Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding

Papaioannou, Anastasios; Kuyucak, Serdar; Kuncic, Zdenka

doi:10.1371/journal.pone.0144058

Cited by 24 publications

(42 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The hydrophobic core and its interactions thus play a critical role in the activation of insulin [23–25]. The hydrophobic core of insulin consists of the residues L11, V12, L15, F24 and Y26 from the B chain and I A 2 and V A 3 from the A chain.…”

Section: Methodsmentioning

confidence: 99%

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations

2016

Self Cite

View full text Add to dashboard Cite

The insulin-family proteins bind to their own receptors, but insulin-like growth factor II (IGF-II) can also bind to the A isoform of the insulin receptor (IR-A), activating unique and alternative signaling pathways from those of insulin. Although extensive studies of insulin have revealed that its activation is associated with the opening of the B chain-C terminal (BC-CT), the activation mechanism of the insulin-like growth factors (IGFs) still remains unknown. Here, we present the first comprehensive study of the insulin-family proteins comparing their activation process and mechanism using molecular dynamics simulations to reveal new insights into their specificity to the insulin receptor. We have found that all the proteins appear to exhibit similar stochastic dynamics in their conformational change to an active state. For the IGFs, our simulations show that activation involves two opening locations: the opening of the BC-CT section away from the core, similar to insulin; and the additional opening of the BC-CT section away from the C domain. Furthermore, we have found that these two openings occur simultaneously in IGF-I, but not in IGF-II, where they can occur independently. This suggests that the BC-CT section and the C domain behave as a unified domain in IGF-I, but as two independent domains in IGF-II during the activation process, implying that the IGFs undergo different activation mechanisms for receptor binding. The probabilities of the active and inactive states of the proteins suggest that IGF-II is hyperactive compared to IGF-I. The hinge residue and the hydrophobic interactions in the core are found to play a critical role in the stability and activity of IGFs. Overall, our simulations have elucidated the crucial differences and similarities in the activation mechanisms of the insulin-family proteins, providing new insights into the molecular mechanisms responsible for the observed differences between IGF-I and IGF-II in receptor binding.

show abstract

Section: Methodsmentioning

confidence: 99%

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations

2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…1C). The contribution of this side chain to the stability of the insulin monomer has recently been investigated by molecular dynamics (MD) simulations (31) and mutagenesis (32).…”

Section: -[Iodo-tyrmentioning

confidence: 99%

Extending Halogen-based Medicinal Chemistry to Proteins

Hage

Pandyarajan²,

Phillips³

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Edited by Norma AllewellInsulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (Tyr B26 ) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum-and molecularmechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-Tyr B26 ]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (Tyr B16 , Phe B24 , Phe B25 , 3-ITyr B26 , and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-Tyr B26 ]insulin analog (determined as an R 6 zinc hexamer). Given that residues B24 -B30 detach from the core on receptor binding, the environment of 3-I-Tyr B26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-Tyr B26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient -hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.Insulin, a small protein critical to metabolic homeostasis (1), provides a model for studies of protein folding and design (2) with long-standing application to human therapeutics (3). The hormone contains two chains, A and B (Fig. 1A), linked by two disulfide bridges (cystines A7-B7 and A20 -B19); the A chain is further stabilized by cystine A6 -A11. In pancreatic ␤-cells, insulin is stored within the secretory granules as zinc-coordinated hexamers. This study has exploited insulin semi-synthesis (4) (simplified through the use of norleucine (Nle) 9 at position B29; arrow in Fig. 1A (5)) to investigate a site-specific modification of an aromatic ring by a single halogen atom (6). The modification, 3-iodo-Tyr at position B26 (3-I-Tyr B26 ), is associated with enhanced binding to the insulin receptor (IR)

show abstract

“…In light of the displaced conformation of the B23-B27 segment in the IR complex (4), it would be of further interest to probe whether such B26 substitutions weaken the attachment of this segment to the insulin core. A recent study of the insulin monomer by molecular-dynamics simulations has predicted that long-range interactions by Tyr B26 in WT insulin regulate transient detachment and re-attachment of this segment through a series of transient conformational substates (78). Use of heteronuclear NMR methods to uncover such "excited-state" conformations represents a promising frontier of protein science (79).…”

Section: B29mentioning

confidence: 99%

Contribution of TyrB26 to the Function and Stability of Insulin

Pandyarajan¹,

Phillips²,

Rege³

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Crystallographic studies of insulin bound to receptor domains have defined the primary hormone-receptor interface. We investigated the role of Tyr B26 , a conserved aromatic residue at this interface. To probe the evolutionary basis for such conservation, we constructed 18 variants at B26. Surprisingly, nonaromatic polar or charged side chains (such as Glu, Ser, or ornithine (Orn)) conferred high activity, whereas the weakestbinding analogs contained Val, Ile, and Leu substitutions. Modeling of variant complexes suggested that the B26 side chains pack within a shallow depression at the solvent-exposed periphery of the interface. This interface would disfavor large aliphatic side chains. The analogs with highest activity exhibited reduced thermodynamic stability and heightened susceptibility to fibrillation. Perturbed self-assembly was also demonstrated in studies of the charged variants (Orn and Glu); indeed, the Glu B26 analog exhibited aberrant aggregation in either the presence or absence of zinc ions. Thus, although Tyr B26 is part of insulin's receptor-binding surface, our results suggest that its conservation has been enjoined by the aromatic ring's contributions to native stability and self-assembly. We envisage that such classical structural relationships reflect the implicit threat of toxic misfolding (rather than hormonal function at the receptor level) as a general evolutionary determinant of extant protein sequences.Insulin, a small globular protein critical to the maintenance of metabolic homeostasis (1), provides a classical model for studies of protein structure and self-assembly (2) with longstanding application to human therapeutics (3). Insulin contains two polypeptide chains, designated A and B, that are linked by two disulfide bridges (cystines A7-B7 and A20-B19); the A chain is further stabilized by an intrachain bridge (cystine A6-A11). In pancreatic ␤-cells, insulin is stored within glucoseregulated secretory granules as zinc-coordinated hexamers (Fig. 1A). The hormone binds to a receptor-tyrosine kinase, designated the insulin receptor (IR). 5 The product of a single gene, the IR precursor is processed in the trans-Golgi network into its final disulfide-linked (␣␤) 2 homodimer conformation. The extracellular ␣ subunit contains hormone-binding elements, whereas the transmembrane ␤ subunit contains the intracellular tyrosine kinase domain (4). Alternative splicing leads to two receptor isoforms, IR-A and IR-B (5). The threedimensional structure of the holoreceptor has been visualized only at low resolution (Ͼ20 Å), but these findings have been inconclusive (for review, see Ref. 6). How extracellular binding of insulin alters the structure of the receptor, leading in turn to activation of the intracellular tyrosine kinase domains, is a major unsolved problem (7).Dissection of the IR into discrete domains has enabled crystallographic analysis of its parts. The relevant structural biology is as follows. (i) Structures of the intracellular tyrosine kinase domains at 1.9 Å resolution have been o...

show abstract

Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding

Cited by 24 publications

References 34 publications

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations

Extending Halogen-based Medicinal Chemistry to Proteins

Contribution of TyrB26 to the Function and Stability of Insulin

Contact Info

Product

Resources

About