Molecular Dynamics Simulations Provide Insights into Structure and Function of Amadoriase Enzymes




Fructosyl amino acid oxidase, Amadoriases, Deglycating enzymes, Molecular dynamics simulation, Enzyme specificity, Binding interactions, HbA1c monitoring, Diabetes monitoring, Glycated haemoglobin


Background. Enzymatic assays based on Fructosyl Amino Acid Oxidases (FAOX) represent a potential, rapid and economical strategy to measure glycated hemoglobin (HbA1c), which is in turn a reliable method to monitor the insurgence and the development of diabetes mellitus. However, the engineering of naturally occurring FAOX to specifically recognize fructosyl-valine (the glycated N-terminal residue of HbA1c) has been hindered by the paucity of information on the tridimensional structures and catalytic residues of the different FAOX that exist in nature, and in general on the molecular mechanisms that regulate specificity in this class of enzymes.

Objective. In this study, we use molecular dynamics simulations and advanced modeling techniques to investigate five different relevant wild-type FAOX (Amadoriase I, Amadoriase II, PnFPOX, FPOX-E and N1-1-FAOD) in order to elucidate the molecular mechanisms that drive their specificity towards polar and nonpolar substrates. Specifically, we compare these five different FAOX in terms of overall folding, ligand entry tunnel, ligand binding residues and ligand binding energies.

Methods. We used a combination of homology modeling and molecular dynamics simulations to provide insights into the structural difference between the five enzymes of the FAOX family.

Results. We first predicted the structure of the N1-1-FAOD and PnFPOX enzymes using homology modelling. Then, we used these models and the experimental crystal structures of Amadoriase I, Amadoriase II and FPOX-E to run extensive molecular dynamics simulations in order to compare the structures of these FAOX enzymes and assess their relevant interactions with two relevant ligands, f-val and f-lys.

Conclusions. Our work will contribute to future enzyme structure modifications aimed at the rational design of novel biosensors for the monitoring of blood glucose levels.

Author Biographies

Federica Rigoldi, Politecnico di Milano

PhD in Bioengineering, Postdoctoral Fellow, Dipartimento di Elettronica, Informazione e Bioingegneria

Ludovica Spero, Politecnico di Milano

MS in Biomedical Engineering, Master Student, Dipartimento di Elettronica, Informazione e Bioingegneria

Andrea Dalle Vedove, Politecnico di Milano

PhD in Chemical Engineering, Postdoctoral Fellow, Dipartimento di Chimica, Materiali e Ingegneria Chimica “G. Natta”

Alberto Redaelli, Politecnico di Milano

PhD in Mechanical Engineering, Full Professor, Dipartimento di Elettronica, Informazione e Bioingegneria

Emilio Parisini, Istituto Italiano di Tecnologia

PhD in Chemistry, Researcher, Center for Nano Science and Technology

Alfonso Gautieri, Politecnico di Milano

PhD in Bioengineering, Postdoctoral Fellow, Dipartimento di Elettronica, Informazione e Bioingegneria


Weykamp C, John WG, Mosca A. A review of the challenge in measuring hemoglobin A1c. J Diabetes Sci Technol. 2009 May;3(3):439-45. DOI 10.1177/193229680900300306

John WG. Haemoglobin A1c: analysis and standardisation. Clin Chem Lab Med. 2003 Sep;41(9):1199-212. DOI 10.1515/CCLM.2003.184

Liu L, Hood S, Wang Y, Bezverkov R, Dou C, Datta A, et al. Direct enzymatic assay for %HbA1c in human whole blood samples. Clin Biochem. 2008 May;41(7-8):576-83. DOI 10.1016/j.clinbiochem.2008.01.013

Miura S, Ferri S, Tsugawa W, Kim S, Sode K. Development of fructosyl amine oxidase specific to fructosyl valine by site-directed mutagenesis. Protein Eng Des Sel. 2008 Apr;21(4):233-9. DOI 10.1093/protein/gzm047

Kim S, Miura S, Ferri S, Tsugawa W, Sode K. Cumulative effect of amino acid substitution for the development of fructosyl valine-specific fructosyl amine oxidase. Enzyme Microb Technol. 2009 Jun;44(1):52-6. DOI 10.1016/j.enzmictec.2008.09.001

