Structure of Monomeric Transthyretin Carrying the Clinically Important T119M Mutation

Mutations in the protein transthyretin can cause as well as protect individuals from transthyretin amyloidosis, an incurable fatal inherited disease. Little is known, however, about the structural basis of pathogenic and clinically protective transthyretin mutants. Here we determined the solution structure of a transthyretin monomer that carries the clinically important T119M mutation. The structure displays a non‐native arrangement that is distinct from all known structures of transthyretin and highlights the importance of high‐resolution studies in solution for understanding molecular processes that lead to amyloid diseases.     

A Dimeric Bis(melamine)‐Substituted Bispidine for Efficient Transmembrane H+/Cl− Cotransport

A 3,7‐diazabicyclo[3.3.1]nonane linking to two melamines is a unique transmembrane H⁺/Cl⁻ carrier. In the solid state, the V‐shaped compound forms a HCl‐bound zig‐zag network through cooperative protonation and hydrogen bond interactions. In the lipid membrane, the receptor forms a dimeric self‐assembly involving multiple H⁺ and Cl⁻ leading to the efficient transport of the acid. The pH‐dependent Cl⁻ efflux observed for the compound was rationalized based on a gradual protonation model that confers an active transmembrane carrier at physiological pH.     

Chemically Triggered C–ON Bond Homolysis in Alkoxyamines. Part 2: DFT Investigation and Application of the pH Effect on NMP

In recent work, a 15‐fold increase in the C–ON bond homolysis rate constant k_d of 4‐pyridylethyl‐SG1‐based alkoxyamine was observed upon protonation of the pyridyl moiety in organic solvent. In this report, the pH dependence of k_d (pK_a = 4.7) is investigated in D₂O/CD₃OD (v/v 1:1). A 64‐fold increase in k_d is observed at acidic pH. Calculations show that the increase in k_d upon protonation is due to both an increase in the stabilization of the protonated 4‐pyridylethyl radical and an increase of the destabilization of the starting materials through an increase in the polarity of the alkyl fragment. This new alkoxyamine is applied to NMP of styrene and sodium styrene sulfonate.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Polyacrylamide gel electrophoresis followed by sodium dodecyl sulfate gradient polyacrylamide gel electrophoresis for the study of the dimer to monomer transition of human transthyretin

Familial amyloidotic polyneuropathy (FAP) is caused by mutations which destabilize transthyretin (TTR) and facilitate the aggregation into extracellular amyloid fibrils preferentially in peripheral nerve and heart tissues. Therapeutic and preventive trials for FAP at the plasma TTR level require a careful study of the destabilization of TTR under variable conditions. We have developed a simple double one-dimensional (D1-D) electrophoretic procedure with polyacrylamide gel electrophoresis (PAGE) followed by sodium dodecylsulfate (SDS) gradient PAGE to study the dimer to monomer transition. TTR is first isolated by PAGE from other plasma proteins. The gel strip containing the TTR fraction is incubated in 2% SDS under varying conditions of temperature, buffer composition, pH, and additives like urea and/or a sulfhydryl-reactive agent, followed by SDS-gradient PAGE for the separation of TTR dimers and monomers. We demonstrate that an unidirectional dimer to monomer transition of normal TTR is achieved at 70-80 degrees C in neutral to mild alkaline buffers or at 37 degrees C and slightly acidic pH (6-7). Addition of urea favors the transition into monomers. Amyloidogenic mutations like amyloidogenic TTR (ATTR)-V30M or ATTR-I107V favor the transition into monomers in buffer systems close to the physiological pH of human plasma. We conclude that this finding has to be considered by any hypothesis on ATTR-derived amyloidogenesis.     

Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses

It is well established that the formation of transthyretin (TTR) amyloid fibrils is linked to the destabilization and dissociation of its tetrameric structure into insoluble aggregates. Isotope labeling is used for the study of TTR by NMR, neutron diffraction, and mass spectrometry (MS). Here MS, thioflavin T fluorescence, and crystallographic data demonstrate that while the X‐ray structures of unlabeled and deuterium‐labeled TTR are essentially identical, subunit exchange kinetics and amyloid formation are accelerated for the deuterated protein. However, a slower subunit exchange is noted in deuterated solvent, reflecting the poorer solubility of non‐polar protein side chains in such an environment. These observations are important for the interpretation of kinetic studies involving deuteration. The destabilizing effects of TTR deuteration are rather similar in character to those observed for aggressive mutations of TTR such as L55P (associated with familial amyloid polyneuropathy).     

