Side-chain Protons Research Articles

Compound-specific, intra-molecular, and clumped 13C fractionations in the thermal generation and decomposition of ethane and propane: A DFT and kinetic investigation

The distribution of stable isotopes in organic compounds within geochemical systems reflects the reactions they undergo, which are often kinetically governed and can be elucidated through quantification based on first principles: employing quantum chemical simulations to derive energy barriers and kinetic isotope effects (KIEs), followed by kinetic calculations using these parameters. In this paper, the distribution of 13C in hydrocarbon gases during the thermal generation and decomposition of ethane and propane has been addressed. The work is based on abundant and systematic isotopic data, including the compound- and position-specific 13C compositions, recent improvements in kinetic networks in hydrocarbon generation, and state-of-the-art quantum chemical methods that can process organic geochemical systems involving solid phases. Density Functional Theory computations validate the carbonium path of hydrocarbon generation and the free-radical path of their decomposition under geological conditions. The first step of each path (alkyl sidechain protonation for generation and hydrogen abstraction for decomposition) is the rate-limiting step and determines the 13C fractionations of gaseous hydrocarbons, with the reaction rate constrained by the concentration or accessibility of the active species (hydrated protons and surface free radicals in the two paths, respectively). Alkyl protonation has normal 13C KIEs, but hydrogen abstraction on the surfaces of solid organic matter has inverse ones (substituting 12C by 13C accelerates the reaction). These inverse KIEs explain three isotopic phenomena in gaseous hydrocarbons in their late thermal evolution: 1) the depletion of 13C in ethane and propane accompanied by their decreased fraction in hydrocarbon gases (isotope “rollover”); 2) the reversed 13C sequence with carbon number (δ13Cmethane > δ13Cethane > δ13Cpropane); and 3) the depletion of 13C in the center carbon atoms of residual propane. Isotopic fractionation between gaseous hydrocarbons upon generation is evaluated using the Successive Random Chain-Scission model. The covariation of δ13C in alkanes shows a depletion in CH4 compared with the values expected from the reciprocal of the carbon numbers, indicating that this deviation may be intrinsic instead of mixing with microbial methane. The comparison of intramolecular 13C fractionation of propane between computational and observed data suggests the contribution of isoprenoids at the beginning of the generation, in addition to isotopic homogenization between the center and end carbon atoms through the ring closure of intermediate cations. The 13C–13C clumping exhibits a weak KIE in both the generation and decomposition of ethane; the clumping is essentially stochastically governed. This work demonstrates how first-principle calculations can provide significant insights into the details of geochemical reactions governing the isotopic distributions.

Inhomogenous broadening of antenna protein chlorophyll site energies due to side chain conformational and protonation states determined by Monte Carlo microstate analysis

Inhomogenous broadening of antenna protein chlorophyll site energies due to side chain conformational and protonation states determined by Monte Carlo microstate analysis

Lasso Peptides: Exploring the Folding Landscape of Nature's Smallest Interlocked Motifs.

Lasso peptides make up a class of natural products characterized by a threaded structure. Given their small size and stability, chemical synthesis would offer tremendous potential for the development of novel therapeutics. However, the accessibility of the pre-folded lasso architecture has limited this advance. To better understand the folding process de novo, simulations are used herein to characterize the folding propensity of microcin J25 (MccJ25), a lasso peptide known for its antimicrobial properties. New algorithms are developed to unambiguously distinguish threaded from nonthreaded precursors and determine handedness, a key feature in natural lasso peptides. We find that MccJ25 indeed forms right-handed pre-lassos, in contrast to past predictions but consistent with all natural lasso peptides. Additionally, the native pre-lasso structure is shown to be metastable prior to ring formation but to readily transition to entropically favored unfolded and nonthreaded structures, suggesting that de novo lasso folding is rare. However, by altering the ring forming residues and appending thiol and thioester functionalities, we are able to increase the stability of pre-lasso conformations. Furthermore, conditions leading to protonation of a histidine imidazole side chain further stabilize the modified pre-lasso ensemble. This work highlights the use of computational methods to characterize lasso folding and demonstrates that de novo access to lasso structures can be facilitated by optimizing sequence, unnatural modifications, and reaction conditions like pH.

