1
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Marton Menendez A, Nesbitt DJ. Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches. Biophys J 2024; 123:3331-3345. [PMID: 39091026 DOI: 10.1016/j.bpj.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
T. maritima and B. subtilis are bacteria that inhabit significantly different thermal environments, ∼80 vs. ∼40°C, yet employ similar lysine riboswitches to aid in the transcriptional regulation of the genes involved in the synthesis and transport of amino acids. Despite notable differences in G-C basepair frequency and primary sequence, the aptamer moieties of each riboswitch have striking similarities in tertiary structure, with several conserved motifs and long-range interactions. To explore genetic adaptation in extreme thermal environments, we compare the kinetic and thermodynamic behaviors in T. maritima and B. subtilis lysine riboswitches via single-molecule fluorescence resonance energy transfer analysis. Kinetic studies reveal that riboswitch folding rates increase with lysine concentration while the unfolding rates are independent of lysine. This indicates that both riboswitches bind lysine through an induced-fit ("bind-then-fold") mechanism, with lysine binding necessarily preceding conformational changes. Temperature-dependent van't Hoff studies reveal qualitative similarities in the thermodynamic landscapes for both riboswitches in which progression from the open, lysine-unbound state to both transition states (‡) and closed, lysine-bound conformations is enthalpically favored yet entropically penalized, with comparisons of enthalpic and entropic contributions extrapolated to a common [K+] = 100 mM in quantitative agreement. Finally, temperature-dependent Eyring analysis reveals the TMA and BSU riboswitches to have remarkably similar folding/unfolding rate constants when extrapolated to their respective (40 and 80°C) environmental temperatures. Such behavior suggests a shared strategy for ligand binding and aptamer conformational change in the two riboswitches, based on thermodynamic adaptations in number of G-C basepairs and/or modifications in tertiary structure that stabilize the ligand-unbound conformation to achieve biocompetence under both hyperthermophilic and mesothermophilic conditions.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado; Department of Chemistry, University of Colorado Boulder, Boulder, Colorado.
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado; Department of Chemistry, University of Colorado Boulder, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
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2
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Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahmoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024; 30:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [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: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.
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Affiliation(s)
- Jonathan W Sun
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph S Thomas
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Julia M Monkovic
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Halle Gibson
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Akash Nagapurkar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jin Kim Montclare
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Radiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Biomaterials, NYU College of Dentistry, New York, New York, USA
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3
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Nicholson DA, Nesbitt DJ. Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na + and K + Cations. J Phys Chem B 2023; 127:6842-6855. [PMID: 37504511 DOI: 10.1021/acs.jpcb.3c01001] [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] [Indexed: 07/29/2023]
Abstract
G-Quadruplexes (G4s) are ubiquitous nucleic acid folding motifs that exhibit structural diversity that is dependent on cationic conditions. In this work, we exploit temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) to elucidate the kinetic and thermodynamic mechanisms by which monovalent cations (K+ and Na+) impact folding topologies for a simple G-quadruplex sequence (5'-GGG-(TAAGGG)3-3') with a three-state folding equilibrium. Kinetic measurements indicate that Na+ and K+ influence G4 formation in two distinctly different ways: the presence of Na+ modestly enhances an antiparallel G4 topology through an induced fit (IF) mechanism with a low affinity (Kd = 228 ± 26 mM), while K+ drives G4 into a parallel/hybrid topology via a conformational selection (CS) mechanism with much higher affinity (Kd = 1.9 ± 0.2 mM). Additionally, temperature-dependent studies of folding rate constants and equilibrium ratios reveal distinctly different thermodynamic driving forces behind G4 binding to K+ (ΔH°bind > 0, ΔS°bind > 0) versus Na+ (ΔH°bind < 0, ΔS°bind < 0), which further illuminates the diversity of the possible pathways for monovalent facilitation of G-quadruplex folding.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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4