An Ethylenediamine‐based Switch to Render the Polyzwitterion Cationic at Tumorous pH for Effective Tumor Accumulation of Coated Nanomaterials

Polyzwitterions are employed as coating polymers for biomaterials to induce an antifouling property on the surface. Fine‐tuning the betaine structure switches the antifouling property to be interactive with anionic tissue constituents in response to a tumorous pH gradient. The ethylenediamine moiety in the carboxybetaine enabled stepwise protonation and initiated the di‐protonation process around tumorous pH (6.5). The net charge of the developed polyzwitterion (PGlu(DET‐Car)) was thus neutral at pH 7.4 for antifouling, but was cationic at pH 6.5 for interaction with anionic constituents. Quantum dots coated with PGlu(DET‐Car) exhibited comparable stealth and enhanced tumor accumulation relative to the PEG system. The present study provides a novel design of smart switchable polyzwitterion based on a precise control of the net charge.     

Chromatographic Framework to Determine the Memantine Binding Mechanism on Human Serum Albumin Surface

In this work, the interaction of memantine with human serum albumin (HSA) immobilized on porous silica particles was studied using a biochromatographic approach. The determination of the enthalpy change at different pH values suggested that the protonated group in the memantine–HSA complex exhibits a heat protonation with a magnitude around 65 kJ mol^?1. This value agrees with the protonation of a guanidinium group, and confirmed that an arginine group may become protonated in the memantine–HSA complex formation. The thermodynamic data showed that memantine–HSA binding, for low temperature (<293 K), is dominated by a positive entropy change. This result suggests that dehydration at the binding interface and charge–charge interactions contribute to the memantine–HSA complex formation. Above 293 K, the thermodynamic data ΔH and ΔS became negative due to van der Waals interactions and hydrogen bonding which are engaged at the complex interface. The temperature dependence of the free energy of binding is weak because of the enthalpy–entropy compensation caused by a large heat capacity change, ΔC _p = ? 3.79 kJ mol^?1 K^?1 at pH = 7. These results were used to determine the potential binding site of this drug on HSA.     

A comparative study between para‐aminophenyl and ortho‐aminophenyl benzothiazoles using NMR and DFT calculations

Ortho‐substituted and para‐substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho‐substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho‐substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o‐aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the ¹H, ¹³C and ¹⁵N NMR chemical shifts and density functional theory calculated structures of the compounds are described. Copyright © 2014 John Wiley & Sons, Ltd.     

Femtosecond Hydrogen Bond Dynamics of Bulk‐like and Bound Water at Positively and Negatively Charged Lipid Interfaces Revealed by 2D HD‐VSFG Spectroscopy

Interfacial water in the vicinity of lipids plays an important role in many biological processes, such as drug delivery, ion transportation, and lipid fusion. Hence, molecular‐level elucidation of the properties of water at lipid interfaces is of the utmost importance. We report the two‐dimensional heterodyne‐detected vibrational sum frequency generation (2D HD‐VSFG) study of the OH stretch of HOD at charged lipid interfaces, which shows that the hydrogen bond dynamics of interfacial water differ drastically, depending on the lipids. The data indicate that the spectral diffusion of the OH stretch at a positively charged lipid interface is dominated by the ultrafast (<～100 fs) component, followed by the minor sub‐picosecond slow dynamics, while the dynamics at a negatively charged lipid interface exhibit sub‐picosecond dynamics almost exclusively, implying that fast hydrogen bond fluctuation is prohibited. These results reveal that the ultrafast hydrogen bond dynamics at the positively charged lipid–water interface are attributable to the bulk‐like property of interfacial water, whereas the slow dynamics at the negatively charged lipid interface are due to bound water, which is hydrogen‐bonded to the hydrophilic head group.     

脱铁伴清蛋白两结合位点不同酪氨酸氢键的特性

The interaction of gallium（Ⅲ） with the ligands containing phenolic group（s）, such as salicylic acid, 8-hydroxyquinoline, N,N＇-bis（2-hydroxybenzyl）ethylenediamine-N,N＇diacetic acid （HBED）, N,N＇-ethylenebis[2-（o- hydroxyphenyl）glycine （EHPG）, and ovotransferrin, was studied, respectively, by means of fluorescence in 0.01 mol/L Hepes at pH 7.4 and room temperature. Fluorescence intensity showed an increase when gallium（Ⅲ） was bound to 8-hydroxyquinoline and HBED. In contrast, it was decreased with the interaction of gallium（Ⅲ） with salicylic acid and EHPG. At pH 7.4, there was N…H-O type intramolecular hydrogen bond in the former, and the latter existed O…H-O type intramolecular hydrogen bond. Fluorescence titration of apoovotransferrin with gallium（Ⅲ） displayed that the fluorescence intensity was decreased at the N-terminal binding site, while enhanced at the C-terminal binding site. It can account for the O…H-O type intramolecular hydrogen bonds for the phenolic groups of Tyr92 and Tyr191 residues at the N-terminal binding site. And there are N…H-O type intramolecular hydrogen bonds for Tyr431 and Tyr524 residues at the C-terminal binding site. In addition, under the same conditions, the conditional binding constant of gallium（Ⅲ） with EHPG or HBED determined by fluorescence method is lg KGa-EHPG=19.18 or lg KGa-HBED= 19.08.     

