Salt Bridge Research Articles

Mechanistic basis of the dynamic response of TWIK1 ionic selectivity to pH

Highly selective for K+ at neutral pH, the TWIK1 channel becomes permeable to Na+ upon acidification. Using molecular dynamics simulations, we identify a network of residues involved in this unique property. Between the open and closed states previously observed by electron microscopy, molecular dynamics simulations show that the channel undergoes conformational changes between pH 7.5–6 involving residues His122, Glu235, Lys246 and Phe109. A complex network of interactions surrounding the selectivity filter at high pH transforms into a simple set of stronger interactions at low pH. In particular, His122 protonated by acidification moves away from Lys246 and engages in a salt bridge with Glu235. In addition, stacking interactions between Phe109 and His122, which stabilize the selectivity filter in its K+-selective state at high pH, disappear upon acidification. This leads to dissociation of the Phe109 aromatic side chain from this network, resulting in the Na+-permeable conformation of the channel.

Phosphorylation-Dependent Regulation of Guanylyl Cyclase (GC)-A and Other Membrane GC Receptors.

Receptor guanylyl cyclases (GCs) are single membrane spanning, multidomain enzymes, that synthesize cGMP in response to natriuretic peptides or other ligands. They are evolutionarily conserved from sea urchins to humans and regulate diverse physiologies. Most family members are phosphorylated on four to seven conserved serines or threonines at the beginning of their kinase homology domains. This review describes studies that demonstrate that phosphorylation and dephosphorylation are required for activation and inactivation of these enzymes, respectively. Phosphorylation sites in GC-A, GC-B, GC-E and sea urchin receptors are discussed as are mutant receptors that mimic the dephosphorylated, inactive or phosphorylated, active forms of GC-A and GC-B, respectively. A salt bridge model is described that explains why phosphorylation is required for enzyme activation. Potential kinases, phosphatases and ATP regulation of GC receptors are also discussed. Critically, knock-in mice with glutamate substitutions for receptor phosphorylation sites are described. The inability of opposing signaling pathways to inhibit cGMP synthesis in mice where GC-A or GC-B cannot be dephosphorylated demonstrates the necessity of receptor dephosphorylation in vivo. Cardiac hypertrophy, oocyte meiosis, long bone growth/achondroplasia, and bone density are regulated by GC phosphorylation, but additional processes are likely to be identified in the future.

Identification and characterization of a TLR4 homologue in Eriocheir sinensis based on structure analysis

Toll-like receptor 4 (TLR4) plays an essential role in the activation of innate immunity by recognizing diverse pathogenic components of bacteria. Six Tolls were found in Eriocheir sinensis but have not yet been identified as mammalian TLR4 homolog. For this purpose, we predicted three-dimensional (3D) structures of EsTolls (EsToll1-6) with AlphaFold2. 3D structure of LRRs and TIR most had high accuracy (pLDDT >70). By structure analysis, 3D structures of EsToll6 had a high overlap with HsTLR4. Moreover, we also predicted potential 11 hydrogen bonds and 3 salt bridges in the 3D structure of EsToll6-EsML1 complex. 18 hydrogen bonds and 7 salt bridges were predicted in EsToll6-EsML2 complex. Co-immunoprecipitation assay showed that EsToll6 could interact with EsML1 and EsML2, respectively. Importantly, TAK242 (a mammalian TLR4-specific inhibitor) could inhibit the generation of ROS stimulated by lipopolysaccharides (LPS) in EsToll6-EsML2-overexpression Hela cells. Collectively, these results implied that EsToll6 was a mammalian TLR4 homolog and provided a new insight for researching mammalian homologs in invertebrates.

Effects of wind shear and thrust coefficient on the induction zone of a porous disk: A wind tunnel study

