1
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Datar PM, Joshi SY, Deshmukh SA, Marsh ENG. Probing the role of protein conformational changes in the mechanism of prenylated-FMN-dependent phenazine-1-carboxylic acid decarboxylase. J Biol Chem 2024; 300:105621. [PMID: 38176649 PMCID: PMC10850782 DOI: 10.1016/j.jbc.2023.105621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Phenazine-1-carboxylic acid decarboxylase (PhdA) is a prenylated-FMN-dependent (prFMN) enzyme belonging to the UbiD family of decarboxylases. Many UbiD-like enzymes catalyze (de)carboxylation reactions on aromatic rings and conjugated double bonds and are potentially valuable industrial catalysts. We have investigated the mechanism of PhdA using a slow turnover substrate, 2,3-dimethylquinoxaline-5-carboxylic acid (DQCA). Detailed analysis of the pH dependence and solvent deuterium isotope effects associated with the reaction uncovered unusual kinetic behavior. At low substrate concentrations, a substantial inverse solvent isotope effect (SIE) is observed on Vmax/KM of ∼ 0.5 when reaction rates of DQCA in H2O and D2O are compared. Under the same conditions, a normal SIE of 4.15 is measured by internal competition for proton transfer to the product. These apparently contradictory results indicate that the SIE values report on different steps in the mechanism. A proton inventory analysis of the reaction under Vmax/KM and Vmax conditions points to a "medium effect" as the source of the inverse SIE. Molecular dynamics simulations of the effect of D2O on PhdA structure support that D2O reduces the conformational lability of the enzyme and results in a more compact structure, akin to the active, "closed" conformer observed in crystal structures of some UbiD-like enzymes. Consistent with the simulations, PhdA was found to be more stable in D2O and to bind DQCA more tightly, leading to the observed rate enhancement under Vmax/KM conditions.
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Affiliation(s)
- Prathamesh M Datar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Rohilla K, Pandey MK. Computational Approach to Elucidating Insulin-Protamine Binding Interactions and Dynamics in Insulin NPH Formulations. ACS OMEGA 2024; 9:4857-4869. [PMID: 38313521 PMCID: PMC10831847 DOI: 10.1021/acsomega.3c08445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Insulin NPH is an intermediate-acting insulin. Its protracted action profile is due to the formation of microcrystalline suspensions when insulin is complexed with a basic peptide protamine, zinc ion, and phenolic ligands. Despite advancements in analytical techniques, the binding epitope and binding mode of the protamine in the insulin-protamine complex are still unknown. In this study, we used bioinformatics tools such as molecular docking and molecular dynamics (MD) simulations to compute the binding sites and energetics of the insulin-protamine complex. We have taken four naturally occurring protamine peptides that are independently docked with the insulin R6 hexamer and subjected them to 200 ns MD simulations to observe the dynamics of the complexes and estimate the binding energies. The arginine-rich protamine peptides were found to bind on the surface of the insulin hexamer through hydrogen bonding, hydrophobic, and electrostatic interactions well supported by the calculated negative binding energies. The overall structure of the insulin hexamer was retained upon binding, highlighting its dynamic stability in the complex. Furthermore, the residues at the termini of the protamine peptides in the complex were seen to be highly dynamic, which stabilize toward the end of the simulation.
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Affiliation(s)
- Ketan
Kumar Rohilla
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Manoj Kumar Pandey
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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3
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Sundaram V, Ramanan RN, Selvaraj M, Ahemad N, Vijayaraghavan R, MacFarlane DR, Ooi CW. Probing the molecular interactions between cholinium-based ionic liquids and insulin aspart: A combined computational and experimental study. Int J Biol Macromol 2023; 253:126665. [PMID: 37689282 DOI: 10.1016/j.ijbiomac.2023.126665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
Despite extensive studies revealing the potential of cholinium-based ionic liquids (ILs) in protein stabilization, the nature of interaction between ILs' constituents and protein residues is not well understood. In this work, we used a combined computational and experimental approach to investigate the structural stability of a peptide hormone, insulin aspart (IA), in ILs containing a choline cation [Ch]+ and either dihydrogen phosphate ([Dhp]-) or acetate ([Ace]-) as anions. Although IA remained stable in both 1 M [Ch][Dhp] and 1 M [Ch][Ace], [Dhp]- exhibited a much stronger stabilization effect than [Ace]-. Both the hydrophilic ILs intensely hydrated IA and increased the number of water molecules in IA's solvation shell. Undeterred by the increased number of water molecules, the native state of IA's hydrophobic core was maintained in the presence of ILs. Importantly, our results reveal the importance of IL concentration in the medium which was critical to maintain a steady population of ions in the microenvironment of IA and to counteract the denaturing effect of water molecules. Through molecular docking, we confirm that the anions exert the dominant effect on the structure of IA, while [Ch]+ have the secondary influence. The computational results were validated using spectroscopic analyses (ultra-violet, fluorescence, and circular dichroism) along with dynamic light scattering measurements. The extended stability of IA at 30 °C for 28 days in 1 M [Ch][Dhp] and [Ch][Ace] demonstrated in this study reveals the possibility of stabilizing IA using cholinium-based ILs.
