Conformational Changes Research Articles

Effect of supramolecular chirality on nano-protein/cell interaction: An experimental and computational investigation

Understanding the unique role of supramolecular chirality in nano-protein/cell interactions, as opposed to molecular chirality, is crucial for elucidating the origin of life. However, this aspect has received inadequate attention. In this study, L/D-glutamic acid-based amphiphiles (L/D-GluC16), which possess molecular chirality, were synthesized. Additionally, through the manipulation of solvent effects, left/right-handed helical nanofibers (M/P-GluC16), endowed with supramolecular chirality, were assembled from L/D-GluC16. With the aid of molecular dynamics (MD) simulations, the interaction between M/P-GluC16, L/D-GluC16, and a model protein (bovine serum albumin, BSA) was investigated at the thermodynamic and spatial orientational levels. Combined with the experimental result of protein adsorption efficiency, a more favorable chirality-dependent binding of M/P-GluC16 to protein compared to L/D-GluC16 was confirmed. Furthermore, driven by the binding-induced conformational changes and subsequent functional disruptions of proteins, M/P-GluC16 exhibited a greater chirality-specific cancer cell inhibitory efficacy compared to L/D-GluC16, highlighting the more significant impact of supramolecular chirality on nano-protein/cell interactions than molecular chirality.

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

Formation of whey protein, pectin, and chlorogenic acid ternary complexes and their application in emulsions

Physicochemical properties, stability, and digestive behavior of lycopene-loaded emulsions prepared by ternary complexes fabricated with different mixing sequences based on whey protein isolate (WPI), high methoxyl pectin (HMP), and chlorogenic acid (CA) were investigated. Spectroscopic and molecular docking analyses confirmed the non-covalent interactions among the compounds within the ternary complexes, as well as the conformational changes in the protein induced by the mixing sequence. The interfacial tension (6.92–9.44 mN/m) influenced by the different mixing sequences of WPI, HMP and CA was HMP-CA-WPI > WPI-CA-HMP > WPI-HMP-CA, and the size of emulsions stabilized by HMP-CA-WPI was approximately 10 nm larger than that of the other two. Complexes with mixing sequence of HMP, CA and WPI outperformed in antioxidant properties (Ferric reducing power absorbance 0.43, ABTS∙ radical scavenging activity 66.04 %), lycopene retention rate (after UV irradiation 85.11 %, after thermal treatment 83.15 %), and storage stability of emulsions than those prepared by WPI-HMP-CA and WPI-CA-HMP. Emulsions stabilized by different ternary complexes showed similar free fatty acid release profiles (39.62 %–41.59 %) and lycopene bio-accessibility (28.87 %–29.94 %) during digestion. This study mat offer novel insights for the rational utilization in emulsions of ternary complexes based on proteins, polysaccharides, and phenolic acids.

Octadentate Bispidine Chelators for Tb(III) Complexation: Pyridine Carboxylate versus Pyridine Phosphonate Donors.

With their rigid and preorganized skeleton, bispidine (3,7-diazabicyclo[3.3.1]nonane) chelators are very appealing for the preparation of metal complexes with high kinetic inertness. With the aim to develop new Tb(III)-based medical imaging probes, this study describes the synthesis and physicochemical properties of two novel terbium(III) complexes with octadentate bispidine-based ligands substituted with either pyridine-phosphonate (H6L1) or picolinate (H4L2) subunits. Thermodynamic stability constants of the corresponding Tb(III) complexes have been determined by potentiometric, UV-visible absorption spectrophotometric and spectrofluorimetric methods. Despite their apparent similarity, these two octadentate ligands differ in their most stable conformation: chair-chair conformation for H4L2 and boat-chair conformation for H6L1, as confirmed by 1H NMR studies and suggested by physicochemical investigations. This conformational change induces different protonation schemes for the two ligands. The kinetic inertness of the Tb complexes has been studied in various media and assessed by transmetalation and transchelation experiments. In particular, Tb(L2) displayed a remarkable kinetic inertness with no measurable dissociation over two months in mouse serum at 10-5 M concentration. The complex was also very inert in the presence of a 50-fold excess of Zn(II) in H2O at pH = 7.4 (7% of dissociation over two months). The complexes with ligand L1 are significantly less inert, emphasizing the influence of the ligand conformation on the kinetic inertness of the Ln(III) complexes. Finally, the luminescence properties of the isolated complexes have also been investigated. A bright green luminescence was observed, especially for Tb(L2), which displays a high quantum yield value of 50% in H2O (60% in D2O; λexc = 263 nm). In addition, luminescence lifetimes of 1.9(2) and 1.7(2) ms have been measured for Tb(L1) and Tb(L2), respectively, hence confirming the formation of nona-coordinated complexes with one inner-sphere water molecule. These data on a bispidine scaffold pave the way for developing bright, inert luminescent probes for bioimaging and for radiolabeling applications with Tb(III) radioisotopes.

