabetabetabetabetaalphaalpha topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive beta-turns that overlap with each other by two residues (triple beta-turn). As putative binding sites with GCN1, a structure-based alignment allowed the identification of several surface residues in alpha-helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin-conjugating enzymes (E2s), with most of the structural differences in the region connecting beta-strand 4 and alpha-helix 3. The structural architecture, including the triple beta-turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins.
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19
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Wong HJ, Stathopulos PB, Bonner JM, Sawyer M, Meiering EM. Non-linear effects of temperature and urea on the thermodynamics and kinetics of folding and unfolding of hisactophilin. J Mol Biol 2005; 344:1089-107. [PMID: 15544814 DOI: 10.1016/j.jmb.2004.09.091] [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] [Received: 03/04/2004] [Revised: 08/17/2004] [Accepted: 09/29/2004] [Indexed: 11/21/2022]
Abstract
Extensive measurements and analysis of thermodynamic stability and kinetics of urea-induced unfolding and folding of hisactophilin are reported for 5-50 degrees C, at pH 6.7. Under these conditions hisactophilin has moderate thermodynamic stability, and equilibrium and kinetic data are well fit by a two-state transition between the native and the denatured states. Equilibrium and kinetic m values decrease with increasing temperature, and decrease with increasing denaturant concentration. The betaF values at different temperatures and urea concentrations are quite constant, however, at about 0.7. This suggests that the transition state for hisactophilin unfolding is native-like and changes little with changing solution conditions, consistent with a narrow free energy profile for the transition state. The activation enthalpy and entropy of unfolding are unusually low for hisactophilin, as is also the case for the corresponding equilibrium parameters. Conventional Arrhenius and Eyring plots for both folding and unfolding are markedly non-linear, but these plots become linear for constant DeltaG/T contours. The Gibbs free energy changes for structural changes in hisactophilin have a non-linear denaturant dependence that is comparable to non-linearities observed for many other proteins. These non-linearities can be fit for many proteins using a variation of the Tanford model, incorporating empirical quadratic denaturant dependencies for Gibbs free energies of transfer of amino acid constituents from water to urea, and changes in fractional solvent accessible surface area of protein constituents based on the known protein structures. Noteworthy exceptions that are not well fit include amyloidogenic proteins and large proteins, which may form intermediates. The model is easily implemented and should be widely applicable to analysis of urea-induced structural transitions in proteins.
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Affiliation(s)
- Hannah J Wong
- Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry, University of Waterloo, ESC 326, Waterloo, Ont., N2L 3G1, Canada
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20
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Hung KW, Kumar TKS, Chi YH, Chiu IM, Yu C. Molecular cloning, overexpression, and characterization of the ligand-binding D2 domain of fibroblast growth factor receptor. Biochem Biophys Res Commun 2004; 317:253-8. [PMID: 15047176 DOI: 10.1016/j.bbrc.2004.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2004] [Indexed: 11/25/2022]
Abstract
Fibroblast growth factors (FGFs) regulate a wide range of important cellular processes. The biological activities of FGFs are mediated by cell surface receptors (FGFRs). In the present study for the first time we report the cloning, expression, and characterization of the ligand (FGF)-binding D2 domain of human FGFR2. D2 domain is expressed in Escherichia coli in high yields (10 mg/L) as inclusion bodies. The protein is recovered by dissolving the inclusion bodies in 8 M urea and subsequently refolding on nickel affinity column. The protein is purified (to approximately 97% purity) to homogeneity using heparin-Sepharose affinity column. Far-UV circular dichroism data and chemical shift index plot based on 1H-alpha, 13C-alpha, 13C-beta, and 13carbonyl group chemical shifts suggest that D2 domain is an all beta-sheet protein consisting of 9 beta-strands. Isothermal titration calorimetry and equilibrium urea unfolding experiments show that recombinant D2 domain is in a biologically active conformation and binds strongly to its ligand (FGF) and to the heparin analog, sucrose octasulfate (SOS). Using a variety of triple resonance NMR experiments, complete assignment of 1H, 15N, and 13C resonances in D2 domain has been accomplished. The findings of the present study not only pave way for an in-depth investigation of the molecular mechanism(s) underlying the activation of FGF signaling but also provide avenues for the rational design of potent inhibitors against FGF-mediated pathogenesis.
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MESH Headings
- Amino Acid Sequence
- Calorimetry/methods
- Circular Dichroism
- Cloning, Molecular
- Escherichia coli/metabolism
- Fibroblast Growth Factors/metabolism
- Humans
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Protein Denaturation
- Protein Renaturation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor, Fibroblast Growth Factor, Type 2
- Receptors, Fibroblast Growth Factor/biosynthesis
- Receptors, Fibroblast Growth Factor/chemistry
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sucrose/analogs & derivatives
- Sucrose/metabolism
- Urea/chemistry
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Affiliation(s)
- Kuo-Wei Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan, ROC
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