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Affiliation(s)
- Vidya Sundaram
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Arkema Thiochemicals Sdn Bhd, Oasis Ara Damansara, 47301 Petaling Jaya, Selangor, Malaysia
| | - Manikandan Selvaraj
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - R Vijayaraghavan
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R MacFarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chien Wei Ooi
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia.
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4
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Jeevanandam J, Paramasivam E, Saraswathi NT. Glycation restrains open-closed conformation of Insulin. Comput Biol Chem 2023; 102:107803. [PMID: 36542957 DOI: 10.1016/j.compbiolchem.2022.107803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
In hyperglycemic conditions, the level of reactive dicarbonyl metabolites concentration is found to be high, which plays a significant role in protein glycation. Despite decades of research, the effect of methylglyoxal on the structure and function of insulin is still unknown. Through a shift in conformation at the B-chain C-terminal (BT-CT) hinge from an "open" to a "wide-open" conformation, insulin binds to the receptor and activates the signal cascade. Insulin resistance, which is the main sign of Type 2 Diabetes, can be caused by a lack of insulin signaling. Methylglyoxal site-specific glycation in residue R22 at B chain forms AGE product Methylglyoxal-hydroimidazolone (MGH1) in insulin. In this work, we present molecular dynamics study of this glycated insulin R22MGH1, which revealed new insights into the conformational and structural changes. We find the following key results: 1) B-chain in insulin undergoes a closed conformational change upon glycation. 2) Glycated insulin shows secondary structure alteration. 3) Glycated insulin retains its closed shape due to an unusually strong hydrophobic contact between B-chain residues. 4) Wide open native conformation of insulin allows the B chain helix to be surrounded by more water molecules compared to the closed conformation of glycated insulin. The closed conformation of glycated insulin impairs its binding to insulin receptor (IR).
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Affiliation(s)
- Jayanth Jeevanandam
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamilnadu, India
| | - Esackimuthu Paramasivam
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamilnadu, India
| | - N T Saraswathi
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamilnadu, India.
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5
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Cook TW, Wilstermann AM, Mitchell JT, Arnold NE, Rajasekaran S, Bupp CP, Prokop JW. Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics. Biomolecules 2023; 13:257. [PMID: 36830626 PMCID: PMC9953665 DOI: 10.3390/biom13020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Insulin is amongst the human genome's most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS-IGF2. This INS-IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS-IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3'UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.