Fluorescent Assay for the Determination of Enrofloxacin Using an Aptamer and SYBR Green I

Enrofloxacin (ENR) is commonly used to treat bacterial infections in animals and can pose a potential threat to human health with overuse. Therefore, the development of an accurate method for enrofloxacin is urgently needed. In this work, we have developed a method for enrofloxacin based on aptamer and SYBR Green I (SG-I). To our knowledge, this strategy is used for the first time for enrofloxacin. The enrofloxacin aptamer had a G-quadruplex structure, which can be identified and modified by SG-I to emit strong fluorescence. In the presence of the analyte, the aptamer preferentially bound causing a conformational change in the double-stranded portion of aptamer, which caused the SG-I fluorescence quenching. The fluorescence exhibited a consistent reduction in proportion to the concentrations of enrofloxacin from 1.95 to 400 nM. The limit of detection was 0.59 nM. Furthermore, the sensor was employed to determine enrofloxacin in food and serum with recovery rates ranging from 98.04% to 103.08%.

Fatty acid influence on zinc and uranyl ion binding to human serum albumin: an all atoms molecular dynamics investigation

The potential health risks associated with radionuclides, particularly actinides, have prompted investigations into their interactions with body fluids in living organisms. Human serum albumin (HSA), a plenteous plasma protein with extraordinary binding capacities, is a key player in these interactions. The present study is intended at understanding the interplay between metal ions, namely, zinc and uranyl ions and fatty acids binding with HSA, using all atom equilibrium and non-equilibrium molecular dynamics simulations. Results highlight distinct behaviours of zinc and uranyl ions, elucidating how their interactions with HSA are influenced by the presence of fatty acids. Hydrogen bonding dynamics analysis reveals the disruption of existing bonds due to fatty acid binding, contrasting with the weakening effect caused by metal binding. The resulting conformational changes have significant implications for HSA’s structure and dynamics. The potential of mean force (PMF) plots reveals binding and unbinding routes for zinc and uranyl ions, both in fatty acid’s presence and absence. Short-range interactions reveal distinct binding behaviours of zinc and uranyl ions, altered by fatty acids, providing insights into unbinding pathways and correlating with the PMF plots.

Recent advances in solid‐state nuclear magnetic resonance studies on membrane fusion proteins

Membrane fusion is an essential biological process that merges two separate lipid bilayers into a whole one. Membrane fusion proteins facilitate this process by bringing lipid bilayers in close proximity to reduce the repulsive energy between membranes. Along with their interactions with membranes, the structures and dynamics of membrane fusion proteins are key to elucidating the mechanisms of membrane fusion. Solid‐state NMR (SSNMR) spectroscopy has unique advantages in determining the structures and dynamics of membrane fusion proteins in their membrane‐bound states. It has been extensively applied to reveal conformational changes in intermediate states of viral membrane fusion proteins and to characterize the critical lipid–membrane interactions that drive the fusion process. In this review, we summarize recent advancements in SSNMR techniques for studying membrane fusion proteins and their applications in elucidating the mechanisms of membrane fusion.

Exploring the Potential of Biomimetic Peptides in Targeting Fibrillar and Filamentous Alpha-Synuclein-An In Silico and Experimental Approach to Parkinson's Disease.

