Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K

Journal article


Lisgarten, D., Palmer, R., Lobley, C., Naylor, C., Chowdhry, B., AL-Kurdi, Z., Badwan, A., Howlin, B., Gibbons, N., Saldanha, J., Lisgarten, J. and Basak, A. 2017. Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K. Chemistry Central Journal. 11 (73), pp. 1-26. https://doi.org/10.1186/s13065-017-0296-y
AuthorsLisgarten, D., Palmer, R., Lobley, C., Naylor, C., Chowdhry, B., AL-Kurdi, Z., Badwan, A., Howlin, B., Gibbons, N., Saldanha, J., Lisgarten, J. and Basak, A.
Abstract

The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6–Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S–S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I).

The results of this comparison are reported.

Year2017
JournalChemistry Central Journal
Journal citation11 (73), pp. 1-26
PublisherSpringer Open
ISSN1752-153X
Digital Object Identifier (DOI)https://doi.org/10.1186/s13065-017-0296-y
Related URLhttp://creativecommons.org/publicdomain/zero/1.0/)
Publication dates
Online01 Aug 2017
Publication process dates
Deposited08 Aug 2017
Accepted12 Jul 2017
Accepted author manuscript
License
Output statusPublished
References

1.Baker EN, Blundell TL, Cutfield JF, Cutfield SM, Dodson EJ, Dodson GG et al (1998) The structure of 2Zn Pig insulin crystals at 1.5 Å resolution. Philos Trans R Soc London Ser B Biol Sci 319(1195):369–456
View ArticleGoogle Scholar

2.Cunha JP (2016) http://www.rxlist.com/humulin-n-side-effects-drug-center.htm

3.Ciszak E, Beals JM, Frank BH, Baker JC, Carter ND, Smith GD (1995) Role of C-terminal B-chain residues in insulin assembly: the structure of hexameric LysB28ProB29-human insulin. Structure 15(3):615–622
View ArticleGoogle Scholar

4.Ishida H, Nagamatsu S (2001) Chemical structure, active sites and receptor binding of the insulin molecule and its signal transduction. Nippon Rinso 59(11):2109–2116 (translated from Japanese by Hideaki Niwa)
Google Scholar

5.Xu B, Q-x Hua, Nakagawa SH, Jia W, Chu Y-C, Katsoyannis PG, Weiss MA (2002) Chiral mutagenesis of insulin’s hidden receptor-binding surface: structure of an Allo-isoleucine A2 analogue. J Mol Biol 316:435–441
View ArticleGoogle Scholar

6.Pullen RA, Lindsay DG, Wood SP, Tickle IJ, Blundell TL, Wollmer A et al (1976) Receptor binding region of insulin. Nature 259:369–373
View ArticleGoogle Scholar

7.Conlon JM (2001) Evolution of the insulin molecule: insights into structure-activity and phylogenetic relationships. Peptides 22(7):1183–1193
View ArticleGoogle Scholar

8.Sakabe N (2013) Personal communication
Google Scholar

9.Incardona M-F, Bourenkov GP, Levik K, Pieritz RA, Popov AN, Svensson O (2009) EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis. J. Synchrotron Radiat 16:872–879. doi:https://doi.org/10.1107/S0909049509036681
View ArticleGoogle Scholar

10.Sakabe N, Sakabe K, Higashi T, Igarashi N, Suzuki M, Watanabe N, Sasaki K (2001) Automatic Weissenberg data collection system for time-resolved protein crystallography. Nucl Instrum Methods Phys 468:1367
View ArticleGoogle Scholar

11.Watanabe N, Suzuki M, Higashi Y, Sakabe N (1999) Rotated-inclined focussing monochromator with simultaneous tuning of asymmetry factor and radius of curvature over a wide wavelength range. J Synchrotron Radiat 6:64
View ArticleGoogle Scholar