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Affiliation(s)
- Taylor W. Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jackson T. Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Nicholas E. Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
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6
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Smith NA, Menting JG, Weiss MA, Lawrence MC, Smith BJ. Single-chain insulin analogs threaded by the insulin receptor αCT domain. Biophys J 2022; 121:4063-4077. [PMID: 36181268 PMCID: PMC9675026 DOI: 10.1016/j.bpj.2022.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022] Open
Abstract
Insulin is a mainstay of therapy for diabetes mellitus, yet its thermal stability complicates global transportation and storage. Cold-chain transport, coupled with optimized formulation and materials, prevents to some degree nucleation of amyloid and hence inactivation of hormonal activity. These issues hence motivate the design of analogs with increased stability, with a promising approach being single-chain insulins (SCIs), whose C domains (foreshortened relative to proinsulin) resemble those of the single-chain growth factors (IGFs). We have previously demonstrated that optimized SCIs can exhibit native-like hormonal activity with enhanced thermal stability and marked resistance to fibrillation. Here, we describe the crystal structure of an ultrastable SCI (C-domain length 6; sequence EEGPRR) bound to modules of the insulin receptor (IR) ectodomain (N-terminal α-subunit domains L1-CR and C-terminal αCT peptide; "microreceptor" [μIR]). The structure of the SCI-μIR complex, stabilized by an Fv module, was determined using diffraction data to a resolution of 2.6 Å. Remarkably, the αCT peptide (IR-A isoform) "threads" through a gap between the flexible C domain and the insulin core. To explore such threading, we undertook molecular dynamics simulations to 1) compare threaded with unthreaded binding modes and 2) evaluate effects of C-domain length on these alternate modes. The simulations (employing both conventional and enhanced sampling simulations) provide evidence that very short linkers (C-domain length of -1) would limit gap opening in the SCI and so impair threading. We envisage that analogous threading occurs in the intact SCI-IR complex-rationalizing why minimal C-domain lengths block complete activity-and might be exploited to design novel receptor-isoform-specific analogs.
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Affiliation(s)
- Nicholas A Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - John G Menting
- WEHI, Parkville, Victoria, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael A Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Michael C Lawrence
- WEHI, Parkville, Victoria, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
| | - Brian J Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
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7
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Sundaram V, Ramanan RN, Selvaraj M, Vijayaraghavan R, MacFarlane DR, Ooi CW. Enhanced structural stability of insulin aspart in cholinium aminoate ionic liquids. Int J Biol Macromol 2022; 208:544-552. [PMID: 35331796 DOI: 10.1016/j.ijbiomac.2022.03.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/14/2022]
Abstract
Cholinium aminoates [Ch][AA] have gained tremendous interest as a promising ionic liquid medium for the synthesis and storage of proteins. However, high alkalinity of [Ch][AA] limits its usage with pH-sensitive proteins. Here, we probed the structure, stability, and interactions of a highly unstable therapeutic protein, insulin aspart (IA), in a range of buffered [Ch][AA] (b-[Ch][AA]) using a combination of biophysical tools and in silico pipeline including ultraviolet-visible, fluorescence, and circular dichroism spectroscopies, dynamic light scattering measurements and molecular docking. b-[Ch][AA] used in the study differed in concentrations and their anionic counterparts. We reveal information on ion and residue specific solvent-protein interactions, demonstrating that the structural stability of IA was enhanced by a buffered cholinium prolinate. In comparison to the glycinate and alaninate anions, the hydrophilic prolinate anions established more hydrogen bonds with the residues of IA and provided a less polar environment that favours the preservation of IA in its active monomeric form, opening new opportunities for utilizing [Ch][AA] as storage medium.
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Affiliation(s)
- Vidya Sundaram
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Biological Enginerring Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar-382055, Gujarat, India
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Manikandan Selvaraj
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - R Vijayaraghavan
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R MacFarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
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8
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Tokhadzé N, Sahnoune M, Devémy J, Dequidt A, Goujon F, Chennell P, Sautou V, Malfreyt P. Insulin Adsorption onto PE and PVC Tubings. ACS APPLIED BIO MATERIALS 2022; 5:2567-2575. [PMID: 35549028 DOI: 10.1021/acsabm.2c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the adsorption of insulin onto PE and PVC materials by using HPLC measurements and computer simulations. We interpret the experiments by calculating the Gibbs free energy profiles during the adsorption process. The values of free energy of adsorption show a good agreement with the experimental measurements. The adsorption of insulin onto the different materials is characterized through the conformational changes with respect to its conformation in water and the interfacial regions, which are described by specific arrangements of polymer chains, water, insulin, and plasticizer molecules.