Alpha-synuclein (ASyn) is a protein that is known to play a critical role in Parkinson's disease (PD) due to its propensity for misfolding and aggregation. Furthermore, this process leads to oxidative stress and the formation of free radicals that cause neuronal damage. In this study, we have utilized a biomimetic approach to design new peptides derived from marine natural resources. The peptides were designed using a peptide scrambling approach where antioxidant moieties were combined with fibrillary inhibition motifs in order to design peptides that would have a dual targeting effect on ASyn misfolding. Of the 20 designed peptides, 12 were selected for examining binding interactions through molecular docking and molecular dynamics approaches, which revealed that the peptides were binding to the pre-NAC and NAC (non-amyloid component) domain residues such as Tyr39, Asn65, Gly86, and Ala85, among others. Because ASyn filaments derived from Lewy body dementia (LBD) have a different secondary structure compared to pathogenic ASyn fibrils, both forms were tested computationally. Five of those peptides were utilized for laboratory validation based on those results. The binding interactions with fibrils were confirmed using surface plasmon resonance studies, where EQALMPWIWYWKDPNGS, PYYYWKDPNGS, and PYYYWKELAQM showed higher binding. Secondary structural analyses revealed their ability to induce conformational changes in ASyn fibrils. Additionally, PYYYWKDPNGS and PYYYWKELAQM also demonstrated antioxidant properties. This study provides insight into the binding interactions of varying forms of ASyn implicated in PD. The peptides may be further investigated for mitigating fibrillation at the cellular level and may have the potential to target ASyn.

Pathological Mutations D169G and P112H Electrostatically Aggravate the Amyloidogenicity of the Functional Domain of TDP-43.

Aggregation of TDP-43 is linked to the pathogenesis of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Notably, electrostatic point mutations such as D169G and P112H, located within the highly conserved functional tandem RNA recognition motif (RRM) domains of the TDP-43 protein (TDP-43tRRM), have been identified in diseased patients as well. In this study, we address how the electrostatic mutations alter both the native state stability and aggregation propensity of TDP-43tRRM. The mutants D169G and P112H show increased chemical stability compared to the TDP-43tRRM at physiological pH. However, at low pH, both the mutants undergo a conformational change to form amyloid-like fibrils, though with variable rates─the P112H mutant being substantially faster than the other two sequences (TDP-43tRRM and D169G mutant) showing comparable rates. Moreover, among the three sequences, only the P112H mutant undergoes a strong ionic strength-dependent aggregability trend. These observations signify the substantial contribution of the excess charge of the P112H mutant to its unique aggregation process. Complementary simulated observables with atomistic resolution assign the experimentally observed sequence-, pH-, and ionic strength-dependent aggregability pattern to the degree of thermal lability of the mutation site-containing RRM1 domain and its extent of dynamical anticorrelation with the RRM2 domain whose combination eventually dictate the extent of generation of aggregation-prone partially unfolded conformational ensembles. Our choice of a specific charge-modulated pathogenic mutation-based experiment-simulation-combination approach unravels the otherwise hidden residue-wise contribution to the individual steps of this extremely complicated multistep aggregation process.

L-Histidine Modulates the Catalytic Activity and Conformational Changes of the HD3 Deoxyribozyme.

Background/Objectives: Riboswitches are functional nucleic acids that regulate biological processes by interacting with small molecules, such as metabolites, influencing gene expression. Artificial functional nucleic acids, including deoxyribozymes, have been developed through in vitro selection for various catalytic functions. In a previous study, an l-histidine-dependent deoxyribozyme was identified, exhibiting RNA cleavage activity in the presence of l-histidine resembling ribonuclease catalytic mechanisms. This study aims to clarify the role of l-histidine in the activity and structural formation of the l-histidine-dependent deoxyribozyme (HD), focusing on the binding properties and conformational changes of its derivative HD3. Methods: Conformational changes in HD3 were analyzed using circular dichroism (CD) under varying concentrations of l-histidine. Direct binding analysis was conducted using carbon-14 (14C)-labeled l-histidine and a liquid scintillation counter. The catalytic activity of HD3 in the presence of different l-histidine concentrations was measured. Results: The binding constant for l-histidine-induced conformational changes (Ka(CD)) was found to be 2.0 × 103 (M-1), whereas for catalytic activity (Ka(Rxn)) and scintillation counting (Ka(RI)), it was approximately 1.0 × 103 (M-1). Conclusions: l-Histidine plays an essential role in both the catalytic activity and structural formation of the HD3 deoxyribozyme. The consistent binding constants across different experimental methods highlight the significant contribution of l-histidine to the active folding of deoxyribozymes.

