Rational design of hyper-glycosylated human luteinizing hormone analogs (a bioinformatics approach)

Glycoengineering is a recently used approach to extend serum half-life of valuable protein therapeutics. One aspect of glycoengineering is to introduce new N-glycosylation site (Asn-X-Thr/Ser, where X ≠ Pro) into desirable positions in the peptide backbone, resulting in the generation of hyper-glycosylated protein. In this study, human luteinizing hormone (LH) was considered for identification of the suitable positions for the addition of new N-linked glycosylation sites. A rational in silico approach was applied for prediction of structural and functional alterations caused by changes in amino acid sequence. As the first step, we explored the amino acid sequence of LH to find out desirable positions for introducing Asn or/and Thr to create new N-glycosylation sites. This exploration led to the identification of 38 potential N-glycan sites, and then the four acceptable ones were selected for further analysis. Three-dimensional (3D) structures of the selected analogs were generated and examined by the model evaluation methods. Finally, two analogs with one additional glycosylation site were suggested as the qualified analogs for hyper-glycosylation of the LH, which can be considered for further experimental investigations. Our computational strategy can reduce laborious and time-consuming experimental analyses of the analogs.

[1]  Shandar Ahmad,et al.  ASAView: Database and tool for solvent accessibility representation in proteins , 2003, BMC Bioinformatics.

[2]  H. Keutmann,et al.  The glycoprotein hormones: recent studies of structure‐function relationships , 1988, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[3]  Ylva Gavel,et al.  Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering , 1990, Protein engineering.

[4]  Mohammad Ali Shokrgozar,et al.  In silico design and analysis of a new hyperglycosylated analog of erythropoietin to improve drug efficacy , 2015, Advanced biomedical research.

[5]  L. Kasturi,et al.  The Amino Acid at the X Position of an Asn-X-Ser Sequon Is an Important Determinant of N-Linked Core-glycosylation Efficiency (*) , 1996, The Journal of Biological Chemistry.

[6]  Rational design of glycoengineered interferon-&bgr; analogs with improved aggregation state: experimental validation , 2017, Protein engineering, design & selection : PEDS.

[7]  S. Rizza,et al.  Synthetic α-Subunit Peptides Stimulate Testosterone Production in Vitro by Rat Leydig Cells , 1990 .

[8]  W A Hendrickson,et al.  Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein. , 1994, Structure.

[9]  P. Roche,et al.  A receptor binding site identified in the region 81–95 of the β-subunit of human luteinizing hormone (LH) and chorionic gonadotropin (hCG) , 1993, Molecular and Cellular Endocrinology.

[10]  M. Samoudi,et al.  Rational design of hyper-glycosylated interferon beta analogs: a computational strategy for glycoengineering. , 2015, Journal of molecular graphics & modelling.

[11]  Alabama.,et al.  Gonadotropin preparations: past, present, and future perspectives. , 2008, Fertility and sterility.

[12]  S. Danishefsky,et al.  Chemical Synthesis of the β-Subunit of Human Luteinizing (hLH) and Chorionic Gonadotropin (hCG) Glycoprotein Hormones , 2014, Journal of the American Chemical Society.

[13]  Mariana Henriques,et al.  Glycosylation: impact, control and improvement during therapeutic protein production , 2014, Critical reviews in biotechnology.

[14]  M. Betenbaugh,et al.  Controlling N-linked glycan site occupancy. , 2005, Biochimica et biophysica acta.

[15]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[16]  P. Fossa,et al.  In silico evaluation of human small heat shock protein HSP27: homology modeling, mutation analyses and docking studies. , 2015, Bioorganic & medicinal chemistry.

[17]  Hossein Saber,et al.  Increasing thermal stability and catalytic activity of glutamate decarboxylase in E. coli: An in silico study , 2016, Comput. Biol. Chem..

[18]  H. Keutmann Receptor-binding regions in human glycoprotein hormones , 1992, Molecular and Cellular Endocrinology.

[19]  R. J. Solá,et al.  Glycosylation of Therapeutic Proteins , 2010, BioDrugs.

[20]  F. Momany,et al.  Validation of the general purpose QUANTA ®3.2/CHARMm® force field , 1992 .

[21]  Roman A. Laskowski,et al.  PDBsum: summaries and analyses of PDB structures , 2001, Nucleic Acids Res..

[22]  M. Etcheverrigaray,et al.  Novel long-lasting interferon alpha derivatives designed by glycoengineering. , 2008, Biochimie.

[23]  Sudhir Kumar,et al.  Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations , 2012, Bioinform..

[24]  Huimin Zhao,et al.  Engineering Of Therapeutic Proteins , 2009 .

[25]  R. Ogden,et al.  Development and characterization of a long-acting recombinant hFSH agonist. , 2003, Human reproduction.

[26]  D. Chang,et al.  Structural Requirements for Additional N-Linked Carbohydrate on Recombinant Human Erythropoietin* , 2004, Journal of Biological Chemistry.

[27]  T. Roitsch,et al.  Structural requirements for protein N-glycosylation. Influence of acceptor peptides on cotranslational glycosylation of yeast invertase and site-directed mutagenesis around a sequon sequence. , 1989, European journal of biochemistry.

[28]  Søren Brunak,et al.  Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function , 2001, Pacific Symposium on Biocomputing.

[29]  Yuliet Mazola,et al.  Integrating Bioinformatics Tools to Handle Glycosylation , 2011, PLoS Comput. Biol..

[30]  J. Pierce,et al.  Glycoprotein hormones: structure and function. , 1981, Annual review of biochemistry.

[31]  A. Decherney,et al.  History and challenges surrounding ovarian stimulation in the treatment of infertility. , 2012, Fertility and sterility.

[32]  A. Zomorodipour,et al.  In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. , 2016, Journal of molecular graphics & modelling.

[33]  L. Buck,et al.  Enhancement of therapeutic protein in vivo activities through glycoengineering , 2003, Nature Biotechnology.

[34]  D. C. Harris,et al.  Crystal structure of human chorionic gonadotropin , 1994, Nature.

[35]  Liang Fu,et al.  Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC. , 2013, Protein engineering, design & selection : PEDS.

[36]  S. Elliott,et al.  Glycoengineering: the effect of glycosylation on the properties of therapeutic proteins. , 2005, Journal of pharmaceutical sciences.

[37]  Y. Combarnous,et al.  Structure–Function Relationships of Glycoprotein Hormones and Their Subunits’ Ancestors , 2015, Front. Endocrinol..

[38]  Z. Li,et al.  Optimal and consistent protein glycosylation in mammalian cell culture. , 2009, Glycobiology.

[39]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Raymond A Dwek,et al.  Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. , 2003, Glycobiology.

[41]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[42]  G. Pérez,et al.  Rates of proximal and distal glycosylation of luteinizing hormone by cultured rat pituitary cells , 1997 .

[43]  María Martín,et al.  Ongoing and future developments at the Universal Protein Resource , 2010, Nucleic Acids Res..

[44]  Y. Levy,et al.  Effect of glycosylation on protein folding: A close look at thermodynamic stabilization , 2008, Proceedings of the National Academy of Sciences.