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Affiliation(s)
- Nicolas Tokhadzé
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Meriem Sahnoune
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- Université Clermont Auvergne, CHU Clermont-Ferrand, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Philip Chennell
- Université Clermont Auvergne, CHU Clermont-Ferrand, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Valérie Sautou
- Université Clermont Auvergne, CHU Clermont-Ferrand, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
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9
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Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022; 13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023] Open
Abstract
Insulin is a peptide hormone known for chiefly regulating glucose level in blood among several other metabolic processes. Insulin remains the most effective drug for treating diabetes mellitus. Insulin is synthesized in the pancreatic β-cells where it exists in a compact hexameric architecture although its biologically active form is monomeric. Insulin exhibits a sequence of conformational variations during the transition from the hexamer state to its biologically-active monomer state. The structural transitions and the mechanism of action of insulin have been investigated using several experimental and computational methods. This review primarily highlights the contributions of molecular dynamics (MD) simulations in elucidating the atomic-level details of conformational dynamics in insulin, where the structure of the hormone has been probed as a monomer, dimer, and hexamer. The effect of solvent, pH, temperature, and pressure have been probed at the microscopic scale. Given the focus of this review on the structure of the hormone, simulation studies involving interactions between the hormone and its receptor are only briefly highlighted, and studies on other related peptides (e.g., insulin-like growth factors) are not discussed. However, the review highlights conformational dynamics underlying the activities of reported insulin analogs and mimetics. The future prospects for computational methods in developing promising synthetic insulin analogs are also briefly highlighted.
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Palanisamy K, Prakash M. The molecular mechanism behind the stabilization of insulin by choline and geranate (CAGE) ionic liquids - computational insights into oral insulin drug formulation. Phys Chem Chem Phys 2021; 23:25298-25307. [PMID: 34746944 DOI: 10.1039/d1cp03349b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Insulin is a principal hormone that is involved in the regulation of glucose levels in the blood. Oral insulin formulation is a recent development in drug delivery systems. Biocompatible choline-based ionic liquids (ILs) show promising antibacterial activity and are useful for oral and transdermal drug delivery applications. Choline and geranate (CAGE) ILs enhance the stability and oral efficacy of insulin delivery. The molecular mechanism behind insulin formulation in the oral form is at issue. In the present work, the molecular-level understanding of CAGE ILs in insulin is scrutinized by employing atomistic molecular dynamics (MD) simulations. To identify the stability of insulin in an IL medium, we have studied a series of concentration (mole fraction 0.05-1.00) of CAGE ILs with an insulin dimer. It can be well evidenced from the experimental reports that in an aqueous medium, there is a refashioning of CAGE nanostructures at 0.50 mole fraction. It is found from our calculations that the first solvation shell of insulin is readily occupied by choline and geranate ions in the presence of water. Moreover, the geranate ions strongly interacted with the water molecules and thereby, eliminating the intermolecular hydrogen bonding (H-bonding) interactions towards the insulin at 0.30-0.50 mole fraction of CAGE ILs. The most desirable 0.30-0.50 mole fraction of CAGE invigorates water-mediated H-bonding interactions with geranate ions, which also enhances the electrostatic behavior around the vicinity of the insulin dimer. These important findings can help in the development of oral insulin drug delivery and related applications.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603203, Chennai, Tamil Nadu, India.
| | - Muthuramalingam Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603203, Chennai, Tamil Nadu, India.
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11
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Sundaram V, Ramanan RN, Selvaraj M, Vijayaraghavan R, MacFarlane DR, Ooi CW. Structural stability of insulin aspart in aqueous cholinium aminoate ionic liquids based on molecular dynamics simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Macháčková K, Mlčochová K, Potalitsyn P, Hanková K, Socha O, Buděšínský M, Muždalo A, Lepšík M, Černeková M, Radosavljević J, Fábry M, Mitrová K, Chrudinová M, Lin J, Yurenko Y, Hobza P, Selicharová I, Žáková L, Jiráček J. Mutations at hypothetical binding site 2 in insulin and insulin-like growth factors 1 and 2 result in receptor- and hormone-specific responses. J Biol Chem 2019; 294:17371-17382. [PMID: 31558604 PMCID: PMC6873181 DOI: 10.1074/jbc.ra119.010072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/23/2019] [Indexed: 11/26/2022] Open
Abstract
Information on how insulin and insulin-like growth factors 1 and 2 (IGF-1 and -2) activate insulin receptors (IR-A and -B) and the IGF-1 receptor (IGF-1R) is crucial for understanding the difference in the biological activities of these peptide hormones. Cryo-EM studies have revealed that insulin uses its binding sites 1 and 2 to interact with IR-A and have identified several critical residues in binding site 2. However, mutagenesis studies suggest that Ile-A10, Ser-A12, Leu-A13, and Glu-A17 also belong to insulin's site 2. Here, to resolve this discrepancy, we mutated these insulin residues and the equivalent residues in IGFs. Our findings revealed that equivalent mutations in the hormones can result in differential biological effects and that these effects can be receptor-specific. We noted that the insulin positions A10 and A17 are important for its binding to IR-A and IR-B and IGF-1R and that A13 is important only for IR-A and IR-B binding. The IGF-1/IGF-2 positions 51/50 and 54/53 did not appear to play critical roles in receptor binding, but mutations at IGF-1 position 58 and IGF-2 position 57 affected the binding. We propose that IGF-1 Glu-58 interacts with IGF-1R Arg-704 and belongs to IGF-1 site 1, a finding supported by the NMR structure of the less active Asp-58–IGF-1 variant. Computational analyses indicated that the aforementioned mutations can affect internal insulin dynamics and inhibit adoption of a receptor-bound conformation, important for binding to receptor site 1. We provide a molecular model and alternative hypotheses for how the mutated insulin residues affect activity.
