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1. Structural Insights Into the 5′UG/3′GU Wobble Tandem in Complex With Ba2+ Cation

   https://doi.org/10.3389/fmolb.2021.762786  

   Ruszkowska, Agnieszka; Zheng, Ya Ying; Mao, Song; Ruszkowski, Milosz; Sheng, Jia (January 2022, Frontiers in Molecular Biosciences)

   G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA] 2 , providing detailed structural insights into the tandem motif I (5′UG/3′GU) complexed with Ba 2+ cation. We compare the electrostatic potential of the presented motif I major groove with previously published structures of tandem motifs I, II (5′GU/3′UG), and III (5′GG/3′UU). A local patch of a strongly negative electrostatic potential in the major groove of the presented structure forms the metal binding site with the contributions of three oxygen atoms from the tandem. These results give us a better understanding of the G•U tandem motif I as a divalent metal binder, a feature essential for RNA functions. 

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2. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity

   https://doi.org/10.1038/s41598-018-32028-7  

   Chen, Jianlin; Liu, Xiaorong; Chen, Jianhan (September 2018, Scientific Reports)

   Abstract Understanding how proteins fold has remained a problem of great interest in biophysical research. Atomistic computer simulations using physics-based force fields can provide important insights on the interplay of different interactions and energetics and their roles in governing the folding thermodynamics and mechanism. In particular, generalized Born (GB)-based implicit solvent force fields can be optimized to provide an appropriate balance between solvation and intramolecular interactions and successfully recapitulate experimental conformational equilibria for a set of helical and β-hairpin peptides. Here, we further demonstrate that key thermodynamic properties and their temperature dependence obtained from replica exchange molecular dynamics simulations of these peptides are in quantitative agreement with experimental results. Useful lessons can be learned on how the interplay of entropy and sequentially long-range interactions governs the mechanism and cooperativity of folding. These results highlight the great potential of high-quality implicit solvent force fields for studying protein folding and large-scale conformational transitions. 

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3. Quantifying reversible nitrogenous ligand binding to Co( ii ) porphyrin receptors at the solution/solid interface and in solution

   https://doi.org/10.1039/D0CP04109B  

   Johnson, Kristen N.; Hipps, K. W.; Mazur, Ursula (November 2020, Physical Chemistry Chemical Physics)

   null (Ed.)

   We present a quantitative study comparing the binding of 4-methoxypyridine, MeOPy, ligand to Co( ii )octaethylporphyrin, CoOEP, at the phenyloctane/HOPG interface and in toluene solution. Scanning tunneling microscopy (STM) was used to study the ligand binding to the porphyrin receptors adsorbed on graphite. Electronic spectroscopy was employed for examining this process in fluid solution. The on surface coordination reaction was completely reversible and followed a simple Langmuir adsorption isotherm. Ligand affinities (or Δ G ) for the binding processes in the two different chemical environments were determined from the respective equilibrium constants. The free energy value of −13.0 ± 0.3 kJ mol −1 for the ligation reaction of MeOPy to CoOEP at the solution/HOPG interface is less negative than the Δ G for cobalt porphyrin complexed to the ligand in solution, −16.8 ± 0.2 kJ mol −1 . This result indicates that the MeOPy–CoOEP complex is more stable in solution than on the surface. Additional thermodynamic values for the formation of the surface ligated species (Δ H c = −50 kJ mol −1 and Δ S c = −120 J mol −1 ) were extracted from temperature dependent STM measurements. Density functional computational methods were also employed to explore the energetics of both the solution and surface reactions. At high concentrations of MeOPy the monolayer was observed to be stripped from the surface. Computational results indicate that this is not because of a reduction in adsorption energy of the MeOPy–CoOEP complex. Nearest neighbor analysis of the MeOPy–CoOEP in the STM images revealed positive cooperative ligand binding behavior. Our studies bring new insights to the general principles of affinity and cooperativity in the ligand–receptor interactions at the solution/solid interface. Future applications of STM will pave the way for new strategies designing highly functional multisite receptor systems for sensing, catalysis, and pharmacological applications. 