AbstractNeglecting the velocity reduction in the induction zone of wind turbines can lead to overestimates of power production predictions, and, thus, of the annual energy production for a wind farm. An experimental study on the induction zone associated with wind turbine operations is performed in the boundary‐layer test section of the BLAST wind tunnel at UT Dallas using stereo particle image velocimetry. This experiment provides a detailed quantification of the wind speed decrease associated with the induction zone for two different incoming flows, namely, uniform flow and boundary layer flow. Operations of wind turbines in different regions of the power curve are modeled in the wind tunnel environment with two porous disks with a solidity of 50.4% and 32.3%, which correspond to thrust coefficients of 0.71 and 0.63, respectively. The porous disks are designed to approximate the wake velocity profiles previously measured for utility‐scale wind turbines through scanning wind LiDARs. The results show that the streamwise velocity at one rotor diameter upwind of both disks decreases 1% more for the boundary layer flow than for the uniform flow. Further, the effect of shear in front of the disk with a higher thrust coefficient can be observed until 1.75 rotor diameter upwind of the disk, whereas for the disk with a lower thrust coefficient, the effect of shear becomes negligible at 1.25 rotor diameter upwind. It is found that at one rotor diameter upwind, for both incoming flows, the disk having a higher thrust coefficient has 2% more velocity reduction than the lower‐thrust‐coefficient disk. The results suggest that the variability in wind shear and rotor thrust coefficient, which is encountered during typical operations of wind turbines, should be considered for the development of improved models for predictions of the rotor induction zone, the respective cumulative effects in the presence of multiple turbines, namely, wind farm blockage, and more accurate predictions of wind farm power capture.

Genome-wide characterization of the NBLRR gene family provides evolutionary and functional insights into blast resistance in pearl millet (Cenchrusamericanus (L.) Morrone).

The investigation is the first report on genome-wide identification and characterization of NBLRR genes in pearl millet. We have shown the role of gene loss and purifying selection in the divergence of NBLRRs in Poaceae lineage and candidate CaNBLRR genes for resistance to Magnaporthe grisea infection. Plants have evolved multiple integral mechanisms to counteract the pathogens' infection, among which plant immunity through NBLRR (nucleotide-binding site, leucine-rich repeat) genes is at the forefront. The genome-wide mining in pearl millet (Cenchrus americanus (L.) Morrone) revealed 146 CaNBLRRs. The variation in the branch length of NBLRRs showed the dynamic nature of NBLRRs in response to evolving pathogen races. The orthology of NBLRRs showed a predominance of many-to-one orthologs, indicating the divergence of NBLRRs in the pearl millet lineage mainly through gene loss events followed by gene gain through single-copy duplications. Further, the purifying selection (Ka/Ks < 1) shaped the expansion of NBLRRs within the lineage of pear millet and other members of Poaceae. Presence of cis-acting elements, viz. TCA element, G-box, MYB, SARE, ABRE and conserved motifs annotated with P-loop, kinase 2, RNBS-A, RNBS-D, GLPL, MHD, Rx-CC and LRR suggests their putative role in disease resistance and stress regulation. The qRT-PCR analysis in pearl millet lines showing contrasting responses to Magnaporthe grisea infection identified CaNBLRR20, CaNBLRR33, CaNBLRR46 CaNBLRR51, CaNBLRR78 and CaNBLRR146 as putative candidates. Molecular docking showed the involvement of three and two amino acid residues of LRR domains forming hydrogen bonds (histidine, arginine and threonine) and salt bridges (arginine and lysine) with effectors. Whereas 14 and 20 amino acid residues of CaNBLRR78 and CaNBLRR20 showed hydrophobic interactions with 11 and 9 amino acid residues of effectors, Mg.00g064570.m01 and Mg.00g006570.m01, respectively. The present investigation gives a comprehensive overview of CaNBLRRs and paves the foundation for their utility in pearl millet resistance breeding through understanding of host-pathogen interactions.

Chemoinformatic study on phytochemicals from Melissa officinalis for ligand based drug design inhibition of aflatoxins synthesis

This study involved extracting 2D structures of fifty-one (51) GC-MS chromatogram-generated compounds from PubChem a free depository database for generating a library of compounds and obtaining the 3D structure of polyketide synthase A, an enzyme recognized for the biosynthesis of aflatoxin in Aspergillus species, from the protein data bank. In silico (molecular docking was performed to assess the interactions of the phytochemicals in the sample and were screened for their inhibitory potential, having higher binding energy, and favorable pharmacokinetics profiles. The docking analysis outcome indicates that nine (9) compounds exhibited binding energies ranging from −11.314 to −8.365 kcal/mol which is higher than the control (PLM) with a binding energy of −8.131 kcal/mol. It is observed that many of the compounds interacted with the target using hydrophobic interaction and only a few added hydrogen bonds and salt bridges. This research has shown a potential of the aerial part of Melissa officinalis vegetable for drug development to inhibit the synthesis of aflatoxins from Aspergillus flavus. The study has showcased good scientific information for the development of natural products for the prevention and treatment of aflatoxin contamination in agricultural products.

Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking.

Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) has emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme active-site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.

Kinase Inhibition via Small Molecule‐Induced Intramolecular Protein Cross‐Linking

Remarkable progress has been made in the development of cysteine‐targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) has emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K‐E/D salt bridge within the enzyme active‐site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D‐targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide‐based small‐molecule inhibitors capable of inducing intramolecular cross‐linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide‐facilitated, ligand‐induced mechanism leading to intramolecular kinase cross‐linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.

Balancing the Affinity and Tumor Cell Binding of a Two-in-One Antibody Simultaneously Targeting EGFR and PD-L1

The optimization of the affinity of monoclonal antibodies is crucial for the development of drug candidates, as it can impact the efficacy of the drug and, thus, the dose and dosing regimen, limit adverse effects, and reduce therapy costs. Here, we present the affinity maturation of an EGFR×PD-L1 Two-in-One antibody for EGFR binding utilizing site-directed mutagenesis and yeast surface display. The isolated antibody variants target EGFR with a 60-fold-improved affinity due to the replacement of a single amino acid in the CDR3 region of the light chain. The binding properties of the Two-in-One variants were confirmed using various methods, including BLI measurements, real-time antigen binding measurements on surfaces with a mixture of both recombinant proteins and cellular binding experiments using flow cytometry as well as real-time interaction cytometry. An AlphaFold-based model predicted that the amino acid exchange of tyrosine to glutamic acid enables the formation of a salt bridge to an arginine at EGFR position 165. This easily adaptable approach provides a strategy for the affinity maturation of bispecific antibodies with respect to the binding of one of the two antigens.

Recovery of metallic lead from End-Of-Life silicon solar modules using salt bridge electrowinning

Toxic lead (Pb) in end-of-life silicon solar modules must be recovered to keep it out of the environment. Present literature on Pb recovery from solar waste is sparse and uses chemicals like nitric or hydrochloric acid. Previously, the authors reported Pb recovery from silicon modules by leaching and electrowinning in acetic acid. However, the Pb recovered from acetic solution contained a small amount of metallic Pb with the rest being lead oxides/acetates. These Pb compounds require further processing to obtain metallic Pb for reuse in solar panel solder, leading to additional cost and chemical waste. This paper reports recovery of metallic Pb using an electrochemical system with two half cells connected through a salt bridge. The salt bridge enables optimized recovery rates of Pb as high as 99.99 % for synthetic leachates. The first experiment to recover Pb from real silicon module waste shows 80 % recovery without optimization. The new method offers a low-cost, closed-loop, direct pathway to metallic Pb recovery from end-of-life silicon solar modules for reuse in new modules.

Role of Histidine 310 in Amydetes vivianii firefly luciferase pH and metal sensitivities and improvement of its color tuning properties.

Firefly luciferases emit yellow-green light and are pH-sensitive, changing the bioluminescence color to red in the presence of heavy metals, acidic pH and high temperatures. These pH and metal-sensitivities have been recently harnessed for intracellular pH indication and toxic metal biosensing. However, whereas the structure of the pH sensor and the metal binding site, which consists mainly of two salt bridges that close the active site (E311/R337 and H310/E354), has been identified, the specific role of residue H310 in pH and metal sensing is still under debate. The Amydetes vivianii firefly luciferase has one of the lowest pH sensitivities among the group of pH-sensitive firefly luciferases, displaying high bioluminescent activity and special spectral selectivity for cadmium and mercury, which makes it a promising analytical reagent. Using site-directed mutagenesis, we have investigated in detail the role of residue H310 on pH and metal sensitivity in this luciferase. Negatively charged residues at position 310 increase the pH sensitivity and metal sensitivity; H310G considerably increases the size of the cavity, severely impacting the activity, H310R closes the cavity, and H310F considerably decreases both pH and metal sensitivities. However, no substitution completely abolished pH and metal sensitivities. The results indicate that the presence of negatively charged and basic side chains at position 310 is important for pH sensitivity and metals coordination, but not essential, indicating that the remaining side chains of E311 and E354 may still coordinate some metals in this site. Furthermore, a metal binding site search predicted that H310 mutations decrease the affinity mainly for Zn, Ni and Hg but less for Cd, and revealed the possible existence of additional binding sites for Zn, Ni and Hg.