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Affiliation(s)
- Kateřina Macháčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Květoslava Mlčochová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Pavlo Potalitsyn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Kateřina Hanková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Anja Muždalo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Michaela Černeková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jelena Radosavljević
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Czech Academy of Sciences, 166 37 Prague 6, Czech Republic
| | - Katarína Mitrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Martina Chrudinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jingjing Lin
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Yevgen Yurenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
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13
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Soleymani H, Ghorbani M, Allahverdi A, Shojaeilangari S, Naderi-Manesh H. Activation of human insulin by vitamin E: A molecular dynamics simulation study. J Mol Graph Model 2019; 91:194-203. [PMID: 31265936 DOI: 10.1016/j.jmgm.2019.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
Lack of perfect insulin signaling can lead to the insulin resistance, which is the hallmark of diabetes mellitus. Activation of insulin and its binding to the receptor for signaling process initiates via B-chain C-terminal hinge conformational change through an open structure to "wide-open" conformation. Observational studies and basic scientific evidence suggest that vitamin D and E directly and/or indirectly prevent diabetes through improving glucose secretion and tolerance, activating calcium dependent endopeptidases and thus improving insulin exocytosis, antioxidant effect and reducing insulin resistance. On the contrary, clinical trials have yielded inconsistent results about the efficacy of vitamin D supplementations for the control of glucose hemostasis. In this work, best binding modes of vitamin D3 and E on insulin obtained from AutoDock Vina were selected for Molecular Dynamic, MD, study. The binding energy obtained from Molecular Mechanics- Poisson Boltzman Surface Area, MM-PBSA method, revealed that Vitamins D3 and E have good affinity to bind to the insulin and vitamin E has higher binding energy (-46 kj/mol) by engaging more residues in binding site. Distance and angle calculation results illustrated that vitamin E changes the B-chain conformation and it causes the formation of wide-open/active form of insulin. Vitamin E increases the ValB12-TyrB26 distance to ∼15 Å and changes the hinge angle to ∼65°. Consequently, essential hydrophobic residues for binding to insulin receptor exposed to surface in the presence of vitamin E. However, our data illustrated that vitamin D3 cannot change B-chain conformation. Thus our MD simulations propose a model for insulin activation through vitamin E interaction for therapeutic approaches.
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Affiliation(s)
- Hossein Soleymani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | - Mohammad Ghorbani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | - Abdollah Allahverdi
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | | | - Hossein Naderi-Manesh
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran; School of Biological Science, Institute for Research in Fundamental Sciences (IPM), 19395-5746, Tehran, Iran.
