1
|
Dao HM, AboulFotouh K, Hussain AF, Marras AE, Johnston KP, Cui Z, Williams RO. Characterization of mRNA Lipid Nanoparticles by Electron Density Mapping Reconstruction: X-ray Scattering with Density from Solution Scattering (DENSS) Algorithm. Pharm Res 2024; 41:501-512. [PMID: 38326530 DOI: 10.1007/s11095-024-03671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/28/2024] [Indexed: 02/09/2024]
Abstract
PURPOSE This study aimed to test the feasibility of using Small Angle X-ray Scattering (SAXS) coupled with Density from Solution Scattering (DENSS) algorithm to characterize the internal architecture of messenger RNA-containing lipid nanoparticles (mRNA-LNPs). METHODS The DENSS algorithm was employed to construct a three-dimensional model of average individual mRNA-LNP. The reconstructed models were cross validated with cryogenic transmission electron microscopy (cryo-TEM), and dynamic light scattering (DLS) to assess size, morphology, and internal structure. RESULTS Cryo-TEM and DLS complemented SAXS, revealed a core-shell mRNA-LNP structure with electron-rich mRNA-rich region at the core, surrounded by lipids. The reconstructed model, utilizing the DENSS algorithm, effectively distinguishes mRNA and lipids via electron density mapping. Notably, DENSS accurately models the morphology of the mRNA-LNPs as an ellipsoidal shape with a "bleb" architecture or a two-compartment structure with contrasting electron densities, corresponding to mRNA-filled and empty lipid compartments, respectively. Finally, subtle changes in the LNP structure after three freeze-thaw cycles were detected by SAXS, demonstrating an increase in radius of gyration (Rg) associated with mRNA leakage. CONCLUSION Analyzing SAXS profiles based on DENSS algorithm to yield a reconstructed electron density based three-dimensional model can be a useful physicochemical characterization method in the toolbox to study mRNA-LNPs and facilitate their development.
Collapse
Affiliation(s)
- Huy M Dao
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Khaled AboulFotouh
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aasim Faheem Hussain
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Alexander E Marras
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
- Materials Science and Engineering Graduate Program, Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Keith P Johnston
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Robert O Williams
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
2
|
Tzeli D, Raugei S, Xantheas SS. Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH 3) 4] q, q = -2, -1, +2, +3. J Chem Theory Comput 2021; 17:6080-6091. [PMID: 34546757 DOI: 10.1021/acs.jctc.1c00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH3)4]2-/1-/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD(T)] methodologies. We show that the nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH3)4] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH3)4]2-/1- complexes and covalent in [Fe(SCH3)4]2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH3)4]2- → [Fe(SCH3)4]- (i.e., FeII → FeIII) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH3)4]2+ → [Fe(SCH3)4]3+ of 16.6 eV, almost half of the ionization potential of Fe2+. The ionic versus covalent bond character influences the Fe-S bond strength and length, that is, ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for FeII) and 0.04 Å (for FeII). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (FeII) and 14.6 eV (FeIII) at the RCCSD(T) level of theory.
Collapse
Affiliation(s)
- Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 84, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 116 35, Greece
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
3
|
Le Breton N, Wright JJ, Jones AJY, Salvadori E, Bridges HR, Hirst J, Roessler MM. Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I. J Am Chem Soc 2017; 139:16319-16326. [PMID: 29039928 DOI: 10.1021/jacs.7b09261] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A(1H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.
Collapse
Affiliation(s)
- Nolwenn Le Breton
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
| | - John J Wright
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
| | - Andrew J Y Jones
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Enrico Salvadori
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom.,London Centre for Nanotechnology, University College London , 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Hannah R Bridges
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
| |
Collapse
|
4
|
Molecular magnetism, quo vadis? A historical perspective from a coordination chemist viewpoint☆. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.004] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
5
|
Khadem-Maaref M, Mehrnejad F, Phirouznia A. Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study. J Mol Graph Model 2017; 73:24-29. [PMID: 28214629 DOI: 10.1016/j.jmgm.2017.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 11/26/2022]
Abstract
Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co2+, Mn2+, and Zn2+, are able to reactivate metal-depleted PZase, while others including Cu2+, Fe2+, and Mg2+, cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations. We calculated the metal-ligand (residue) binding energy and the atomic partial charges in the presence of various ions. The results indicated that the tendency of alkaline earth metals to bind to PZase MCS is very low and not suitable for enzyme structural and catalytic function. In contrast, Co2+ and Ni2+ ions have very high binding affinity and are favorable to the structural and functional properties of the enzyme. Furthermore, we observed that the rate at which Ni2+, Co2+ and Fe2+ ions in PZase MCS polarize the OH bond of coordinated water molecules is much higher than the polarization rate created by other ions. This finding suggests that the coordination of Ni2+, Co2+, or Fe2+ to PZase facilitates the deprotonation of coordinated water molecules to generate a nucleophile that catalyzes the enzymatic reaction.
Collapse
Affiliation(s)
- Mahmoud Khadem-Maaref
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Arash Phirouznia
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| |
Collapse
|