Miura S, Ferri S, Tsugawa W, Kim S, Sode K. Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis. Biotechnol Lett. 2006 Dec;28(23):1895-900. DOI 10.1007/s10529-006-9173-9

Kim S, Nibe E, Ferri S, Tsugawa W, Sode K. Engineering of dye-mediated dehydrogenase property of fructosyl amino acid oxidases by site-directed mutagenesis studies of its putative proton relay system. Biotechnol Lett. 2010 Aug;32(8):1123-9. DOI 10.1007/s10529-010-0267-z

Kim S, Nibe E, Tsugawa W, Kojima K, Ferri S, Sode K. Construction of engineered fructosyl peptidyl oxidase for enzyme sensor applications under normal atmospheric conditions. Biotechnol Lett. 2012 Mar;34(3):491-7. DOI 10.1007/s10529-011-0787-1

Mennella C, Borrelli RC, Vinale F, Ruocco M, Fogliano V. Substrate specificity of amadoriase I from Aspergillus fumigatus. Ann N Y Acad Sci. 2005 Jun;1043:837-44. DOI 10.1196/annals.1333.096

Wu X, Palfey BA, Mossine VV, Monnier VM. Kinetic studies, mechanism, and substrate specificity of amadoriase I from Aspergillus sp. Biochemistry. 2001 Oct 30;40(43):12886-95. DOI 10.1021/Bi011244e

Qian Y, Zheng J, Lin Z. Loop engineering of amadoriase II and mutational cooperativity. Appl Microbiol Biotechnol. 2013 Oct;97(19):8599-607. DOI 10.1007/s00253-013-4705-4

Zheng J, Guan H, Xu L, Yang R, Lin Z. Engineered amadoriase II exhibiting expanded substrate range. Appl Microbiol Biotechnol. 2010 Mar;86(2):607-13. DOI 10.1007/s00253-009-2319-7

Collard F, Zhang J, Nemet I, Qanungo KR, Monnier VM, Yee VC. Crystal structure of the deglycating enzyme fructosamine oxidase (amadoriase II). J Biol Chem. 2008 Oct 3;283(40):27007-16. DOI 10.1074/jbc.M804885200

Gan W, Gao F, Xing K, Jia M, Liu H, Gong W. Structural basis of the substrate specificity of the FPOD/FAOD family revealed by fructosyl peptide oxidase from Eupenicillium terrenum. Acta Crystallogr F Struct Biol Commun. 2015 Apr;71(Pt 4):381-7. DOI 10.1107/S2053230X15003921

Rigoldi F, Gautieri A, Dalle Vedove A, Lucarelli AP, Vesentini S, Parisini E. Crystal structure of the deglycating enzyme amadoriase i in its free form and substrate-bound complex. Proteins. 2016 Jun;84(6):744-58. DOI 10.1002/prot.25015

Masic A, Bertinetti L, Schuetz R, Chang S, Metzger TH, Buehler MJ, et al. Osmotic pressure induced tensile forces in tendon collagen. Nat Commun. 2015 Jun;6:1-8. DOI 10.1038/ncomms6942

Qin Z, Buehler MJ. Impact tolerance in mussel thread networks by heterogeneous material distribution. Nat Commun. 2013 July;4:2187. DOI 10.1038/ncomms3187

Gautieri A, Redaelli A, Buehler MJ, Vesentini S. Age- and diabetes-related nonenzymatic crosslinks in collagen fibrils: Candidate amino acids involved in Advanced Glycation End-products. Matrix Biol. 2014 Feb;34:89-95. DOI 10.1016/j.matbio.2013.09.004

Gautieri A, Vesentini S, Redaelli A, Ballarini R. Modeling and measuring visco-elastic properties: From collagen molecules to collagen fibrils. Int J Non Linear Mech. 2013 Apr;56:25-33. DOI 10.1016/j.ijnonlinmec.2013.03.012

Gautieri A, Vesentini S, Redaelli A. How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations. J Mol Model. 2010 Dec;16(12):1845-51. DOI 10.1007/s00894-010-0687-7