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Marton Menendez A, Nesbitt DJ. Ionic Cooperativity between Lysine and Potassium in the Lysine Riboswitch: Single-Molecule Kinetic and Thermodynamic Studies. J Phys Chem B 2023; 127:2430-2440. [PMID: 36916791 DOI: 10.1021/acs.jpcb.3c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Functionality in many biological systems, including proteins and nucleic acid structures, including protein and nucleic acid riboswitch structures, can depend on cooperative kinetic behavior between multiple small molecule ligands. In this work, single-molecule FRET data on the Bacillus subtilis lysine riboswitch reveals that affinity for the cognate lysine ligand increases significantly with K+, providing evidence for synergism between lysine/K+ binding to the aptamer and successful folding of the riboswitch. To describe/interpret this more complex kinetic scenario, we explore the conventional 4-state ("square") model for aptamer binding as a function of K+. Extension into this additional dimension generates a novel "cube" model for riboswitch folding dynamics with respect to lysine/K+ binding, revealing that riboswitch folding (kfold) and unfolding (kunfold) rate constants increase and decrease dramatically with K+, respectively. Furthermore, temperature-dependent single-molecule kinetic studies indicate that the presence of K+ entropically enhances the transition state barrier to folding but partially compensates for this by increasing the overall exothermicity for lysine binding. We rationalize this behavior as evidence that K+ facilitates hydrogen bonding between the negatively charged carboxyl group of lysine and the RNA, increasing structural rigidity and lowering entropy in the binding pocket. Finally, we explore the effects of cation size with Na+ and Cs+ studies to demonstrate that K+ is optimally suited for bridging interactions between lysine and the riboswitch aptamer domain. Regulation of lysine production and transport, dictated by the riboswitch's ability to recognize and bind lysine, is therefore intimately tied to the presence of K+ in the binding pocket and is strongly modulated by local cation conditions. The results suggest an increase in lysine riboswitch functionality by sensitivity to additional species in the cellular riboswitch environment.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Sung HL, Nesbitt DJ. Synergism in the Molecular Crowding of Ligand-Induced Riboswitch Folding: Kinetic/Thermodynamic Insights from Single-Molecule Spectroscopy. J Phys Chem B 2022; 126:6419-6427. [PMID: 35981263 DOI: 10.1021/acs.jpcb.2c03507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conformational dynamics in riboswitches involves ligand binding and folding of RNA, each of which can be influenced by excluded volume effects under "crowded" in vivo cellular conditions and thus incompletely characterized by in vitro studies under dilute buffer conditions. In this work, temperature-dependent single-molecule fluorescence resonance energy transfer (FRET) spectroscopy is used to characterize the thermodynamics of (i) cognate ligand and (ii) molecular crowders (PEG, polyethylene glycol) on folding of the B. subtilis LysC lysine riboswitch. With the help of detailed kinetic analysis, we isolate and study the effects of PEG on lysine binding and riboswitch folding steps individually, from which we find that PEG crowding facilitates riboswitch folding primarily via a surprising increase in affinity for the cognate ligand. This is furthermore confirmed by temperature-dependent studies, which reveal that PEG crowding is not purely entropic and instead significantly impacts both enthalpic and entropic contributions to the free energy landscape for folding. The results indicate that PEG molecular crowding/stabilization of the lysine riboswitch is more mechanistically complex and requires extension beyond the conventional picture of purely repulsive solvent-solute steric interactions arising from excluded volume and entropy. Instead, the current experimental FRET data support an alternative multistep mechanism, whereby PEG first entropically crowds the unfolded riboswitch into a "pre-folded" conformation, which in turn greatly increases the ligand binding affinity and thereby enhances the overall equilibrium for riboswitch folding.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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6
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Marton Menendez A, Nesbitt DJ. Lysine-Dependent Entropy Effects in the B. subtilis Lysine Riboswitch: Insights from Single-Molecule Thermodynamic Studies. J Phys Chem B 2021; 126:69-79. [PMID: 34958583 DOI: 10.1021/acs.jpcb.1c07833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Riboswitches play an important role in RNA-based sensing/gene regulation control for many bacteria. In particular, the accessibility of multiple conformational states at physiological temperatures allows riboswitches to selectively bind a cognate ligand in the aptamer domain, which triggers secondary structural changes in the expression platform, and thereby "switching" between on or off transcriptional or translational states for the downstream RNA. The present work exploits temperature-controlled, single-molecule total internal reflection fluorescence (TIRF) microscopy to study the thermodynamic landscape of such ligand binding/folding processes, specifically for the Bacillus subtilis lysine riboswitch. The results confirm that the riboswitch folds via an induced-fit (IF) mechanism, in which cognate lysine ligand first binds to the riboswitch before structural rearrangement takes place. The transition