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP‐Binding RNA Aptamer

RNA tertiary structure motifs are stabilized by a wide variety of hydrogen‐bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pK _a values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP‐binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pK _a value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pK _a for A nucleotides in single‐stranded RNA. This is the largest pK _a shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pK _a shifts observed for amino acid side chains in proteins. Both RNA pre‐folding and ligand binding contribute to the pK _a shift.     

Inherent Conformational Preferences of Ac‐Gln‐Gln‐NHBn: Sidechain Hydrogen Bonding Supports a β‐Turn in the Gas Phase

Gas‐phase single‐conformation spectroscopy is used to study Ac‐Gln‐Gln‐NHBn in order to probe the interplay between sidechain hydrogen bonding and backbone conformational preferences. This small, amide‐rich peptide offers many possibilities for backbone–backbone, sidechain–backbone, and sidechain–sidechain interactions. The major conformer observed experimentally features a type‐I β‐turn with a canonical 10‐membered ring C=O—H?N hydrogen bond between backbone amide groups. In addition, the C=O group of each Gln sidechain participates in a seven‐membered ring hydrogen bond with the backbone NH of the same residue. Thus, sidechain hydrogen‐bonding potential is satisfied in a manner that is consistent with and stabilizes the β‐turn secondary structure. This turn‐forming propensity may be relevant to pathogenic amyloid formation by polyglutamine segments in human proteins.     

Synthesis and characterization of potent bivalent amyloidosis inhibitors that bind prior to transthyretin tetramerization

The misfolding of transthyretin (TTR), including rate-limiting tetramer dissociation and partial monomer denaturation, is sufficient for TTR misassembly into amyloid and other abnormal quaternary structures associated with senile systemic amyloidosis, familial amyloid polyneuropathy, and familial amyloid cardiomyopathy. Monovalent small molecules that bind to one or both of the unoccupied thyroid hormone binding sites at the TTR quaternary structure interface stabilize the native state, raising the kinetic barrier for tetramer dissociation sufficiently that the rate of dissociation, and therefore amyloidosis, becomes slow. Bivalent amyloid inhibitors that bind to both binding sites simultaneously are reported herein. The candidate bivalent inhibitors are generally unable to bind to the native TTR tetramer and typically do not engage in monovalent binding owing to a strong inhibitor orientation preference. However, the TTR quaternary structure can assemble around several of the bivalent inhibitors if the inhibitor intercepts the protein before assembly occurs. Some of the wild-type TTR.bivalent inhibitor complexes prepared in this fashion retain a tetrameric structure when subjected to substantial denaturation stresses (8 M urea, 120 h). The best bivalent inhibitor reduced acid-mediated TTR (3.6 microM) amyloid fibril formation to 6% of that exhibited by TTR in the absence of inhibitor, a significant improvement over the approximately 30% observed for the best monovalent inhibitors (3.6 microM, 72 h). The apparent dissociation rate of the best bivalent inhibitor is effectively zero, consistent with the idea that TTR tetramer dissociation and inhibitor dissociation are linked-as a result of the inhibitor-templating tetramer assembly. X-ray cocrystal structures of two of the complexes demonstrate that the bivalent inhibitors simultaneously occupy both sites in TTR, consistent with the 1:1 binding stoichiometry derived from HPLC analysis. The purpose of this study was to demonstrate that bivalent inhibitors could be useful; what resulted are the best inhibitors produced to date. In this context, molecules capable of intercepting TTR during folding and assembly in the lumen of the endoplasmic reticulum would be of obvious interest.     

Polychlorinated biphenyls inhibit amyloid fibril formation

In this issue of Chemistry & Biology, Purkey et al. [1] compare the binding of PCBs and hydroxylated PCBs (polychlorinated biphenyls) with the human serum protein transthyretin. Hydroxylated PCBs appear to bind with higher selectivity to transthyretin relative to other serum proteins and in so doing inhibit amyloid fibril formation.     