Tokareva O, Jacobsen M, Buehler M, Wong J, Kaplan DL. Structure-function-property-design interplay in biopolymers: Spider silk. Acta Biomater. 2014 Apr;10(4):1612-26. DOI 10.1016/j.actbio.2013.08.020

Takeuchi M, Iwaki M, Takino J, Shirai H, Kawakami M, Bucala R, et al. Immunological detection of fructose-derived advanced glycation end-products. Lab Invest. 2010 Jul;90(7):1117-27. DOI 10.1038/labinvest.2010.62

Solar MI, Buehler MJ. Composite materials: Taking a leaf from nature’s book. Nat Nanotechnol. 2012 May;7(7):417-9. DOI 10.1038/nnano.2012.86

Kim S, Ferri S, Tsugawa W, Mori K, Sode K. Motif-based search for a novel fructosyl peptide oxidase from genome databases. Biotechnol Bioeng. 2010 Jun 15;106(3):358-66. DOI 10.1002/bit.22710

Hirokawa K, Gomi K, Kajiyama N. Molecular cloning and expression of novel fructosyl peptide oxidases and their application for the measurement of glycated protein. Biochem Biophys Res Commun. 2003 Nov 7;311(1):104-11. DOI 10.1016/j.bbrc.2003.09.169

Lin Z, Zheng J. Occurrence, characteristics, and applications of fructosyl amine oxidases (amadoriases). Appl Microbiol Biotechnol. 2010 May;86(6):1613-9. DOI 10.1007/s00253-010-2523-5

Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007 Nov 1;23(21):2947-8. DOI 10.1093/bioinformatics/btm404

Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406-25.

Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111-20.

Takahashi M, Pischetsrieder M, Monnier VM. Molecular cloning and expression of amadoriase isoenzyme (fructosyl amine:oxygen oxidoreductase, EC 1.5.3) from Aspergillus fumigatus. J Biol Chem. 1997 May 9;272(19):12505-7. DOI 10.1074/jbc.272.19.12505

Wu XL, Takahashi M, Chen SG, Monnier VM. Cloning of amadoriase I isoenzyme from Aspergillus sp.: Evidence of FAD covalently linked to Cys342. Biochemistry. 2000 Feb 15;39(6):1515-21. DOI 10.1021/bi992031g

Takahashi M, Pischetsrieder M, Monnier VM. Isolation, purification, and characterization of amadoriase isoenzymes (fructosyl amine-oxygen oxidoreductase EC 1.5.3) from Aspergillus sp. J Biol Chem. 1997 Feb 7;272(6):3437-43. DOI 10.1074/jbc.272.6.3437

Ferri S, Miyamoto Y, Sakaguchi-Mikami A, Tsugawa W, Sode K. Engineering fructosyl peptide oxidase to improve activity toward the fructosyl hexapeptide standard for HbA1c measurement. Mol Biotechnol. 2013 Jul;54(3):939-43. DOI 10.1007/s12033-012-9644-2

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. DOI 10.1038/msb.2011.75

McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600. DOI 10.1093/nar/gkt376

Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, et al. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4. DOI 10.1093/nar/gkv279

Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W320-4. DOI 10.1093/nar/gku316

Ferri S, Kim S, Tsugawa W, Sode K. Review of fructosyl amino acid oxidase engineering research: a glimpse into the future of hemoglobin A1c biosensing. J Diabetes Sci Technol. 2009 May;3(3):585-92. DOI 10.1177/193229680900300324

Hirokawa K, Gomi K, Bakke M, Kajiyama N. Distribution and properties of novel deglycating enzymes for fructosyl peptide in fungi. Arch Microbiol. 2003 Sep;180(3):227-31. DOI 10.1007/s00203-003-0584-x




How to Cite

Rigoldi F, Spero L, Dalle Vedove A, Redaelli A, Parisini E, Gautieri A. Molecular Dynamics Simulations Provide Insights into Structure and Function of Amadoriase Enzymes. Innov Biosyst Bioeng [Internet]. 2017Dec.19 [cited 2024Jun.13];1(1):57-71. Available from: