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The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF1R) are homodimeric transmembrane glycoproteins that transduce signals across the membrane on binding of extracellular peptide ligands. The structures of IR/IGF1R fragments in apo and liganded states have revealed that the extracellular subunits of these receptors adopt -shaped configurations to which are connected the intracellular tyrosine kinase (TK) domains. The binding of peptide ligands induces structural transitions in the extracellular subunits leading to potential dimerization of transmembrane domains (TMDs) and autophosphorylation in TKs. However, the activation mechanisms of IR/IGF1R, especially the role of TMDs in coordinating signalinducing structural transitions, remain poorly understood, in part due to the lack of structures of full-length receptors in apo or liganded states. While atomistic simulations of IR/IGF1R TMDs showed that these domains can dimerize in single component membranes, spontaneous unbiased dimerization in a plasma membrane having a physiologically representative lipid composition has not been observed. We address this limitation by employing coarse-grained (CG) molecular dynamics simulations to probe the dimerization propensity of IR/IGF1R TMDs. We observed that TMDs in both receptors spontaneously dimerized independent of their initial orientations in their dissociated states, signifying their natural propensity for dimerization. In the dimeric state, IR TMDs predominantly adopted X-shaped configurations with asymmetric helical packing and significant tilt relative to the membrane normal, while IGF1R TMDs adopted symmetric V-shaped or parallel configurations with either no tilt or a small tilt relative to the membrane normal. Our results suggest that IR/IGF1R TMDs spontaneously dimerize and adopt distinct dimerized configurations. 

Light-induced self-assembly (LISA) is a non-invasive method for tuning material properties. Photoresponsive ligands coated on the surfaces of nanoparticles are often used to achieve LISA. We report simulation studies for a photoresponsive ligand, azobenzene dithiol (ADT), which switches from a trans-to-cis configuration on exposure to ultraviolet light, allowing self-assembly in ADT-coated gold nanoparticles (NPs). This is attributed to a higher dipole moment of cis-ADT over trans-ADT which leads to a dipole–dipole attraction facilitating self-assembly. Singh and Jha [Comput. Theor. Chem., 2021, 1206, 113492] used quantum-chemistry calculations to quantify the interaction energy of a pair of ADT ligands in their cis and trans conformations. The interaction energy between ligands was fit to a potential energy function of the Lennard–Jones (LJ) form having distinct exponents for attractive and repulsive contributions. Using this generalized equation for the ligand–ligand interaction energy, we calculated the total effective interaction energy between a pair of cis as well as trans ADT-coated NPs. Specifically, we calculated the effective interaction energies between cis/trans-NPs using discrete as well as continuous approaches. Given the limitations of experiments in probing individual ligand conformations, we also studied the effect of varying the functional ligand length on the interaction energy between NPs and identified the optimal functional ligand length to capture the steric and conformational effects. Finally, using the effective interaction energy, we obtained a generalized potential energy function, which was applied in Langevin dynamics simulations to capture self-assembly in NPs. 

Self-assembly of colloidal particles is emerging as a promising approach for producing novel materials. These colloidal particles can be synthesized with protrusions (lobes) on their surfaces that allow the formation of porous structures with a wide range of applications. Using Langevin dynamics simulations, we studied self-assembly in the binary mixtures of lobed colloidal particles with variations in their lobe sizes to investigate the feasibility of using dumbbell particles (with two lobes) as cross-linkers to increase the porosity in self-assembled morphologies. Each binary system was formed by mixing the dumbbell particles with one of the following types of particles: trigonal planar (three lobes), tetrahedral (four lobes), trigonal bipyramidal (five lobes), and octahedral (six lobes). We observed that the lobe size on each particle can be tuned to favor the formation of random aggregates and spherical aggregates when the lobes are larger and well-ordered crystalline structures when the lobes are smaller. We also observed that these polydisperse systems form self-assembled structures characterized by porosities higher than those of the structures formed by the monodisperse systems. These results indicate that the lobe size is an important design feature that can be optimized to achieve desired structures with distinct morphologies and porosities, and the dumbbell particles are effective cross-linking agents to enhance the porosity in self-assembled structures. 

The insulin receptor (IR), the insulin-like growth factor-1 receptor (IGF1R), and the insulin/IGF1 hybrid receptors (hybR) are homologous transmembrane receptors. The peptide ligands, insulin and IGF1, exhibit significant structural homology and can bind to each receptor via site-1 and site-2 residues with distinct affinities. The variants of the Iridoviridae virus family show capability in expressing single-chain insulin/IGF1 like proteins, termed viral insulin-like peptides (VILPs), which can stimulate receptors from the insulin family. The sequences of VILPs lacking the central C-domain (dcVILPs) are known, but their structures in unbound and receptor-bound states have not been resolved to date. We report all-atom structural models of three dcVILPs (dcGIV, dcSGIV, and dcLCDV1) and their complexes with the receptors (μIR, μIGF1R, and μhybR), and probed the peptide/receptor interactions in each system using all-atom molecular dynamics (MD) simulations. Based on the nonbonded interaction energies computed between each residue of peptides (insulin and dcVILPs) and the receptors, we provide details on residues establishing significant interactions. The observed site-1 insulin/μIR interactions are consistent with previous experimental studies, and a residue-level comparison of interactions of peptides (insulin and dcVILPs) with the receptors revealed that, due to sequence differences, dcVILPs also establish some interactions distinct from those between insulin and IR. We also designed insulin analogs and report enhanced interactions between some analogs and the receptors. 

We report coarse-grained Langevin dynamics simulations of homogeneous mixtures of lobed colloidal particles with opposite charges. We show that dumbbell, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, and octahedral shaped particles form distinct self-assemblies including chains, sheets, crystalline, and spherical structures. The dumbbell and square planar particles predominantly form chains and sheets while other particles form network-like self-assembled morphologies. At higher temperatures and lower charges, non-planar particles form three-dimensional aggregates. We further report on packing arrangements of particles which lead to differences in porosities within self-assembled morphologies. Our results show that the trigonal planar particles form larger porous structures. The self-assembled structures that we report are potentially useful in designing porous biomaterials for biomedical applications.