12.Sakabe K, Sasaki K, Watanabe N, Suzuki M, Wang G, Miyahra J, Sakabe N (1997) Large-format imaging plate and Weissenberg camera for accurate protein crystallography data collection using synchrotron radiation. J Synchrotron Radiat 4:136
View ArticleGoogle Scholar

13.Katayama C, Sakabe N, Sakabe K (1972) A statistical evaluation of absorption. Acta Cryst A28:293
View ArticleGoogle Scholar

14.Higashi T (1989) The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J App Crystallogr 22:9
View ArticleGoogle Scholar

15.Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66(Pt 2):125–132
View ArticleGoogle Scholar

16.Evans PR (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62(Pt 1):72–82
View ArticleGoogle Scholar

17.Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Cryst 30:1022–1025
View ArticleGoogle Scholar

18.Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Cryst D67:355–367. doi:https://doi.org/10.1107/S0907444911001314
Google Scholar

19.Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Cryst D66:486–501
Google Scholar

20.Afonine PV, Grosse-Kunstleve RW, Adams PD (2005) CCP4 Newsl. 42, contribution 8. PHENIX
Google Scholar

21.Sheldrick GM (2008) A short history of SHELX. Acta Cryst A64:112
View ArticleGoogle Scholar

22.Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Cryst D66:12–21
Google Scholar

23.Accelerys Corporation (2012) Discovery Studio Software version 3.5. http://accelrys.com/products/datasheets/whats-new-in-discovery-studi...

24.Smith GD, Pangborn WA, Blessing RH (2003) The structure of T6 human insulin at 1.0 Å resolution. Acta Crystallogr Sect D 59:474–482. doi:https://doi.org/10.1107/S0907444902023685
View ArticleGoogle Scholar

25.Addlagatta A, Krzywda S, Czapinska H, Otlewski J, Jaskolski M (2001) Ultrahigh-resolution structure of a BPTI mutant. Acta Crystallogr Sect D 57:649–663
View ArticleGoogle Scholar

26.Panijpan B (1977) Chirality of the disulfide bond in biomolecules. J Chem Educ 54(11):670
View ArticleGoogle Scholar

27.Zimmerman RE, Stokell DJ, Akers MP (2012) Elona Biotechnologies Liquid insulin compositions and methods of making the same US Patent Publication Number US20120214964 A1, August 2012
Google Scholar

28.Owens DR, Landgraf W, Schmidt A, Bretzel RG, Kuhlmann MK (2012) The emergence of biosimilar insulin preparations–a cause for concern? Diabetes Technol Ther 14(11):989–996. doi:https://doi.org/10.1089/dia.2012.0105
View ArticleGoogle Scholar

29.HyperChem 8 Professional(™) (Hypercube Inc, Gainsville, FL, USA)
Google Scholar

30.Weiner PK, Kollman PA (1981) AMBER: Assisted Model Building with Energy Refinement. A general program for modeling molecules and their interactions. J Comp Chem 2:287–303
View ArticleGoogle Scholar

31.Polak E, Ribiere G (1969) Note on the convergence of methods of conjugate directions. Revue Francaise d’Informatique et de Recherche Operationnelle 3(16):35–43
Google Scholar

32.Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684
View ArticleGoogle Scholar

33.Hockney RW (1970) The potential calculation and some applications. Methods Comput Phys 9:136–211
Google Scholar

34.Ciszak E, Beals JM, Frank BH, Baker JC, Carter ND, Smith GD (1995) Role of C-terminal B-chain residues in insulin assembly: the structure of hexameric Lys B28 Pro B29-human insulin. Structure 3:615–622
View ArticleGoogle Scholar

35.Dassault Systèmes BIOVIA (2016) Discovery studio modeling environment, release 2017. Dassault Systèmes, San Diego
Google Scholar

36.Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer. An environment for comparative protein modelling. Electrophoresis 18:2714–2723
View ArticleGoogle Scholar

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