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14
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Ong SC, Belgi A, van Lierop B, Delaine C, Andrikopoulos S, MacRaild CA, Norton RS, Haworth NL, Robinson AJ, Forbes BE. Probing the correlation between insulin activity and structural stability through introduction of the rigid A6-A11 bond. J Biol Chem 2018; 293:11928-11943. [PMID: 29899115 DOI: 10.1074/jbc.ra118.002486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/10/2018] [Indexed: 11/06/2022] Open
Abstract
The development of fast-acting and highly stable insulin analogues is challenging. Insulin undergoes structural transitions essential for binding and activation of the insulin receptor (IR), but these conformational changes can also affect insulin stability. Previously, we substituted the insulin A6-A11 cystine with a rigid, non-reducible C=C linkage ("dicarba" linkage). A cis-alkene permitted the conformational flexibility of the A-chain N-terminal helix necessary for high-affinity IR binding, resulting in surprisingly rapid activity in vivo Here, we show that, unlike the rapidly acting LysB28ProB29 insulin analogue (KP insulin), cis-dicarba insulin is not inherently monomeric. We also show that cis-dicarba KP insulin lowers blood glucose levels even more rapidly than KP insulin, suggesting that an inability to oligomerize is not responsible for the observed rapid activity onset of cis-dicarba analogues. Although rapid-acting, neither dicarba species is stable, as assessed by fibrillation and thermodynamics assays. MALDI analyses and molecular dynamics simulations of cis-dicarba insulin revealed a previously unidentified role of the A6-A11 linkage in insulin conformational dynamics. By controlling the conformational flexibility of the insulin B-chain helix, this linkage affects overall insulin structural stability. This effect is independent of its regulation of the A-chain N-terminal helix flexibility necessary for IR engagement. We conclude that high-affinity IR binding, rapid in vivo activity, and insulin stability can be regulated by the specific conformational arrangement of the A6-A11 linkage. This detailed understanding of insulin's structural dynamics may aid in the future design of rapid-acting insulin analogues with improved stability.
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Affiliation(s)
- Shee Chee Ong
- From the College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia
| | - Alessia Belgi
- the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Bianca van Lierop
- the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Carlie Delaine
- From the College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia
| | - Sofianos Andrikopoulos
- the Department of Medicine, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Naomi L Haworth
- the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia.,the Research School of Chemistry, Australian National University, Acton, Australian Capital Territory 2601, Australia, and.,the School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Andrea J Robinson
- the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Briony E Forbes
- From the College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia,
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15
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Afanasyeva A, Bockwoldt M, Cooney CR, Heiland I, Gossmann TI. Human long intrinsically disordered protein regions are frequent targets of positive selection. Genome Res 2018; 28:975-982. [PMID: 29858274 PMCID: PMC6028134 DOI: 10.1101/gr.232645.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species, it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here, we address this question by investigating the evolutionary pattern of more than 6600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs fourfold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts.
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Affiliation(s)
- Arina Afanasyeva
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S102TN, United Kingdom.,Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg 195251, Russia.,Petersburg Nuclear Physics Institute, B.P. Konstantinov NRC Kurchatov Institute, Gatchina, Leningrad District 188300, Russia.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki City, Osaka 567-0085, Japan
| | - Mathias Bockwoldt
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Christopher R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S102TN, United Kingdom
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S102TN, United Kingdom
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16
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Singh R, Bansal R, Rathore AS, Goel G. Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics. Biophys J 2017; 112:1571-1585. [PMID: 28445749 DOI: 10.1016/j.bpj.2017.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 03/03/2017] [Accepted: 03/20/2017] [Indexed: 12/29/2022] Open
Abstract
Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding. The highest lifetime, lowest free-energy ensemble identified consisted of native conformations adopted by a folded insulin monomer in solution, namely, the R-, the Rf-, and the T-states of insulin. The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x-ray structure. The second longest-lived metastable state was an unfolded, compact monomer with little similarity to the native structure. We have identified three additional long-lived, metastable states from the bin-based model. We then carried out an exhaustive structural characterization of metastable states on the basis of tertiary contact maps and per-residue accessible surface areas. We have also determined the lowest free-energy path between two longest-lived metastable states and confirm earlier findings of non-two-state folding for insulin through a folding intermediate. The ensemble containing the monomeric intermediate retained 58% of native hydrophobic contacts, however, accompanied by a complete loss of native secondary structure. We have discussed the relative importance of nativelike versus nonnative tertiary contacts for the folding transition. We also provide a simple measure to determine the importance of an individual residue for folding transition. Finally, we have compared and contrasted this intermediate with experimental data obtained in spectroscopic, crystallographic, and calorimetric measurements during early stages of insulin aggregation. We have also determined stability of monomeric insulin by incubation at a very low concentration to isolate protein-protein interaction effects.
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Affiliation(s)
- Richa Singh
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Rohit Bansal
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag Singh Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India.