Elucidating Daptomycin's Antibacterial Efficacy: Insights into the Tripartite Complex with Lipid II and Phospholipids in Bacterial Septum Membrane.

This study elucidated the mechanism of formation of a tripartite complex containing daptomycin (Dap), lipid II, and phospholipid phosphatidylglycerol in the bacterial septum membrane, which was previously reported as the cause of the antibacterial action of Dap against gram-positive bacteria via molecular dynamics and enhanced sampling methods. Others have suggested that this transient complex ushers in the inhibition of cell wall synthesis by obstructing the downstream polymerization and cross-linking processes involving lipid II, which is absent in the presence of cardiolipin lipid in the membrane. In this work, we observed that the complex was stabilized by Ca2+-mediated electrostatic interactions between Dap and lipid head groups, hydrophobic interaction, hydrogen bonds, and salt bridges between the lipopeptide and lipids and was associated with Dap concentration-dependent membrane depolarization, thinning of the bilayer, and increased lipid tail disorder. Residues Orn6 and Kyn13, along with the DXDG motif, made simultaneous contact with constituent lipids, hence playing a crucial role in the formation of the complex. Incorporating cardiolipin into the membrane model led to its competitively displacing lipid II away from the Dap, reducing the lifetime of the complex and the nonexistence of lipid tail disorder and membrane depolarization. No evidence of water permeation inside the membrane hydrophobic interior was noted in all of the systems studied. Additionally, it was shown that using hydrophobic contacts between Dap and lipids as collective variables for enhanced sampling gave rise to a free energy barrier for the translocation of the lipopeptide. A better understanding of Dap's antibacterial mechanism, as studied through this work, will help develop lipopeptide-based antibiotics for rising Dap-resistant bacteria.

Screening and construction of nanobodies against human CD93 using phage libraries and study of their antiangiogenic effects

BackgroundCluster of Differentiation 93 (CD93) plays an important role in angiogenesis and is considered an important target for inhibiting tumor angiogenesis, but there are currently no therapeutic antibodies against CD93 in the clinic. Thus, we describe the screening of novel nanobodies (Nbs) targeting human CD93 from a phage library of shark-derived Nbs.MethodsScreening and enrichment of phage libraries by enzyme-linked immunosorbent assay (ELISA). Anti-CD93 Nbs were purified by expression in E. coli. The binding affinity of anti-CD93 Nbs NC81/NC89 for CD93 was examined by flow cytometry (FC) and ELISA. The thermal stability of NC81/NC89 was examined by ELISA and CD spectroscopy. Afterward, the anti-angiogenic ability of NC81/NC89 was examined by MTT, wound healing assay, and tube formation assay. The expression level of VE-cadherin (VE-Ca) and CD93 was detected by Western Blot (WB). The binding sites and binding forms of NC81/NC89 to CD93 were analyzed by molecular docking.ResultsThe anti-CD93 Nbs were screened in a phage library, expressed in E. coli, and purified to &amp;gt;95% purity. The results of FC and ELISA showed that NC81/NC89 have binding ability to human umbilical vein endothelial cells (HUVECs). The results of ELISA and CD spectroscopy showed that NC81/NC89 retained the ability to bind CD93 at 80°C and that the secondary structure remained stable. In vitro, the results showed that NC81 and NC89 significantly inhibited the proliferation and migration of human umbilical vein endothelial cells (HUVECs) as well as tube formation on Matrigel. Western Blot showed that NC81 and NC89 also inhibited the expression of VE-Ca thereby increasing vascular permeability. It was found during molecular docking that the CDR regions of NC81 and NC89 could be attached to CD93 by strong hydrogen bonds and salt bridges, and the binding sites were different.ConclusionWe have successfully isolated NC81 and NC89, which bind CD93, and both Nbs significantly inhibit angiogenesis and increase vascular permeability. These results suggest that NC81 and NC89 have potential clinical applications in angiogenesis-related therapies.

