In silico interaction of insulin-like growth factor binding protein 3 with insulin-like growth factor 1

Elham Jafari , Ali Gheysarzadeh, Karim Mahnam, Rezvan Shahmohammadi, Amir Ansari, Hadi Bakhtyari, Mohammad Reza Mofid


Insulin-like growth factor binding protein-3 (IGFBP-3) is a vital protein exist in circulation which interacts with high affinity to insulin-like growth factor (IGFs) altering their activities. Therefore, the interaction between IGFs and IGFBP-3 has a key role altering large spectrum of activities such as cell cycle progression, proliferation and apoptosis. Despite decades of research, the crystal structure of IGFBP-3 has not been identified possibly due to some technical challenge in its crystallizing. The three-dimensional (3D) structure of IGFBP-3 was predicted using homology modeling, Phyre2, and molecular dynamic. Its interaction with IGF-1 was also identified by HADDOCK software. IGFBP-3 has the most identity with other IGFBPs in N and C-domain; however, its linker domain has lower identity. Our data predicted that IGF-1 structurally interacts with N- domain and linker domain of IGFBP-3. Some conserved residues of IGFBP-3 such as Glu33, Arg36, Gly39, Arg60, Arg66, Asn109, and Ile146 interacts with Glu3, Asp12, Phe16, Gly19, Asp20, Arg21, and Glu58 of IGF-1. In addition, our data predict that the linker domain has a loop structure which covers post translational modification and interacts with IGF-1. The phosphorylation of Ser111 in linker domain, which previously has been shown to induce apoptosis make a repulsive force interrupting this interaction to IGF-1, which enables IGFBP-3 to induce apoptosis. The present study suggests that the linker domain has a key role in recognition of IGFBP-3 with IGF-1.


Docking study; IGF-1; IGFBP-3; Linker domain; Molecular dynamic

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Jones JI, Clemmons DR. Insulin-like growth factors and their binding proteins: biological actions. Endocr Rev. 1995;16(1):3-34.

Clemmons DR. Role of IGF binding proteins in regulating metabolism. Trends Endocrinol Metab. 2016;27(6):375-391.

Brahmkhatri VP, Prasanna C, Atreya HS. Insulin-like growth factor system in cancer: novel targeted therapies. Biomed Res Int. 2015;2015. Article ID 538019. DOI: 10.1155/2015/538019.

Nissley P, Lopaczynski W. Insulin-like growth factor receptors. Growth Factors. 1991;5(1):29-43.

Singh P, Alex JM, Bast F. Insulin receptor (IR) and insulin-like growth factor receptor 1 (IGF-1R) signaling systems: novel treatment strategies for cancer. Med Oncol. 2014;31(1):805-818.

Rechler MM. Insulin-like growth factor binding proteins. In: McCormick D , editor. Vitamins and Hormones. Vol 47. San Deigo: Academic Press; 1993. pp. 8-14.

Murekatete B, Shokoohmand A, McGovern J, Mohanty L, Meinert C, Hollier BG, et al. Targeting Insulin-Like Growth Factor-I and Extracellular Matrix Interactions in Melanoma Progression. Sci Rep. 2018;8(1):583-594.

Clemmons DR. Insulin-like growth factor binding proteins and their role in controlling IGF actions. Cytokine Growth Factor Rev. 1997;8(1):45-62.

Denley A, Cosgrove LJ, Booker GW, Wallace JC, Forbes BE. Molecular interactions of the IGF system. Cytokine Growth Factor Rev. 2005;16(4-5):421-439.

Khodadadi E, Panjepour M, Abbasian M, Broujeni ZK, Mofid MR. Cloning and expression of full-length human insulin-like growth factor binding protein 3 (IGFBP3) in the Escherichia coli. Adv Biomed Res. 2015;4:66-74.

Oh Y, Rosenfeld RG. IGF-independent actions of the IGF binding proteins. In: Contemporary Endocrinology. Totowa: Humana Press; 1999. pp. 257-272.

Ansari A, Gheysarzadeh, A., Mofid, M.R. The interaction of insulin-like growth factor binding protein 3 (IGFBP-3) in insulin-like growth factor (IGF)-independent system. JIMS. 2017;35(451):1452-1461..

Rechler MM, Clemmons DR. Regulatory actions of insulin-like growth factor-binding proteins. Trends Endocrinol Metab. 1998;9(5):176-183.

Alkharobi H, Alhodhodi A, Hawsawi Y, Alkafaji H, Devine D, El-Gendy R, et al. IGFBP-2 and-3 co-ordinately regulate IGF1 induced matrix mineralisation of differentiating human dental pulp cells. Stem Cell Res. 2016;17(3):517-522.

Wu C, Liu X, Wang Y, Tian H, Xie Y, Li Q, et al. Insulin-like factor binding protein-3 promotes the G1 cell cycle arrest in several cancer cell lines. Gene. 2013;512(1):127-133.