Protein deuteration via algal amino acids to circumvent proton back-exchange for 1H-detected solid-state NMR.

With perdeuteration, solid-state NMR spectroscopy of large proteins suffers from incomplete amide-proton back-exchange. Using a 72 kDa micro-crystalline protein, we show that deuteration exclusively via deuterated amino acids, well-established in solution to suppress sidechain protonation without proton back-exchange obstacles, provides spectral resolution comparable to perdeuterated preparations at intermediate spinning frequencies.

Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties.

Photoconvertible fluorescent proteins (PCFP) are important cellular markers in advanced imaging modalities such as photoactivatable localization microscopy (PALM). However, their complex photophysical and photochemical behavior hampers applications such as quantitative and single-particle-tracking PALM. This work employs multidimensional NMR combined with ensemble fluorescence measurements to show that the popular mEos4b in its Green state populates two conformations (A and B), differing in side-chain protonation of the conserved residues E212 and H62, altering the hydrogen-bond network in the chromophore pocket. The interconversion (protonation/deprotonation) between these two states, which occurs on the minutes time scale in the dark, becomes strongly accelerated in the presence of UV light, leading to a population shift. This work shows that the reversible photoswitching and Green-to-Red photoconversion properties differ between the A and B states. The chromophore in the A-state photoswitches more efficiently and is proposed to be more prone to photoconversion, while the B-state shows a higher level of photobleaching. Altogether, this data highlights the central role of conformational heterogeneity in fluorescent protein photochemistry.

Theoretical study to gain fundamental insight into reaction mechanism of N-S acyl transfer of N-sulfanylethylanilide-based protein labeling reagent on protein surface.

Elucidation of protein function is one of the central issues in the field of life sciences. To study the function of proteins not in isolation, but in a cell or its lysate, thus, it is necessary to selectively label the target protein in a mixture. Affinity labeling is one of several widely used methods for selective labeling; however, this method has the disadvantage that the labeling reagent is always activated, albeit weakly. Therefore, fine-tuning of the reactivity and/or reaction conditions is generally required for successful target-selective labeling. We previously developed a new affinity labeling reagent with N-sulfanylethylanilide (SEAlide) as a key reactive unit. It was designed based on the following hypotheses. SEAlide is less reactive and does not label in the absence of a target protein. Upon target binding, amino acid side-chain functional groups on the target surface convert SEAlide into a thioester form via N-S acyl transfer, allowing the target to be labeled. However, no evidence has been obtained so far to directly prove the hypothesis. In this study, we examine whether amino acid side-chain functional groups can activate SEAlide from the viewpoint of theoretical chemistry. The theoretical studies show that the activation free energy and enthalpy of the acyl transfer of SEAlide are reduced in the presence of methylammonium, which is a model for the protonated side chain of Lys, and acetate, which is a model for the deprotonated side chain of Asp/Glu. It suggests that Lys and Asp/Glu side chains could potentially stabilize the activation transition states to accelerate the thioester formation. Furthermore, the significant decrease in the activation enthalpy indicates that the contribution of entropy to the transition state is large. This result supports the original hypothesis that the SEAlide-based labeling reagent is efficiently activated by binding to the target protein.

Basis for Accurate Protein pKa Prediction with Machine Learning.

pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by pKa's. To accelerate pH-dependent molecular mechanism research in the life sciences or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pKa data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa, which was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it is revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proven an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery, and so on.

Molecular Anions Perspective.