Molecular spectra and docking simulations investigated the binding mechanisms of tetracycline onto E. coli extracellular polymeric substances

Extracellular polymeric substances (EPS), which were an important fraction of natural organic matter (NOM), played an important role in various environmental processes. However, the heterogeneity, complexity, and dynamics of EPS make their interactions with antibiotics elusive. Using advanced multispectral technology, this study examined how EPS interacts with different concentrations of tetracycline (TC) in the soil system. Our results demonstrated that protein-like (C1), fulvic-like (C2), and humic-like (C3) fractions were identified from EPS. Two-dimensional synchronous correlation spectroscopy (2D-SF-COS) indicated that the protein-like fraction gave faster responses than the fulvic-like fraction during the TC binding process. The sequence of structural changes in EPS due to TC binding was revealed by two-dimensional Fourier Transformation Infrared correlation spectroscopy (2D-FTIR-COS) as follows: 1550 > 1660 > 1395 > 1240 > 1087 cm−1. It is noteworthy that the sensitivity of the amide group to TC has been preserved, with its intensity gradually increasing to become the primary binding site for TC. The integration of hetero-2DCOS maps with moving window 2D correlation spectroscopy (MW2DCOS) provided a unique insight into understanding the correlation between EPS fractions and functional groups during the TC binding process. Moreover, molecular docking (MD) discovered that the extracellular proteins would provide plenty of binding sites with TC through salt bridges, hydrogen bonds, and π-π base-stacking forces. With these results, systematic investigations of the dynamic changes in EPS components under different concentrations of antibiotic exposure demonstrated the advanced capabilities of multispectral technology in examining intricate interactions with EPS in the soil environment.

Synthesis and application of anthraquinone quaternary phosphonium salt electroplating copper leveler based on expanded electrostatic adsorption area strategy and physicochemical salt bridge mechanism

Four anthraquinone quaternary phosphate molecules (AQS-a, AQS-b, AQS-c, AQS-d) with different electrostatic adsorption areas were constructed as electroplating levelers based on the strategy of expanding the electrostatic adsorption area of the molecules. AQS-d with the largest electrostatic adsorption area was demonstrated to have the most excellent electrochemical performance by electrochemical tests. The physicochemical adsorption sites and interactions with copper ions of AQS levelers were proposed by theoretical calculations, molecular dynamics simulations, Raman spectroscopy and fluorescence absorption spectroscopy, and the electroplating salt bridge mechanism was proposed. Based on optical microscope, scanning electron microscope, atomic force microscope and X-ray diffractometer, it is proved that AQS-d has the ability to perfectly fill the microvia in actual plating by actual PCB blind hole filling experiment.

Preparation and drug release performance of different gelation type polysaccharide/β-lactoglobulin fiber composite gels

Self-assembled protein fibers have attracted much attention in the fields of medicine and food because of their high aspect ratio, polymorphic structure and strong surface hydrophobicity. In this study, three different gelation types of polysaccharides/β-lactoglobulin fiber (Fblg) composite gels, including ionic alginate-Fblg gels, synergistic xanthan-Fblg gels, and double network agar-Fblg gels, were first prepared. The interactions between the polysaccharides and the Fblgs, the microstructure and mechanical properties of the composite gels were investigated using the light scattering, scanning electron microscopy, rheology and texture analysis in order to reveal their formation mechanisms. Then the loading and release properties of the water-soluble drug 5-fluorouracil (5-FU) and the hydrophobic drug curcumin (Cur) through these composite gels were further studied with release mechanisms determined by fitting different release models. It was found that the mechanical properties of the composite gels were determined by the mesh density of the three-dimensional networks formed inside the gels. The network structure and mechanical strength of the alginate-Fblg gels became weaker with the increase of Fblg content at pH 4 due to their attractive interaction which hindered the binding of Ca2+ to ALG, while the network and the strength of the alginate-Fblg gels didn't change much at pH 7 due to the repulsion between Alg and Fblg. The xanthan-Fblg gels formed lamellar structures with enhanced gel network and mechanical strength due to the hydrogen bonding and the electrostatic interaction with Fblg. The Agar-Fblg composite gel formed at 60 °C (above the gelation temperature of agar of 40 °C) had a denser double network structure and higher mechanical strength than that formed at 0 °C due to inhibition of diffusion of Ca2+ as salt bridges for Fblg. The hydrophilic drugs were loaded in the meshes of the composite gels and their release was determined by the structure of the composite gel networks, whereas the hydrophobic drugs were loaded by attaching to the Fblgs in the composite gels and their release was determined by the loading ability and strength of the gels. The study not only provided a new idea for the preparation and application of polysaccharide-protein fiber composite hydrogels, but also provided insights for improving the efficiency of drug carriers.