Perks C, McCaig C, Holly J. Differential insulin‐like growth factor (IGF)-independent interactions of IGF binding protein-3 and IGF binding protein-5 on apoptosis in human breast cancer cells. Involvement of the mitochondria. J Cell Biochem. 2001;80(2):248-258.

Baxter RC. Insulin-like growth factor binding proteins in the human circulation: a review. Horm Res Paediatr. 1994;42(4-5):140-144.

Cobb LJ, Mehta H, Cohen P. Enhancing the apoptotic potential of insulin-like growth factor-binding protein-3 in prostate cancer by modulation of CK2 phosphorylation. Mol Endocrinol. 2009;23(10):1624-1633.

Hollowood A, Stewart C, Perks C, Pell J, Lai T, Alderson D, et al. Evidence implicating a mid‐region sequence of IGFBP-3 in its specific IGF-independent actions. J Cell Biochem. 2002;86(3):583-589.

Zhang Q, Soderland D, Steinle JJ. TNFα Inhibits IGFBP-3 through Activation of p38α and Casein Kinase 2 in Human Retinal Endothelial Cells. PLoS One. 2014;9(7):e103578.

Kim ST, Jang H-L, Lee J, Park SH, Park YS, Lim HY, et al. Clinical significance of IGFBP-3 methylation in patients with early stage gastric cancer. Transl Oncol. 2015;8(4):288-294.

Fu T, Pappou EP, Guzzetta AA, de Freitas Calmon M, Sun L, Herrera A, et al. IGFBP-3 gene methylation in primary tumor predicts recurrence of stage II colorectal cancers. Ann Surg. 2016;263(2):337-344.

Ho GY, Zheng SL, Cushman M, Perez-Soler R, Kim M, Xue X, et al. Associations of insulin and IGFBP-3 with lung cancer susceptibility in current smokers. J Natl Cancer Inst. 2016;108(7). DOI: 10.1093/jnci/djw012.

Scully T, Scott CD, de Silva HC, Firth SM, Twigg SM, Pintar JE, et al. Insulin-like growth factor binding protein-3 (IGFBP-3) enhances obesity-related breast tumorigenesis. Oncotarget. 2016; 7(34): 55491–55505.

Watanabe K, Uemura K, Asada M, Maesako M, Akiyama H, Shimohama S, et al. The participation of insulin-like growth factor-binding protein 3 released by astrocytes in the pathology of Alzheimer’s disease. Mol Brain. 2015;8(1):82-95.

Bernhard FP, Heinzel S, Binder G, Weber K, Apel A, Roeben B, et al. Insulin-like growth factor 1 (IGF-1) in Parkinson's disease: potential as trait-, progression-and prediction marker and confounding factors. PLoS One. 2016;11(3):e0150552.

Retnakaran R. The Insulin-Like Growth Factor Axis: A New Player in Gestational Diabetes Mellitus? Diabetes. 2016;65(11):3246-3248.

Lofqvist C, Chen J, Connor KM, Smith AC, Aderman CM, Liu N, et al. IGFBP3 suppresses retinopathy through suppression of oxygen-induced vessel loss and promotion of vascular regrowth. Proc Natl Acad Sci U S A. 2007;104(25):10589-10594.

Janssen J, Stolk R, Pols H, Grobbee D, Lamberts S. Serum total IGF-I, free IGF-I, and IGFBP-1 levels in an elderly population: relation to cardiovascular risk factors and disease. Arterioscler Thromb Vasc Biol. 1998;18(2):277-282.

Schwab S, Spranger M, Krempien S, Hacke W, Bettendorf M. Plasma insulin-like growth factor I and IGF binding protein 3 levels in patients with acute cerebral ischemic injury. Stroke. 1997;28(9):1744-1748.

Forbes BE, McCarthy P, Norton R. Insulin-like growth factor binding proteins: a structural perspective. Front Endocrinol (Lausanne). 2012;3:38-50.

Kalus W, Zweckstetter M, Renner C, Sanchez Y, Georgescu J, Grol M, et al. Structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions. EMBO J. 1998;17(22):6558-6572.

Żesławski W, Beisel HG, Kamionka M, Kalus W, Engh RA, Huber R, et al. The interaction of insulin‐like growth factor-I with the N-terminal domain of IGFBP-5. EMBO J. 2001;20(14):3638-3644.

Sitar T, Popowicz GM, Siwanowicz I, Huber R, Holak TA. Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins. Proc Natl Acad Sci U S A. 2006;103(35):13028-13033.

Siwanowicz I, Popowicz GM, Wisniewska M, Huber R, Kuenkele K-P, Lang K, et al. Structural basis for the regulation of insulin-like growth factors by IGF binding proteins. Structure. 2005;13(1): 155-167.

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10(6):845-858.