The Glu86 Residue in TBX4 Proves Critical for Human Lung Development.

T-box transcription factors are a group of evolutionarily conserved T-box-containing regulators of mesoderm specification and development. Heterozygous single nucleotide variants (SNVs) or copy-number variant (CNV) deletions involving dosage-sensitive TBX4 have been associated with pulmonary arterial hypertension (PAH), ischiocoxopodopatellar syndrome with or without PAH, and lethal lung developmental disorders (LLDDs), including acinar dysplasia (AcDys), congenital alveolar dysplasia (CAD), and other unspecified primary pulmonary hypoplasias. Loss- and gain-of-function variants have been proposed to cause pediatric PAH and LLDDs, and adult forms of PAH, respectively. Of more than 50 missense SNVs scattered across the entire TBX4, only three have been reported in patients with LLDDs, all mapping to the T-box domain. Here, we report a recurrence of a pathogenic substitution Glu86Lys identified in an unrelated patient with AcDys. In silico predictions of the conformational changes of TBX4 resulting from this and another substitution, Glu86Gln, suggest the loss of most intermolecular hydrogen bonds involving residue 86, including those with Tyr230 that directly interact with DNA. Functional assays on the TBX4 variants in fetal lung fibroblasts confirmed their deleterious character. We propose that Glu86 is critically involved in maintaining TBX4 structure and function essential for airway branching during early stages of human lung development. Substitutions of this residue may act in a dominant negative manner, leading to AcDys and CAD.

Exploring the interaction of hesperetin-mediated green synthesised gold and silver nanoparticles with human serum albumin: A comparative analysis

This study focused on evaluating the potential of hesperetin-functionalized silver (H-AgNPs) and gold nanoparticles (H-AuNPs) for biomedical use, with a primary objective of understanding their relative binding affinity to human serum albumin (HSA). We evaluated the strength and possible binding mechanisms of the interaction between the nanoparticles and HSA based on analyses from fluorescence studies, UV–visible absorption, lifetime measurements and isothermal titration calorimetry (ITC). Circular dichroism analysis was employed to examine the conformational changes in HSA upon complexation with H-AgNPs and H-AuNPs. Furthermore, the thermodynamic parameters derived from ITC provided insights into the stabilising forces driving the endothermic binding processes. Consistently, the binding constants derived from spectroscopic and calorimetric investigations elucidated the superior binding efficiency of H-AuNPs compared to H-AgNPs with HSA. Antibacterial study revealed that H-AgNPs exhibited significant activity against S. aureus and E. coli, revealing promising antibacterial effects. Contrarily, H-AuNPs demonstrated no activity in the study. From the MTT assay results, we observed that H-AgNPs exhibited higher anticancer activity against human lung cancer cells compared to H-AuNPs, while H-AuNPs demonstrated lower cytotoxicity than H-AgNPs. Based on our research findings, both nanoparticles hold promise as potential candidates for diverse applications in the therapeutic field.

Computational Simulation and Biophysical Study on Cerium Chloride-Induced B-to-Z Transition in (CG) n DNA.