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17
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Computational study of the activity, dynamics, energetics and conformations of insulin analogues using molecular dynamics simulations: Application to hyperinsulinemia and the critical residue B26. Biochem Biophys Rep 2017; 11:182-190. [PMID: 28955783 PMCID: PMC5614686 DOI: 10.1016/j.bbrep.2017.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/13/2017] [Indexed: 12/15/2022] Open
Abstract
Due to the increasing prevalence of diabetes, finding therapeutic analogues for insulin has become an urgent issue. While many experimental studies have been performed towards this end, they have limited scope to examine all aspects of the effect of a mutation. Computational studies can help to overcome these limitations, however, relatively few studies that focus on insulin analogues have been performed to date. Here, we present a comprehensive computational study of insulin analogues-three mutant insulins that have been identified with hyperinsulinemia and three mutations on the critical B26 residue that exhibit similar binding affinity to the insulin receptor-using molecular dynamics simulations with the aim of predicting how mutations of insulin affect its activity, dynamics, energetics and conformations. The time evolution of the conformers is studied in long simulations. The probability density function and potential of mean force calculations are performed on each insulin analogue to unravel the effect of mutations on the dynamics and energetics of insulin activation. Our conformational study can decrypt the key features and molecular mechanisms that are responsible for an enhanced or reduced activity of an insulin analogue. We find two key results: 1) hyperinsulinemia may be due to the drastically reduced activity (and binding affinity) of the mutant insulins. 2) Y26BS and Y26BE are promising therapeutic candidates for insulin as they are more active than WT-insulin. The analysis in this work can be readily applied to any set of mutations on insulin to guide development of more effective therapeutic analogues.
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18
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El Hage K, Pandyarajan V, Phillips NB, Smith BJ, Menting JG, Whittaker J, Lawrence MC, Meuwly M, Weiss MA. Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY. J Biol Chem 2016; 291:27023-27041. [PMID: 27875310 PMCID: PMC5207135 DOI: 10.1074/jbc.m116.761015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/31/2016] [Indexed: 12/13/2022] Open
Abstract
Insulin, 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 (TyrB26) 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 molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]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 (TyrB16, PheB24, PheB25, 3-I-TyrB26, 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-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 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-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.
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Affiliation(s)
- Krystel El Hage
- From the Department of Chemistry, University of Basel, Klingelbergstrasse 80 CH-4056 Basel, Switzerland
| | | | | | - Brian J Smith
- the La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - John G Menting
- the The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and
| | | | - Michael C Lawrence
- the The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and
- the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Markus Meuwly
- From the Department of Chemistry, University of Basel, Klingelbergstrasse 80 CH-4056 Basel, Switzerland,
| | - Michael A Weiss
- the Departments of Biochemistry,
- Medicine, and
- Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
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19
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Papaioannou A, Kuyucak S, Kuncic Z. Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations. PLoS One 2016; 11:e0161459. [PMID: 27548502 PMCID: PMC4993506 DOI: 10.1371/journal.pone.0161459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/05/2016] [Indexed: 12/27/2022] Open
Abstract
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.
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Affiliation(s)
- Anastasios Papaioannou
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
- School of Physics, University of Sydney, Sydney, NSW, Australia
- * E-mail: (AP); (ZK)
| | - Serdar Kuyucak
- School of Physics, University of Sydney, Sydney, NSW, Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
- School of Physics, University of Sydney, Sydney, NSW, Australia
- * E-mail: (AP); (ZK)
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20
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Pandyarajan V, Phillips NB, Rege N, Lawrence MC, Whittaker J, Weiss MA. Contribution of TyrB26 to the Function and Stability of Insulin: STRUCTURE-ACTIVITY RELATIONSHIPS AT A CONSERVED HORMONE-RECEPTOR INTERFACE. J Biol Chem 2016; 291:12978-90. [PMID: 27129279 DOI: 10.1074/jbc.m115.708347] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/06/2022] Open
Abstract
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, non-aromatic polar or charged side chains (such as Glu, Ser, or ornithine (Orn)) conferred high activity, whereas the weakest-binding 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.
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Affiliation(s)
| | | | | | - Michael C Lawrence
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Michael A Weiss
- From the Departments of Biochemistry, Medicine, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106,
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