Akbari V, Moghim S, Mofid MR. Comparison of epothilone and taxol binding in yeast tubulin using molecular modeling. Avicenna J Med Biotechnol. 2011;3(4):167-175.

Lovell SC, Davis IW, Arendall WB, De Bakker PI, Word JM, Prisant MG, et al. Structure validation by Cα geometry:phi,psi and Cbeta deviation. Proteins. 2003;50(3):437-450.

Hess B, Kutzner C, Van Der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4(3):435-447.

Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein− protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003;125(7):1731-1737.

Payet LD, Wang X-H, Baxter RC, Firth SM. Amino-and carboxyl-terminal fragments of insulin-like growth factor (IGF) binding protein-3 cooperate to bind IGFs with high affinity and inhibit IGF receptor interactions. Endocrinology. 2003;144(7):2797-2806.

Moreno-Santos I, Castellano-Castillo D, Lara MF, Fernandez-Garcia JC, Tinahones FJ, Macias-Gonzalez M. IGFBP-3 Interacts with the Vitamin D Receptor in Insulin Signaling Associated with Obesity in Visceral Adipose Tissue. Int J Mol Sci. 2017;18(11):2349-2364.

Shimasaki S, Shimonaka M, Zhang H-P, Ling N. Identification of five different insulin-like growth factor binding proteins (IGFBPs) from adult rat serum and molecular cloning of a novel IGFBP-5 in rat and human. J Biol Chem. 1991;266(16): 10646-10653.

Jafari S, Babaeipour V, Seyedi HE, Rahaie M, Mofid M, Haddad L, et al. Recombinant production of mecasermin in E. coli expression system. Res Pharm Sci. 2014;9(6):453-461.

Brown J, Delaine C, Zaccheo OJ, Siebold C, Gilbert RJ, Van Boxel G, et al. Structure and functional analysis of the IGF-II/IGF2R interaction. EMBO J. 2008;27(1):265-276.

Sitar T, Popowicz GM, Siwanowicz I, Huber R, Holak TA. Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins. Proc Natl Acad Sci U S A. 2006;103(35):13028-13033

Sato A, Koyama S, Yamada H, Suzuki S, Tamura K, Kobayashi M, et al. Three-dimensional solution structure of a disulfide bond isomer of the human insulin-like growth factor-I. Chem Biol Drug Des. 2000;56(4):218-230.

Dubaquié Y, Lowman HB. Total alanine-scanning mutagenesis of insulin-like growth factor I (IGF-I) identifies differential binding epitopes for IGFBP-1 and IGFBP-3. Biochemistry. 1999;38(20):6386-6396.

Blundell T, Bedarkar S, Rinderknecht E, Humbel R. Insulin-like growth factor: a model for tertiary structure accounting for immunoreactivity and receptor binding. Proc Natl Acad Sci U S A. 1978;75(1):180-184.

Hong J, Zhang G, Dong F, Rechler MM. Insulin-like growth factor (IGF)-binding protein-3 mutants that do not bind IGF-I or IGF-II stimulate apoptosis in human prostate cancer cells. J Biol Chem. 2002;277(12):10489-10497.

Imai Y, Moralez A, Andag U, Clarke JB, Busby WH, Clemmons DR. Substitutions for hydrophobic amino acids in the N-terminal domains of IGFBP-3 and-5 markedly reduce IGF-I binding and alter their biologic actions. J Biol Chem. 2000;275(24): 18188-18194.

Carrick FE, Forbes BE, Wallace JC. BIAcore analysis of bovine insulin-like growth factor (IGF)-binding protein-2 identifies major IGF binding site determinants in both the amino- and carboxyl-terminal domains. J Biol Chem. 2001;276(29):27120-27128.

Fowlkes JL, Thrailkill KM, George-Nascimento C, Rosenberg CK, Serra DM. Heparin-binding, highly basic regions within the thyroglobulin type-1 repeat of insulin-like growth factor (IGF)-binding proteins (IGFBPs) -3, -5, and -6 inhibit IGFBP-4 degradation. Endocrinology. 1997;138(6):2280-2285.

Yan X, Forbes BE, McNeil KA, Baxter RC, Firth SM. Role of N-and C-terminal residues of insulin-like growth factor (IGF)-binding protein-3 in regulating IGF complex formation and receptor activation. J Biol Chem. 2004;279(51):53232-53240.

Shand JH, Beattie J, Song H, Phillips K, Kelly SM, Flint DJ, et al. Specific amino acid substitutions determine the differential contribution of the N- and C-terminal domains of insulin-like growth factor (IGF)-binding protein-5 in binding IGF-I. J Biol Chem. 2003;278(20):17859-17866.

Hoeck WG, Mukku VR. Identification of the major sites of phosphorylation in IGF binding protein‐3. J Cell Biochem. 1994;56(2):262-273.


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