Rare earth elements have been shown to trigger the B-to-Z DNA transition in diverse self-assembled branched DNA architectures. Herein, we investigated the influence of cerium chloride on the conformational changes of DNA sequences containing repeated cytosine-guanine (CG)6-12 or guanine-cytosine (GC)6-12 sequences. The CD results show that (CG)6-12 repeats were susceptible to the formation of Z-DNA at low concentrations of CeCl3. On the other hand, (GC)6-12 is unable to undergo B-Z DNA transition and instead exhibits condensation with a similar amount of CeCl3. The CD signature was found to be different and unique in both alternate repeats during the interaction with CeCl3. The sequence-specific effects on the B-Z transition are based on the order of nucleotides in DNA. With the addition of EDTA, the Z-form of DNA is reverted to the native B-form. Further, we have reported the positive zeta potential of CeCl3-induced Z-DNA in contrast to the negative zeta potential of B-DNA. The differential zeta-potential value during the B-Z transition is complementary to the conformational changes of DNA. The molecular simulation study also supports the sequence-specific conformational change between the B- and Z-forms of DNA molecules. This newly described reversible topological and sequence-dependent transition is crucial for understanding the structural and biological roles of Z-DNA in response to CeCl3.

Water in peripheral TM-interfaces of Orai1-channels triggers pore opening

The activation of the Ca2+-channel Orai1 via the physiological activator stromal interaction molecule 1 (STIM1) requires structural rearrangements within the entire channel complex involving a series of gating checkpoints. Focusing on the gating mechanism operating along the peripheral transmembrane domain (TM) 3/TM4-interface, we report here that some charged substitutions close to the center of TM3 or TM4 lead to constitutively active Orai1 variants triggering nuclear factor of activated T-cell (NFAT) translocation into the nucleus. Molecular dynamics simulations unveil that this gain-of-function correlates with enhanced hydration at peripheral TM-interfaces, leading to increased local structural flexibility of the channel periphery and global conformational changes permitting pore opening. Our findings indicate that efficient dehydration of the peripheral TM-interfaces driven by the hydrophobic effect is critical for maintaining the closed state of Orai1. We conclude that a charge close to the center of TM3 or TM4 facilitates concomitant hydration and widening of peripheral TM interfaces to trigger constitutive Orai1 pore opening to a level comparable to or exceeding that of native activated Orai1.

Complexity associated with caprylate binding to bovine serum albumin: Dimerization, allostery, and variance between the change in free energy and enthalpy of binding.

Isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and pressure perturbation calorimetry (PPC) were used to study different aspects of the diverse interaction between the fatty acid caprylate and bovine serum albumin (BSA). The ITC thermogram was consistent with exothermic binding to a single site on BSA, which was electrostatic but had little or no hydrophobic contribution. ITC revealed that small changes to solution conditions and temperature were associated with apparent enthalpy-entropy compensation, causing large changes in enthalpy (ΔH) during binding, but with little corresponding changes in free energy (ΔG). ITC also detected a slower endothermic interaction at a low mole ratio. Dynamic light scattering suggested that this was due to dimerization or similar self-association. DSC demonstrated that further interactions took place at higher mole ratios. This was consistent with weak binding of caprylate to multiple binding sites which had a considerable impact on the structural conformation of BSA. PPC showed that the conformational change of BSA was accompanied with a reduction in surface hydrophobicity of the protein. PPC also demonstrated that in solution caprylate's hydrocarbon tail is hidden from water as no clathrate-like water is evident, which is consistent with the lack of hydrophobic contribution during binding. Cumulatively, the three calorimetric techniques offer a comprehensive view of caprylate and BSA interactions, highlighting the role of electrostatic interaction in binding accompanied by probably dimerization and considerable structural change associated with weaker binding to BSA.

RNA sample optimization for cryo-EM analysis.

RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs. A variety of methods and pipelines have been developed to facilitate cryo-EM structure determination of challenging RNA targets with small molecular weights at subnanometer to near-atomic resolutions. While a wide range of conditions have been used to prepare RNAs for cryo-EM analysis, correlations between the variables in these conditions and cryo-EM visualizations and reconstructions remain underexplored, which continue to hinder optimizations of RNA samples for high-resolution cryo-EM structure determination. Here we present a protocol that describes rigorous screenings and iterative optimizations of RNA preparation conditions that facilitate cryo-EM structure determination, supplemented by cryo-EM data processing pipelines that resolve RNA dynamics and conformational changes and RNA modeling algorithms that generate atomic coordinates based on moderate- to high-resolution cryo-EM density maps. The current protocol is designed for users with basic skills and experience in RNA biochemistry, cryo-EM and RNA modeling. The expected time to carry out this protocol may range from 3 days to more than 3 weeks, depending on the many variables described in the protocol. For particularly challenging RNA targets, this protocol could also serve as a starting point for further optimizations.

Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, , where is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo.

The Trajectory of Damaged-Base Eversion into the Active Site of Apurinic/Apyrimidinic Endonuclease APE1 Regulates This Enzyme's Substrate Specificity.

Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for the hydrolysis of the phosphodiester bond on the 5' side of an apurinic/apyrimidinic site during base excision repair. Moreover, in DNA, this enzyme can recognize nucleotides containing such damaged bases as 5,6-dihydro-2'-deoxyuridine (DHU), 2'-deoxyuridine (dU), alpha-2'-deoxyadenosine (αA), and 1,N6-ethenoadenosine (εA). Previously, by pulsed electron-electron double resonance spectroscopy and pre-steady-state kinetic analysis, we have revealed multistep DNA rearrangements during the formation of the catalytic complex. In the present study, the modeling of the eversion trajectory of nucleotides with various damaged bases was performed by directed molecular dynamics simulations. It was found that each damaged base at the beginning of the eversion interacts with protein loop Val196-Arg201, which should be moved to enable further nucleotide eversion. This movement involves a shift in loop Val196-Arg201 away from loop Asn253-Thr257 and requires the disruption of contacts between these loops. The Glu260Ala substitution facilitates the separation of the two loops. Moreover, conformational changes in the Asn253-Thr257 loop should occur in the second half of the lesion eversion trajectory. All these perturbations within the protein globule tend to reduce steric interactions of each damaged base with the protein during the eversion of the nucleotide from DNA and movement to the active site. These perturbations are important determinants of substrate specificity of endonuclease APE1.

Deep eutectic solvents assisted laccase pretreatment for improving enzymatic hydrolysis of corn stover.

The efficient and eco-friendly removal of lignin is a critical challenge for bioethanol production from lignocellulosic biomass. Herein, we report the integration of laccase with deep eutectic solvents (DESs) for the pretreatment of corn stover to enhance the production of reducing sugars. Three betaine-based DESs were prepared and tested for their effects on the activity and stability of a bacterial laccase from Bacillus amyloliquefaciens LC02. The aqueous solution of DESs showed no adverse influence on laccase activity, and the laccase thermostability was improved in the presence of DESs. More than 95% of the laccase activity was retained in the DESs solution during the first hour of incubation at 70°C. A red shift in the fluorescence spectra was observed for the laccase in the presence of DESs, indicating conformational changes. The laccase was able to degrade a dimeric lignin model compound by cleaving its β-O-4 bond. The transformation products were identified using LC-MS. The maximal lignin removal from corn stover was achieved by pretreatment using laccase in combination with the betaine-glycerol DES, which also resulted in a yield of fermentable sugar that was 130% higher than the control. This combination strategy provides guidance on the application of laccase and DESs in the pretreatment of lignocellulosic biomass.

R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

The recent progress in RNA structure determination methods has resulted in a surge of newly solved RNA 3D structures. However, there is an absence of a user-friendly browser-based tool that can facilitate the comparison and visualization of RNA motifs across multiple 3D structures. We introduce R3DMCS, a web server that allows users to compare selected RNA nucleotides across all 3D structures of a given molecule from a given species, or across all 3D structures mapped to a single Rfam family. Starting from one instance of the motif, R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures. With R3DMCS, one can explore conformational changes of motifs due to 3D structures being solved in different functional states or different experimental conditions. One can also investigate conservation of 3D structure across species, or changes in 3D structure due to changes in sequence. R3DMCS is open-source software and freely available at https://rna.bgsu.edu/correspondence/ and https://github.com/BGSU-RNA/RNA-3D-correspondence . Supplementary data are available at Bioinformatics online.