This Perspective attempts to shed light on developments in the theoretical and experimental study of molecular anions highlighting more recent workers in the field. The species I discuss include (i) valence-bound (singly and multiply charged) anions including atmospheric, catalytic, superhalogen, interfacial, and more; (ii) dipole- and correlation-bound anions including their role as doorways to other states and their appearance "in space", and (iii) metastable anions focusing on tools needed for their theoretical treatment. I also briefly discuss angular distributions of photodetached electrons and their growing utilization in experiments and theory. A recurring theme is the dependence of electron binding energies (EBEs) on the surrounding environment. Some anions that are nonexistent as isolated species evolve to be stable but with small EBEs when weakly solvated (e.g., as in a cluster or at an air-solvent interface). Others existing in isolation only as metastable species become stable when the underlying molecular framework contains one or more positively charged group (e.g., protonated side chains in a peptide) that generates a stabilizing Coulomb potential. On the other hand, a destabilizing Coulomb potential between/among negative sites in a multiply charged anion decreases the EBEs of each such site and generates a repulsive Coulomb barrier that can affect stability.

Membrane composition drives sidechain ionization and assembly of transmembrane protein domains.

Ionization states of amino acid residues play significant roles in membrane protein assembly and function; however, they are difficult to decipher experimentally. The analysis is further complicated by the dearth of data on gradients in polarity, electric potentials, and hydration at the protein-membrane interface. Here we examine how electrostatic interactions, suggested to be essential for T-cell receptor (TCR) membrane assembly, could be manipulated by modifying the membrane composition. Novel pH-sensitive ionizable EPR labels were employed to profile heterogeneous dielectric environment along the transmembrane protein-lipid interfaces. Transmembrane α-helical WALP peptide was used for obtaining the profile of effective pK(a) as a function of membrane depth. It was found that effective pK(a) of membrane-buried sidechains can be significantly shifted by varying the membrane surface charge density. A peptide corresponding to the transmembrane domain of TCRα was labeled with pH-sensitive nitroxide and incorporated into liposomes. EPR of this label reported on the sidechain protonation state, membrane insertion, and association of the helices within the membrane. It was found that an increase in negative change density at the membrane surface alters the protonation state of membrane-buried ionizable sidechain in the transmembrane domain of TCRα. Hyperfine Correlation Spectroscopy (HYSCORE) was used to assess effects of sidechain ionization state on water penetration at membrane-peptide interface while Double Electron-Electron Resonance (DEER) quantified the domain agglomeration. Turning the charge of the sidechain “off” increases tendency of the transmembrane domain to agglomerate - a phenomenon that could be critical for the TCR assembly and its degradation. Overall, EPR of ionizable probes is informative for uncovering mechanisms as to how the changes in local environment along the protein-lipid interface, can result in a “tunable” pKa of the ionizable sidechains and drive the structural changes in membrane proteins.

Improvement of proton conductivity and efficiency of SPEEK-based composite membrane influenced by dual-sulfonated flexible comb-like polymers for vanadium flow battery

A sulfonated poly(ether ether ketone)-based composite membrane (S/SMA-SN) is developed by introducing dual-sulfonated flexible comb-like polymer (SMA-SN), varying from 0.1 to 1.5 wt%, which was prepared from the poly(styrene-co-maleic anhydride)-ethylenediamine through a main-/side-chain two-step sulfonation procedure. The S/SMA-SN composite membranes demonstrate ultrahigh proton conductivity and excellent cell performance at ultralow contents of SMA-SN polymers. Synergistic main-/side-chain proton channels formed by SPEEK and SMA-SN offer the highest proton conductivity (49.2 mS cm-1) and the lowest vanadium ion permeability (19.6 × 10-7 cm2 min-1) for S/SMA-SN-0.5, which is superior to SPEEK and Nafion membranes. Moreover, S/SMA-SN-0.5 displays its remarkable energy efficiency (72–81.3%) at 100–200 mA cm-2 current density, further illustrating the tradeoff effect of conductivity and resistance. Even at 150 mA cm-2 current density, stable coulombic efficiency (97%) and energy efficiency (80%) maintained after 500 charge-discharge cycles confirms the stable membrane structure and increased chemical stability, which originated from the main-/side-chain synergistic structure. This opens a promising method to explore the high-performance proton exchange membrane for vanadium flow battery application by the side-chain structuralized comb-like polymer at ultralow concentrations.