Hydrogen‐Bond‐Guided Self‐Assembly of Nucleotides on a Receptor‐Array Surface

The hydrogen‐bond‐guided self‐assembly of 5′‐ribonucleotides bearing adenine(A), cytosine (C), uracil (U), or guanine (G) bases from aqueous solution on a lipid‐like surface decorated with synthetic bis(Zn^II–cyclen) (cyclen=1,4,7,10‐tetraazacyclodododecane) metal–complex receptor sites is described. The process was studied by using surface plasmon resonance spectroscopy. The data show that the mechanism of nucleotide binding to the 2D template is influenced by the chemistry of the bases and the pH value of the solution. In a neutral solution of pH 7.5, the process is cooperative and selective with respect to Watson–Crick pairs (A–U and C–G), which form stable double planes in accordance with the Chargaff rule. In a more acidic solution at pH 6.0, the interactions between complementary partners become non‐cooperative and the surface also stabilizes mismatched and wobble pairs due to the pH‐induced changes in the receptor coordination state. The results suggest that hydrogen bonding plays a key role in the self‐assembly of complementary nucleotides at the lipid‐like interface, and the cooperative character of the process stems from the ideal matching of the orientation and chemistry of all the interacting components with respect to each other in neutral solution.     

The N Terminus of α‐Synuclein Forms CuII‐Bridged Oligomers

The oligomerization of α‐synuclein (αSyn) is one of the defining features of Parkinson’s disease. Binding of divalent copper to the N terminus of αSyn has been implicated in both its function and dysfunction. Herein, the molecular details of the Cu^II/αSyn binding interface have been revealed using a library of synthetic 56‐residue αSyn peptides containing site‐specific isotopic labels. Using electron paramagnetic resonance spectroscopy, αSyn is shown to coordinate Cu^II with high affinity via two pH‐dependent coordination modes between pH 6.5–8.5. Most remarkably, the data demonstrate that the dominant mode is associated with binding to oligomers (antiparallel dimers and/or cyclic trimers) in which Cu^II ions occupy intermolecular bridging sites. The findings provide a molecular link between Cu^II‐bound αSyn and its associated quaternary oligomeric structure.     

A non‐natural dinucleotide containing an isomeric l‐related deoxy­nucleoside: dinucleotide inhibitors of anti‐HIV integrase activity

The first X‐ray crystal structure of a non‐natural dinucleotide, 5′‐O‐phosphoryl‐1′‐deoxy‐2′‐isoadenylyl‐(3′ → 5′)‐cytidine 6.5‐hydrate (pIsodApC), C₁₉H₂₆N₈O₁₃P₂·6.5H₂O, belonging to a family of dinucleotides that contain an isomeric nucleoside component, is described. A complex system of hydrogen bonds between water mol­ecules and various sites on the dinucleotide was found. All H atoms were located from electron‐density difference maps, which allowed identification of protonation sites. Compounds of this family have been found to bind at the active site of HIV integrase and to be inhibitors of this key viral enzyme. These dinucleotides are completely resistant to cleavage by exonucleases; an abnormal dihedral angle twist in an inter­nucleotide phosphate bond revealed in the X‐ray crystal structure may be contributing to this unusual stability towards nucleases.     

Molecular dynamics studies of the inhibitory mechanism of copper（Ⅱ） on aggregation of amyloid β-peptide

The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H 13, acting as the anchoring site, and the backbone＇s deprotoned amide nitogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.     

Inner Workings of a Cinchona Alkaloid Catalyzed Oxa‐Michael Cyclization: Evidence for a Concerted Hydrogen‐Bond‐Network Mechanism

Cinchona alkaloids catalyze the oxa‐Michael cyclization of 4‐(2‐hydroxyphenyl)‐2‐butenoates to benzo‐2,3‐dihydrofuran‐2‐yl acetates and related substrates in up to 99 % yield and 91 % ee (ee=enantiomeric excess). Catalyst and substrate variation studies reveal an important role of the alkaloid hydroxy group in the reaction mechanism, but not in the sense of a hydrogen‐bonding activation of the carbonyl group of the substrate as assumed by the Hiemstra–Wynberg mechanism of bifunctional catalysis. Deuterium labeling at C‐2 of the substrate shows that addition of RO? H to the alkenoate occurs with syn diastereoselectivity of ≥99:1, suggesting a mechanism‐based specificity. A concerted hydrogen‐bond network mechanism is proposed, in which the alkaloid hydroxy group acts as a general acid in the protonation of the α‐carbanionic center of the product enolate. The importance of concerted hydrogen‐bond network mechanisms in organocatalytic reactions is discussed. The relative stereochemistry of protonation is proposed as analytical tool for detecting concerted addition mechanisms, as opposed to ionic 1,4‐additions.