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4. Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

   https://doi.org/10.1371/journal.pcbi.1011059  

   Estelle, Aidan B.; George, August; Barbar, Elisar J.; Zuckerman, Daniel M. (April 2023, PLOS Computational Biology)

   Keskin, Ozlem (Ed.)

   Multistep protein-protein interactions underlie most biological processes, but their characterization through methods such as isothermal titration calorimetry (ITC) is largely confined to simple models that provide little information on the intermediate, individual steps. In this study, we primarily examine the essential hub protein LC8, a small dimer that binds disordered regions of 100+ client proteins in two symmetrical grooves at the dimer interface. Mechanistic details of LC8 binding have remained elusive, hampered in part by ITC data analyses employing simple models that treat bivalent binding as a single event with a single binding affinity. We build on existing Bayesian ITC approaches to quantify thermodynamic parameters for multi-site binding interactions impacted by significant uncertainty in protein concentration. Using a two-site binding model, we identify positive cooperativity with high confidence for LC8 binding to multiple client peptides. In contrast, application of an identical model to the two-site binding between the coiled-coil NudE dimer and the intermediate chain of dynein reveals little evidence of cooperativity. We propose that cooperativity in the LC8 system drives the formation of saturated induced-dimer structures, the functional units of most LC8 complexes. In addition to these system-specific findings, our work advances general ITC analysis in two ways. First, we describe a previously unrecognized mathematical ambiguity in concentrations in standard binding models and clarify how it impacts the precision with which binding parameters are determinable in cases of high uncertainty in analyte concentrations. Second, building on observations in the LC8 system, we develop a system-agnostic heat map of practical parameter identifiability calculated from synthetic data which demonstrates that the ability to determine microscopic binding parameters is strongly dependent on both the parameters themselves and experimental conditions. The work serves as a foundation for determination of multi-step binding interactions, and we outline best practices for Bayesian analysis of ITC experiments. 

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5. Thermodynamic and kinetic studies of H ₂ and N ₂ binding to bimetallic nickel-group 13 complexes and neutron structure of a Ni(η ² -H ₂ ) adduct

   https://doi.org/10.1039/C9SC02018G  

   Cammarota, Ryan C.; Xie, Jing; Burgess, Samantha A.; Vollmer, Matthew V.; Vogiatzis, Konstantinos D.; Ye, Jingyun; Linehan, John C.; Appel, Aaron M.; Hoffmann, Christina; Wang, Xiaoping; et al (July 2019, Chemical Science)

   Understanding H 2 binding and activation is important in the context of designing transition metal catalysts for many processes, including hydrogenation and the interconversion of H 2 with protons and electrons. This work reports the first thermodynamic and kinetic H 2 binding studies for an isostructural series of first-row metal complexes: NiML, where M = Al ( 1 ), Ga ( 2 ), and In ( 3 ), and L = [N( o -(NCH 2 P i Pr 2 )C 6 H 4 ) 3 ] 3− . Thermodynamic free energies (Δ G °) and free energies of activation (Δ G ‡ ) for binding equilibria were obtained via variable-temperature 31 P NMR studies and lineshape analysis. The supporting metal exerts a large influence on the thermodynamic favorability of both H 2 and N 2 binding to Ni, with Δ G ° values for H 2 binding found to span nearly the entire range of previous reports. The non-classical H 2 adduct, (η 2 -H 2 )NiInL ( 3 -H 2 ), was structurally characterized by single-crystal neutron diffraction—the first such study for a Ni(η 2 -H 2 ) complex or any d 10 M(η 2 -H 2 ) complex. UV-Vis studies and TD-DFT calculations identified specific electronic structure perturbations of the supporting metal which poise NiML complexes for small-molecule binding. ETS-NOCV calculations indicate that H 2 binding primarily occurs via H–H σ-donation to the Ni 4p z -based LUMO, which is proposed to become energetically accessible as the Ni(0)→M( iii ) dative interaction increases for the larger M( iii ) ions. Linear free-energy relationships are discussed, with the activation barrier for H 2 binding (Δ G ‡ ) found to decrease proportionally for more thermodynamically favorable equilibria. The Δ G ° values for H 2 and N 2 binding to NiML complexes were also found to be more exergonic for the larger M( iii ) ions. 

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