High and fast: NMR protein-proton side-chain assignments at 160 kHz and 1.2 GHz.

The NMR spectra of side-chain protons in proteins provide important information, not only about their structure and dynamics, but also about the mechanisms that regulate interactions between macromolecules. However, in the solid-state, these resonances are particularly difficult to resolve, even in relatively small proteins. We show that magic-angle-spinning (MAS) frequencies of 160 kHz, combined with a high magnetic field of 1200 MHz proton Larmor frequency, significantly improve their spectral resolution. We investigate in detail the gain for MAS frequencies between 110 and 160 kHz MAS for a model sample as well as for the hepatitis B viral capsid assembled from 120 core-protein (Cp) dimers. For both systems, we found a significantly improved spectral resolution of the side-chain region in the 1H-13C 2D spectra. The combination of 160 kHz MAS frequency with a magnetic field of 1200 MHz, allowed us to assign 61% of the aliphatic protons of Cp. The side-chain proton assignment opens up new possibilities for structural studies and further characterization of protein-protein or protein-nucleic acid interactions.

Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS

The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H–1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95–100 kHz MAS.

Acidic pH Promotes Refolding and Macroscopic Assembly of Amyloid β (16-22) Peptides at the Air-Water Interface.

Assembly by amyloid-beta (Aβ) peptides is vital for various neurodegenerative diseases. The process can be accelerated by hydrophobic interfaces such as the cell membrane interface and the air–water interface. Elucidating the assembly mechanism for Aβ peptides at hydrophobic interface requires knowledge of the microscopic structure of interfacial peptides. Here we combine scanning force microscopy, sum-frequency generation spectroscopy, and metadynamics simulations to probe the structure of the central fragment of Aβ peptides at the air–water interface. We find that the structure of interfacial peptides depends on pH: at neutral pH, the peptides adopt a less folded, bending motif by forming intra-hydrogen bonds; at acidic pH, the peptides refold into extended β-strand fibril conformation, which further promotes their macroscopic assembly. The conformational transition of interfacial peptides is driven by the reduced hydrogen bonds, both with water and within peptides, resulting from the protonation of acidic glutamic acid side chains.

Better force fields start with better data: A data set of cation dipeptide interactions

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.

Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.

The nucleocapsid (N) protein is one of the four structural proteins of the SARS-CoV-2 virus and plays a crucial role in viral genome organization and, hence, replication and pathogenicity. The N-terminal domain (NNTD) binds to the genomic RNA and thus comprises a potential target for inhibitor and vaccine development. We determined the atomic-resolution structure of crystalline NNTD by integrating solid-state magic angle spinning (MAS) NMR and X-ray diffraction. Our combined approach provides atomic details of protein packing interfaces as well as information about flexible regions as the N- and C-termini and the functionally important RNA binding, β-hairpin loop. In addition, ultrafast (100 kHz) MAS 1H-detected experiments permitted the assignment of side-chain proton chemical shifts not available by other means. The present structure offers guidance for designing therapeutic interventions against the SARS-CoV-2 infection.

Continuous Variation of Secondary Structural Contents of Interfacial Peptides Induced by Hydrogel Fusion.

Three-dimensional assemblies formed by multi-biopolymers perform important biological functions by maintaining the vital activities of living organisms through biochemical reactions that occur at the interfaces of these structures. In this study, we investigated the mechanism of the continuous variation of the secondary structural contents of interfacial peptides induced by the fusion of hydrogels with different charges. The hydrogel fusion induced continuous pH changes at the interface through ionic diffusion from the hydrogel matrices, and the pH value increased rapidly during the early stage (0-200 min) of the fusion process. In addition, the secondary structural content of the interfacial peptides changed continuously between the β-sheet and random coil conformations during the early stage of the fusion process. The continuous variation in the secondary structural contents of the interfacial peptides was caused by (1) the protonation of peptide molecule amino acid side-chains in the region of pH change and (2) charge shielding due to the electrostatic interactions between the intramolecular peptides, intermolecular peptides, and intramolecular and intermolecular peptides.

Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment.

Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.

Electrostatically induced pKa shifts in oligopeptides: the upshot of neighboring side chains

pKa values of homorepeat hexapeptides with a 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) chromophore attached at the peptide C termini, through an asparagine derivative (Dbo), namely His6-Dbo (H6), Lys6-Dbo (K6), and Arg6-Dbo (R6), were determined by a novel fluorescence-based method. The fluorescence lifetime of Dbo in the peptides (τ) was measured as a function of pH. The side chains collide with Dbo intramolecularly and quench it efficiently only when they are deprotonated (i.e., pH ≥ side chain pKa). The pKa values of the H6, K6, and R6 peptides, attributable to side chain ionization, were found to be depressed compared to the pKa values of the His, Lys, and Arg residues in their free amino acid forms. We further looked into the structural changes of the peptides by molecular dynamics (MD) simulations; the peptides were structurally more expanded when their side chains are protonated. The structural expansion of the peptides reflects an electrostatic repulsion between the protonated side chain residues, which also accounts for the observed decrease in pKa values, which corresponds to a facilitated deprotonation, assisted by electrostatic repulsion.

Enhanced proton conductivity of poly (arylene ether ketone sulfone) containing uneven sulfonic acid side chains by incorporating imidazole functionalized metal-organic framework

In this study, the side-chain type hybrid proton exchange membranes which based on metal-organic frameworks (MOFs) and organic matrix of sulfonated poly (arylene ether ketone sulfone) containing both long and short sulfonic acid side chains (S-C-SPAEKS) were prepared. MOF-801 was used as a template and then imidazole was encapsulated into MOF-801 as additional proton carriers. In imidazole -MOF-801, imidazole was used as a functional group to coordinate with the zirconium metal site of the functional group. Imidazole-MOF-801 and hybrid membranes were characterized by XRD, 1H NMR and FT-IR. These hybrid membranes exhibited excellent proton conductivities and good thermal stabilities. Compared to pure S-C-SPAEKS (0.0487 S cm−1 at 30 °C, 0.0809 S cm−1 at 80 °C), S-C-SPAEKS/0.5% Im-MOF-801 showed a great improvement (0.1205 S cm−1 at 30 °C, 0.1992 S cm−1 at 80 °C), which was about 2.5 times higher than that of pure S-C-SPAEKS and 2 times higher than that of commercial Nafion117 (0.1003 S cm−1 at 80 °C). The results indicated that imidazole functionalized MOFs and uneven side chain structure synergistically made an important contribution to proton transport. This series of hybrid membranes have the potential to be used as alternative proton exchange membranes.

Probing Adsorption of Dipeptides on Anatase in H2 O and D2 O: Thermodynamics and Molecular Geometry.

Considering the vast importance of peptide and protein interactions with inorganic surfaces, probing hydrogen bonding during their adsorption on metal oxide surfaces is a relevant task that could shed light on the essential features of their interplay. This work is devoted to studying the dipeptides' adsorption on anatase nanoparticles (ANs) in light and heavy water to reveal differences arising upon the change of the major hydrogen bonding carrier. Thermodynamic study of six native dipeptides' adsorption on ANs in both media shows a strong influence of the solvent on the Gibbs free energy and the effect of side-chain mobile protons on the entropy of the process. The adsorption is endothermic irrespective of the medium and is entropy-driven. Computer simulations of peptide adsorption in both media shows similarity in binding via an amino group and demonstrates structural features of protonated and deuterated peptides in obtained complexes. Calculated peptide- anatase nanoparticle (AN) descriptors indicate surface oxygens as points of peptide-nanoparticle contacts.