Jul 2026· Journal of Physical Chemistry B· Vol 130, pp. 7867 - 7875· 0 citations· 74 references
Medicine
TL;DR
The computed C p profile of the unmodified tRNA displayed a well-defined peak consistent with experimentally reported C p thermograms for various tRNAs, and the effects of different monovalent ions, distinct interatomic potentials, and varying melting temperature values on the key thermophysical properties of the tRNA isodecoder were probed.
Abstract
The heat capacity (C p ) is a fundamental thermodynamic property widely used to characterize biomolecular conformational stability. Despite extensive investigations into changes in the heat capacity (ΔC p ) associated with protein folding, these effects remain incompletely characterized in the folding of ribonucleic acid (RNA) molecules. In this work, we report on the thermophysical properties of a transfer RNA (tRNA) isodecoder in its chemically unmodified form as well as two modified forms, each having a distinct chemical modification, N 2,N 2-dimethylguanosine (m2,2G) or N 7-methylguanosine (m7G). The computed C p profile of the unmodified tRNA displayed a well-defined peak consistent with experimentally reported C p thermograms for various tRNAs. Based on the consistency between the computed thermophysical properties and experimental observations, we further probed the effects of different monovalent ions, distinct interatomic potentials, and varying melting temperature values on the key thermophysical properties of the tRNA isodecoder.
The reactivity and function of biopolymers depend on their structure and flexibility. There is a limited number of methods that can be used for their studies in solutions. Among them, Raman optical activity (ROA) provides excellent sensitivity to conformational changes. So far, ROA studies of nucleic acid systems are relatively rare because of the complexity of these molecules and difficulties in interpretation of the spectra. To explore the link between spectral shapes and the structure, and to advance the experimental and computational methodologies, we measured Raman and ROA spectra of four oligonucleotides (polyA, polyC, polyG, and polyU) in a wide wavenumber range. Molecular dynamics (MD) and density functional theory (DFT) were used for the spectra simulations. Temperature-dependent vibrational spectral changes are consistent with melting curves obtained from electronic circular dichroism (ECD). The results show that the spectra well-reflect molecular geometry, including changes caused by temperature variation. Comparison of theoretical and experimental Raman and ROA intensities appears as a convenient way to validate and potentially develop MD force fields; the RNA.Shaw force field provided results superior to the RNA.OL3 one. The combined spectroscopic and computational methodology thus can be used as a powerful means to study solution properties of nucleic acids.
Mohammed Siddhique Para Kkadan, Josef Kapitán, Jiří Kessler et al.· Chemistry· 0 citations
We present a coarse-grained model that describes the unfolding process and thermodynamics of ribonucleic acid (RNA) molecules. We obtained and analyzed a set of 1944 three-dimensional RNA structures of various molecular weights and under diverse conditions from the Protein Data Bank. We reduced the description of these molecules from an all-atom representation to a single interacting point per nucleotide, located at its center of mass. From this information, we calculated characteristic properties of the RNA chains, such as the bond distribution function and the contour length, which allowed us to estimate the most probable distance between two nucleotides linked by a phosphodiester bond as a = 5.5 ± 0.4 Å. We also calculated the radius of gyration of these chains, through which we obtained an estimate of the Flory exponent, ν = 0.33 ± 0.01, and a fractal dimension, d F = 3.03 ± 0.09. Furthermore, we determined the persistence length to be l p = 9.5 ± 4.1 Å. On the other hand, the different molecular configurations were used to improve the statistics of the pair distribution functions for various degrees of freedom. These were employed to obtain effective interaction potentials in a previous model [Villada-Balbuena, M.; Carbajal-Tinoco, M. D. J. Chem. Phys. 2024, 161, 165104.], which underwent a series of improvements, reducing the number of fitting parameters and enhancing the description of the radial-angular interaction. The fitting parameters of these potentials were optimized through Brownian dynamics (BD) simulations using the iterative Boltzmann inversion algorithm. The optimized potentials were used in steered BD simulations to model the mechanical unfolding at a constant velocity of a series of hairpins and pseudoknots. The results of these simulations are contrasted with experimental data, achieving excellent agreement. During the unfolding process, we monitored the configurational temperature (CT) of the model’s different degrees of freedom as well as the total CT. We used Jarzynski’s equality to calculate the Helmholtz free energy change, ΔA. Through ΔA and the integral of the force–extension curve, we obtained the Gibbs free energy change ΔG, which was successfully compared with the experimental results of RNA molecules unfolding using optical tweezers. Finally, based on the internal energy change values from the simulations, we estimated the entropy change ΔS. These values were compared with entropy changes from theoretical models. Finally, we utilized our model to calculate the changes in the aforementioned thermodynamic functions for molecules associated with viral protein expression.