Wastewater remediation and bioelectricity generation in dual chambered salt bridge microbial fuel cell: A mini‐review

AbstractThe purpose of this article is to assess the feasibility analysis of microbial fuel cells (MFCs), particularly in the configuration of dual chamber salt bridge microbial fuel cell (DCSB‐MFC), as a promising approach for simultaneous bioelectricity generation and wastewater remediation. The application of a salt bridge presents an economically viable alternative to the use of a proton exchange membrane, which is known for its high cost, in the construction of MFCs. This arrangement has been demonstrated to offer significant benefits in terms of enhancing the performance of new elements and evaluating operational parameters. However, it also encounters issues related to the total internal resistance (Rint) of the MFCs as well as power density (P). In addition, it has been found that traditional packing materials such activated carbon and gravel demonstrate poor permeability, internal resistance, and slow biofilm growth. Furthermore, there is a necessity to search for electrodes that possess high resistance to corrosion and are cost‐effective to achieve optimal bioelectricity generation. Therefore, this article aims to emphasize the research areas that require attention. By addressing these areas, the actual implementation of this configuration can be brought closer to practical implementation.

Thermodynamics of a hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9

Hyperthermostable enzymes are highly desirable biocatalysts due to their exceptional stability at extreme temperatures. Recently, a hyperthermostable carboxylesterase EstD9 from Anoxybacillus geothermalis D9 was biochemically characterized. The enzyme exhibited remarkable stability at high temperature. In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new β-sheets at 80 °C, making the core of the hydrolase fold more stable. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, which resided at the interface between the large and cap domains. To further investigate the structural adaptation in extreme conditions, the intramolecular interactions of the native structure were investigated. EstD9 revealed 18 hydrogen bond networks, 7 salt bridges, and 9 hydrophobic clusters, which is higher than the previously reported thermostable Est30. Collectively, the analysis indicates that intramolecular interactions and structural dynamics play distinct roles in preserving the overall EstD9 structure at elevated temperatures. This work is relevant to both fundamental and applied research involving protein engineering of industrial thermostable enzymes.

NMR Structure of Retinal Guanylate Cyclase Activating Protein 5 (GCAP5) with R22A Mutation That Abolishes Dimerization and Enhances Cyclase Activation.

Guanylate cyclase activating protein-5 (GCAP5) in zebrafish photoreceptors promotes the activation of membrane receptor retinal guanylate cyclase (GC-E). Previously, we showed the R22A mutation in GCAP5 (GCAP5R22A) abolishes dimerization of GCAP5 and activates GC-E by more than 3-fold compared to that of wild-type GCAP5 (GCAP5WT). Here, we present ITC, NMR, and functional analysis of GCAP5R22A to understand how R22A causes a decreased dimerization affinity and increased cyclase activation. ITC experiments reveal GCAP5R22A binds a total of 3 Ca2+, including two sites in the nanomolar range followed by a single micromolar site. The two nanomolar sites in GCAP5WT were not detected by ITC, suggesting that R22A may affect the binding of Ca2+ to these sites. The NMR-derived structure of GCAP5R22A is overall similar to that of GCAP5WT (RMSD = 2.3 Å), except for local differences near R22A (Q19, W20, Y21, and K23) and an altered orientation of the C-terminal helix near the N-terminal myristate. GCAP5R22A lacks an intermolecular salt bridge between R22 and D71 that may explain the weakened dimerization. We present a structural model of GCAP5 bound to GC-E in which the R22 side-chain contacts exposed hydrophobic residues in GC-E. Cyclase assays suggest that GC-E binds to GCAP5R22A with ∼25% higher affinity compared to GCAP5WT, consistent with more favorable hydrophobic contact by R22A that may help explain the increased cyclase activation.

Structural Basis of Conformational Dynamics in the PROTAC-Induced Protein Degradation.

Pronounced conformational dynamics is unveiled upon analyzing multiple crystal structures of the same proteins recruited to the same E3 ligases by PROTACs, and yet, is largely permissive for targeted protein degradation due to the intrinsic mobility of E3 assemblies creating a large ubiquitylation zone. Mathematical modelling of ternary dynamics on ubiquitylation probability confirms the experimental finding that ternary complex rigidification need not correlate with enhanced protein degradation. Salt bridges are found to prevail in the PROTAC-induced ternary complexes, and may contribute to a positive cooperativity and prolonged half-life. The analysis highlights the importance of presenting lysines close to the active site of the E2 enzyme while constraining ternary dynamics in PROTAC design to achieve high degradation efficiency.