Abstract
Insulin crystallizes in different forms, some of which show different conformations for the different molecules in the asymmetric unit. This observation leads to the question as to which conformation the molecule will adopt in solution. Molecular dynamics computer simulations of rhombohedral 2 Zn pig insulin have been carried out for both monomers (1 and 2) independently in order to study their behaviour in the absence of quaternary structure and crystal packing forces.
These preliminary 120 ps simulations suggest that both monomers converge in solution to very similar conformations which differ from the X-ray structures of both monomer 1 and 2 (Chinese nomenclature), but are closer to the former, as has previously been suggested by an analysis of the crystal packing (Chothia et al. 1983) and by energy minimization (Wodak et al. 1984). The secondary structure of the molecules is basically preserved, as expected. A detailed description of the conformational changes is given.
Similar content being viewed by others
Abbreviations
- MD:
-
Molecular dynamics (simulations)
- EM:
-
Energy minimization
- X1:
-
X-ray structure of molecule 1
- X2:
-
X-ray structure of molecule 2
- MD1:
-
mean simulated structure of molecule 1
- MD2:
-
mean simulated structure of molecule 2
- A N helix:
-
helix at the N-terminal part of the insulin A-chain
- A C helix:
-
helix at the C-terminal part of the insulin A-chain. One and three-letter abbreviations for amino acids are used.
References
Åqvist J, Gunsteren WF van, Leijonmarck M, Tapia O (1985) A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. J Mol Biol 183:461–477
Berendsen HJC, Postma JPM, Gunsteren WF van, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690
Chothia C, Lesk AM, Dodson GG, Hodgkin DC (1983) Transmission of conformational change in insulin. Nature 302:500–505
Chou K-C, Nemethy G, Scheraga HA (1983) Energetic approach to the packing of α-helices. 1. Equivalent helices. J Phys Chem 87:2869–2881
Cutfield JF, Cutfield SM, Dodson EJ, Dodson GG, Reynolds CD, Vallely D (1981) Similarities and differences in the crystal structures of insulin. In: Dodson G, Glusker JP, Sayre D (eds) Structural studies on molecules of biological interest—A volume in honour of Dorothy Hodgkin. Clarendon Press, Oxford, pp 527–546
Gunsteren WF van (1986) GROMOS Program System. Distributed through BIOMOS biomolecular software b.v. Laboratory of Physical Chemistry, University of Groningen, NL
Gunsteren WF van, Berendsen HJC (1977) Algorithms for macromolecular dynamics and constrained dynamics. Mol Phys 34:1311–1327
Gunsteren WF van, Berendsen HJC (1985) Molecular dynamics simulations: Techniques and applications to proteins. In: Hermans J (ed) Molecular dynamics and protein structure. Polycrystal Book Service, Western Springs, Illinois, USA, pp 5–14
Gunsteren WF van, Karplus M (1982) Effect of constraints on the dynamics of macromolecules. Macromolecules 15: 1528–1544
Gunsteren WF van, Berendsen HJC, Hermans J, Hol WGJ, Postma JPM (1983) Computer simulation of the dynamics of hydrated protein crystals and its comparison with X-ray data. Proc Natl Acad Sci USA 80:4315–4319
Kobayashi M, Ohgaku S, Iwasaki M, Maegawa H, Shigeta Y, Inouye K (1982) Supernormal insulin: d-Phe B24 insulin with increased affinity for insulin receptors. Biochem Biophys Res Commun 107:329–336
Krüger P, Straßburger W, Wollmer A, Gunsteren WF van (1985) A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal. Eur Biophys J 13:77–88
Lesk AM, Hardman KD (1982) Computer-generated schematic diagrams of protein structures. Science 216:539–540
McCammon JA, Karplus M (1979) Dynamics of acitvated processes in globular proteins. Proc Natl Acad Sci USA 76:3585–3589
McCammon JA, Lee CY, Northrup SH (1983) Side-chain rotational isomerization in proteins: A mechanism involving gating and transient packing defects. J Am Chem Soc 105:2232–2237
Mercola D, Wollmer A (1981) The crystal structure of insulin and solution phenomena: use of the high-resolution structure in the calculation of the optical activity of the tyrosyl residues. In: Dodson G, Glusker JP, Sayre D (eds) Structural studies on molecules of biological interest—A volume in honour of Dorothy Hodgkin. Clarendon Press, Oxford, pp 557–582
Smith GD, Duax WL, Dodson EJ, Dodson GG, de Graaf RAG, Reynolds CD (1982) The structure of des-Phe B1 bovine insulin. Acta Crystallogr B 38:3028–3032
Straßburger W (1986) Molekulare Dynamik von Proteinen. Habilitationsschrift, RWTH Aachen
Wodak SJ, Alard P, Delhaise P, Renneboog-Squilbin C (1984) Simulation of conformational changes in 2 Zn insulin. J Mol Biol 181:317–322
Wollmer A, Fleischhauer J, Straßburger W, Thiele H, Brandenburg D, Dodson G, Mercola D (1977) Side-chain mobility and the calculation of tyrosyl circular dichroism of proteins. Implications of a test with insulin and des-B1-phenylalanine insulin. Biophys J 20:233–243
Wollmer A, Straßburger W, Hoenjet E, Glatter U, Fleischhauer J, Mercola DA, de Graaf RAG, Dodson EJ, Dodson GG, Smith DG, Brandenburg D, Danho W (1980) Correlation of structural details of insulin in the crystal and in solution. In: Brandenburg D, Wollmer A (eds) Insulin — chemistry, structure and function of insulin and related hormones. Walter de Gruyter, Berlin New York, pp 27–35
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Krüger, P., Straßburger, W., Wollmer, A. et al. The simulated dynamics of the insulin monomer and their relationship to the molecule's structure. Eur Biophys J 14, 449–459 (1987). https://doi.org/10.1007/BF00293254
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00293254