The Role of Water in the Stability of Wild-type and Mutant Insulin Dimers

Monophasic coamorphous sulpiride: a leap in physicochemical attributes and dual inhibition of GlyT1 and P-glycoprotein, supported by experimental and computational insights

Study aimed to design and development of a supramolecular formulation of sulpiride (SUL) to enhance its solubility, dissolution and permeability by targeting a novel GlyT1 inhibition mechanism. SUL is commonly used to treat gastric and duodenal ulcers, migraine, anti-emetic, anti-depressive and anti-dyspeptic conditions. Additionally, Naringin (NARI) was incorporated as a co-former to enhance the drug's intestinal permeability by targeting P-glycoprotein (P-gp) efflux inhibition. NARI, a flavonoid has diverse biological activities, including anti-apoptotic, anti-oxidant, and anti-inflammatory properties. This study aims to design and develop a supramolecular formulation of SUL with NARI to enhance its solubility, dissolution, and permeability by targeting a novel GlyT1 inhibition mechanism, extensive experimental characterization was performed using solid-state experimental techniques in conjunction with a computational approach. This approach included quantum mechanics-based molecular dynamics (MD) simulation and density functional theory (DFT) studies to investigate intermolecular interactions, phase transformation and various electronic structure-based properties. The findings of the miscibility study, radial distribution function (RDF) analysis, quantitative simulations of hydrogen/π-π bond interactions and geometry optimization aided in comprehending the coamorphization aspects of SUL-NARI Supramolecular systems. Molecular docking and MD simulation were performed for detailed binding affinity assessment and target validation. The solubility, dissolution and ex-vivo permeability studies demonstrated significant improvements with 31.88-fold, 9.13-fold and 1.83-fold increments, respectively. Furthermore, biological assessments revealed superior neuroprotective effects in the SUL-NARI coamorphous system compared to pure SUL. In conclusion, this study highlights the advantages of a drug-nutraceutical supramolecular formulation for improving the solubility and permeability of SUL, targeting novel schizophrenia treatment approaches through combined computational and experimental analyses.Communicated by Ramaswamy H. Sarma.

Computational Approach to Elucidating Insulin-Protamine Binding Interactions and Dynamics in Insulin NPH Formulations

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.

Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics

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.

Quantitative molecular simulations

All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.

Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─Quo Vadis?

Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.

Progress in Simulation Studies of Insulin Structure and Function

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.

Structural Stability of Insulin Oligomers and Protein Association-Dissociation Processes: Free Energy Landscape and Universal Role of Water

Association and dissociation of proteins are important biochemical events. In this Feature Article, we analyze the available studies of these processes for insulin oligomers in aqueous solution. We focus on the solvation of the insulin monomer in water, stability and dissociation of its dimer, and structural integrity of the hexamer. The intricate role of water in solvation of the dimer- and hexamer-forming surfaces, in long-range interactions between the monomers and the stability of the oligomers, is discussed. Ten water molecules inside the central cavity stabilize the structure of the insulin hexamer. We discuss how different order parameters can be used to understand the dissociation of the insulin dimer. The calculation of the rate using a recently computed multidimensional free energy provides considerable insight into the interplay between protein and water dynamics.

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic molecular dynamics simulations and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer and a twisted state with a structure that appears to reflect a ∼55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin's B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its side-chain packing. The MSM kinetics predict that these configurations exchange on a 14 μs time scale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically ¹³C¹⁸O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.

Site-selective dynamics of azidolysozyme

The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN₃) in lysozyme are characterized. It is found that AlaN₃ is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm^-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm^-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ₂ range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ₀ ∼ 0 ps^-1) or to a remaining, static contribution of ∼0.5 ps^-1 (corresponding to 2.5 cm^-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.

Spectroscopy, Dynamics, and Hydration of S-Nitrosylated Myoglobin

S-Nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the -SNO group, it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO agrees with experimental findings on other proteins as is the observation of buried -SNO. For MbSNO the observed relocation of the EF loop in the simulations by ∼3 Å is consistent with the available X-ray structure, and the conformations adopted by the -SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the -SNO group compared with -SH, MbSNO recruits more water molecules in the first two hydration shells due to stronger electrostatic interactions. Similarly, when comparing the hydration between the A- and H-helices, they differ by up to 30% between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.

Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin

The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric forms in the region of the amide-I vibration differs for residues B24-B26 and D24-D26, which are involved in dimerization of the hormone. Also, the spectroscopic signatures change for mutations at position B24 from phenylalanine, which is conserved in many organisms and is known to play a central role in insulin aggregation, to alanine or glycine. Using three different methods to determine the frequency trajectories (solving the nuclear Schrödinger equation on an effective 1-dimensional potential energy curve, using instantaneous normal modes, and using parametrized frequency maps) leads to the same overall conclusions. The spectroscopic response of monomeric WT and mutant insulin differs from that of their respective dimers, and the spectroscopy of the two monomers in the dimer is also not identical. For the WT and F24A and F24G monomers, spectroscopic shifts are found to be ∼20 cm^-1 for residues (B24-B26) located at the dimerization interface. Although the crystal structure of the dimer is that of a symmetric homodimer, dynamically the two monomers are not equivalent on the nanosecond time scale. Together with earlier work on the thermodynamic stability of the WT and the same mutants, it is concluded that combining computational and experimental infrared spectroscopy provides a potentially powerful way to characterize the aggregation state and dimerization energy of modified insulins.

Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding

The protein hormone insulin exists in various oligomeric forms, and a key step in binding its cellular receptor is dissociation of the dimer. This dissociation process and its corresponding association process have come to serve as paradigms of coupled (un)folding and (un)binding more generally. Despite its fundamental and practical importance, the mechanism of insulin dimer dissociation remains poorly understood. Here, we use molecular dynamics simulations, leveraging recent developments in umbrella sampling, to characterize the energetic and structural features of dissociation in unprecedented detail. We find that the dissociation is inherently multipathway with limiting behaviors corresponding to conformational selection and induced fit, the two prototypical mechanisms of coupled folding and binding. Along one limiting path, the dissociation leads to detachment of the C-terminal segment of the insulin B chain from the protein core, a feature believed to be essential for receptor binding. We simulate IR spectroscopy experiments to aid in interpreting current experiments and identify sites where isotopic labeling can be most effective for distinguishing the contributions of the limiting mechanisms.

Revealing the Dynamical Role of Co-solvents in the Coupled Folding and Dimerization of Insulin

Solvent-protein interactions are important for protein biological functions, especially for a coupled folding and binding system such as insulin. By monitoring the change in the conformation of insulin dimers during dissociation with temperature-jump infrared spectroscopy, we show that co-solvents can significantly destabilize the dimers by perturbing their hydrophobic center. The transition from the native to intermediate dimer state is observed as the buried residues are exposed to solvents in the presence of 10% dimethyl sulfoxide and with α-helices unfolding when ethanol is present, which reduces the dissociation time dramatically to 50% and 20% of the value in a D₂O solution, respectively. We propose a self-consistent analysis using complementary methods to resolve this coupled folding and binding process and obtain a much higher rate of monomer association than of intermediate folding. Our results demonstrate that the conformational changes are critical in dimer formation and strongly affected by co-solvents.

Calculating the absolute binding free energy of the insulin dimer in an explicit solvent

Insulin is a significant hormone in the regulation of glucose level in the blood. Its monomers bind to each other to form dimers or hexamers through a complex process. To study the binding of the insulin dimer, we first calculate its absolute binding free energy by the steered molecular dynamics method and the confinement method based on a fictitious thermodynamic cycle. After considering some special correction terms, the final calculated binding free energy at 298 K is −8.97 ± 1.41 kcal mol⁻¹, which is close to the experimental value of −7.2 ± 0.8 kcal mol⁻¹. Furthermore, we discuss the important residue–residue interactions between the insulin monomers, including hydrophobic interactions, π–π interactions and hydrogen bond interactions. The analysis reveals five key residues, Vla^B12, Tyr^B16, Phe^B24, Phe^B25, and Tyr^B26, for the dimerization of the insulin. We also perform MM-PBSA calculations for the wild-type dimer and some mutants and study the roles of the key residues by the change of the binding energy of the insulin dimer.

In this paper, we calculate the absolute binding free energy of an insulin dimer by steered MD method. The result of −8.97 kcal mol⁻¹ is close to the experimental value −7.2 kcal mol⁻¹. We also analyze the residue–residue interactions.

The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy

Protein aggregation is believed to be a significant biological mechanism related to neurodegenerative disease, which makes the early-stage detection of aggregates a major concern. We demonstrated the use of terahertz (THz) time-domain spectroscopy to study protein-water interaction of monomeric and dimeric bovine insulin in aqueous samples. Regulated by changing pH and verified by size-exclusion chromatography and dynamic light scattering, we then measured their concentration-dependent changes in THz absorption between 0.5 and 3.0 THz and quantitatively deduced the extended hydration shell thickness by cubic distribution model and random distribution model. Under a random distribution assumption, the extended hydration thickness is 15.4 ± 0.4 Å for monomeric insulin and 17.5 ± 0.5 Å for dimeric insulin, with the hydration number of 6700 and 11,000, respectively. The hydration number of dimeric insulin is not twice but 1.64 times that of monomeric insulin, further supported by the ratio of solvent-accessible surface area. This "1.64-times" relation probably originates from the structural and conformational changes accompanied with dimerization. Combined with the investigations on insulin samples with different single amino acid mutations, residue B24 is believed to play an important role in the dimerization process. It is demonstrated that THz time-domain spectroscopy is a useful tool and has the sensitivity to provide the hydration information of different protein aggregates at an early stage.

Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy

The monomer-dimer equilibrium for insulin is one of the essential steps in forming the receptor-binding competent monomeric form of the hormone. Despite this importance, the thermodynamic stability, in particular for modified insulins, is quite poorly understood, in part, due to experimental difficulties. This work explores one- and two-dimensional infrared spectroscopy in the range of the amide-I band for the hydrated monomeric and dimeric wild-type hormone. It is found that for the monomer the frequency fluctuation correlation function (FFCF) and the one-dimensional infrared spectra are position sensitive. The spectra of the -CO probes at the dimerization interface (residues Phe24, Phe25, and Tyr26) split and indicate an asymmetry despite the overall (formal) point symmetry of the dimer structure. Also, the decay times of the FFCF for the same -CO probe in the monomer and the dimer can differ by up to 1 order of magnitude, for example, for residue PheB24, which is solvent exposed for the monomer but at the interface for the dimer. The spectroscopic shifts correlate approximately with the average number of hydration waters and the magnitude of the FFCF at time zero. However, this correlation is only qualitative due to the heterogeneous and highly dynamical environment. Based on density functional theory calculations, the dominant contribution for solvent-exposed -CO is found to arise from the surrounding water (∼75%), whereas the protein environment contributes considerably less. The results suggest that infrared spectroscopy is a positionally sensitive probe of insulin dimerization, in particular in conjunction with isotopic labeling of the probe.