Mario Villada-Balbuena, M. D. Carbajal-Tinoco· Journal of Chemical Theory a...· 0 citations
It is shown that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding and uncovers a previously underappreciated role for nucleic acid in proteostasis and offers a new strategy for studying nucleic acid structure-function relationship at residue level.
Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides, utilizing a ∼32 Å chain of proton-coupled electron transfer (PCET) reactions spanning two protein subunits to generate a catalytic cysteine radical. Two cryogenic electron microscopy structures of the active complex of E. coli RNR are currently available. One structure was trapped in the preturnover state, prior to radical translocation, and the other structure was trapped in the midturnover state, with the radical in the active site. Herein, we use molecular dynamics simulations to investigate the differences in hydrogen-bonding interactions and conformational motions between the preturnover and midturnover states. Our simulations show that Y731, an interfacial tyrosine that participates in the PCET pathway, samples multiple conformations in both states, allowing it to participate in forward and reverse PCET between subunits. We also observe interfacial water channels between the protein subunits in both states. Moreover, our simulations show that E623, which is near Y730 in the preturnover structure and was shown by previous simulations to mediate PCET between Y731 and Y730, can also sample conformations distal to Y730 in the preturnover state, similar to its position in the midturnover structure. Our mixed quantum mechanical/molecular mechanical free energy simulations indicate that forward radical transfer from Y731 to Y730 is thermodynamically favorable with a reasonable free energy barrier, even in the absence of mediation by E623. These results provide insights into the critical role of conformational motions and flexibility in regulating PCET reactions at and near the protein subunit interface of RNR.
Matthew Tremblay, Sharon Hammes-Schiffer· Biochemistry· 0 citations
The dynamics and stabilities (i.e., physicochemical properties) of proteins and protein complexes are dictated by the solution environment. Changes in the solution environment may alter the distribution of states present in solution (i.e., the free-energy landscape) and thus their physicochemical properties. This work examines the effects of temperature (4 °C, 21 °C, and 37 °C), electrospray ionization buffers (ammonium acetate (AmAc) and triethylammonium acetate (TEAA)), and solvent (H2O and D2O) on the physicochemical characteristics of the myoglobin/heme complex using limited proteolysis (i.e., trypsin digestion) and ion mobility-mass spectrometry (IM-MS). Electrospray ionization mass spectra of peptides formed by limited proteolysis showed increased peptide abundances at higher temperatures and in the absence of buffer molecules relative to the intact precursors. Interestingly, peptide abundances in D2O are more consistent across the temperature range studied relative to the peptide abundances in H2O, which demonstrates that D2O not only stabilizes proteins but acts as a kinetic trap for specific protein conformations. As an example, buffer components and D2O stabilize the myoglobin/heme interaction, as is evidenced by the modulation of peptide 64–77, an α-helical region that interacts with heme, and by shifts in the abundances of unfolded protein precursors. Lastly, IM-MS analysis of digested peptides suggests that AmAc alters the tertiary structure of the myoglobin/heme complex, whereas TEAA alters the secondary structure of the complex. The preservation of secondary structure in TEAA is further illustrated by the shift in arrival time distributions of 1+ ions in TEAA relative to the 2+, 3+, 4+, and 5+ ions present in other buffer conditions. Overall, the data show that buffer-solvent interactions govern the hydration of myoglobin and consequently, the physicochemical properties of the complex.
Carter Lantz, Leila Minian, Roza Avetisyan et al.· ACS Measurement Science Au· 0 citations
Chemical modifications to RNA play essential roles in regulating structure, stability, and biological function, yet a unifying physicochemical framework for understanding how these structural modifications perturb the underlying electronic landscape and influence intrinsic reactivity remains lacking. Here, we apply density functional theory to compute electronic-structure descriptors for a comprehensive set of naturally occurring modified ribonucleosides. By analyzing HOMO–LUMO gaps as measures of global electronic softness and Wiberg bond indices as local descriptors of glycosidic bond strength, we establish systematic relationships linking stereoelectronic substitution patterns and nucleobase π-conjugation to molecular reactivity and hydrolytic stability. We find that sulfur and selenium incorporation and major-groove substitutions tend to narrow HOMO–LUMO gaps and weaken glycosidic bonds, whereas C-glycosides (as in pseudouridines) confer electronic stabilization. These results reveal physical principles governing the intrinsic reactivity of modified RNA building blocks and provide a predictive framework for anticipating modification-dependent behavior relevant to RNA stability, degradation, and next-generation sequencing technologies used to characterize the epitranscriptome.
Volga Kojasoy, R. T. Raines· Physical Chemistry, Chemical...· 0 citations
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