state to folding is found to be enthalpically favored (ΔHfold‡ < 0), yet with a free-energy barrier that is predominantly entropic (-TΔSfold‡ > 0), which results in folding (unfolding) rate constants strongly dependent (independent) of lysine concentration. Analysis of the single-molecule kinetic "trajectories" reveals this rate constant dependence of kfold on lysine to be predominantly entropic in nature, with the additional lysine conferring preferential advantage to the folding process by the presence of ligands correctly oriented with respect to the riboswitch platform. By way of contrast, van't Hoff analysis reveals enthalpic contributions to the overall folding thermodynamics (ΔH0) to be surprisingly constant and robustly independent of lysine concentration. The results demonstrate the crucial role of hydrogen bonding between the ligand and riboswitch platform but with only a relatively modest fraction (45%) of the overall enthalpy change needed to access the transition state and initiate transcriptional switching.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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7
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Nicholson DA, Jia B, Nesbitt DJ. Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level. J Phys Chem B 2021; 125:9719-9726. [PMID: 34415161 DOI: 10.1021/acs.jpcb.1c05555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Measurements of the thermodynamic properties of biomolecular folding (ΔG°, ΔH°, ΔS°, etc.) provide a wealth of information on the folding process and have long played a central role in biophysical investigation. In particular, the excess heat capacity of folding (ΔCP) is crucial, as typically measured in bulk ensemble studies by differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). Here, we report the first measurements of ΔCP at the single-molecule level using the single-molecule fluorescence resonance energy transfer (smFRET) as well as the very first measurements of the heat capacity change associated with achieving the transition state (ΔC‡P) for nucleic acid folding. The deoxyribonucleic acid (DNA) hairpin used in these studies exhibits an excess heat capacity for hybridization (ΔCP = -340 ± 60 J/mol/K per base pair) consistent with the range of literature expectations (ΔCP = -100 to -420 J/mol/K per base pair). Furthermore, the measured activation heat capacities (ΔC‡P) for such hairpin unfolding are consistent with a folding transition state containing few fully formed base pairs, in agreement with prevailing models of DNA hybridization.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Bin Jia
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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8
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Nicholson DA, Nesbitt DJ. Pushing Camera-Based Single-Molecule Kinetic Measurements to the Frame Acquisition Limit with Stroboscopic smFRET. J Phys Chem B 2021; 125:6080-6089. [PMID: 34097408 DOI: 10.1021/acs.jpcb.1c01036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) experiments permit detailed examination of microscopic dynamics. However, kinetic rate constants determined by smFRET are susceptible to systematic underestimation when the rate constants are comparable to the data acquisition rate. We demonstrate how such systematic errors in camera-based total internal reflection fluorescence microscopy experiments can be greatly reduced by using stroboscopic illumination/detection, allowing accurate rate constant determination up to the data sampling rate and yielding an order of magnitude increase in the dynamic range. Implementation of these stroboscopic smFRET ideas is straightforward, and the stroboscopically obtained data are compatible with multiple trajectory analysis methods, including dwell-time analysis and hidden Markov modeling. Such stroboscopic methods therefore offer a remarkably simple yet valuable addition to the smFRET toolkit, requiring only relatively modest modification to the normal data collection and analysis procedures.
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Affiliation(s)
- David A Nicholson
- National Institute of Standards and Technology and University of Colorado, JILA, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- National Institute of Standards and Technology and University of Colorado, JILA, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021; 12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) inherits the strategy of measurement from the effective "spectroscopic ruler" FRET and can be utilized to observe molecular behaviors with relatively high throughput at nanometer scale. The simplicity in principle and configuration of smFRET make it easy to apply and couple with other technologies to comprehensively understand single-molecule dynamics in various application scenarios. Despite its widespread application, smFRET is continuously developing and novel studies based on the advanced platforms have been done. Here, we summarize some representative examples of smFRET research of recent years to exhibit the versatility and note typical strategies to further improve the performance of smFRET measurement on different biomolecules.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yi Xing
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing 100191, China;
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
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