Conformational Flexibility Tunes the Propensity of Transthyretin to Form Fibrils Through Non‐Native Intermediate States

The formation of partially unfolded intermediates through conformational excursions out of the native state is the starting point of many diseases involving protein aggregation. Therapeutic strategies often aim to stabilize the native structure and prevent the formation of intermediates that are also cytotoxic in vivo. However, their transient nature and low population makes it difficult to characterize these intermediates. We have probed the backbone dynamics of transthyretin (TTR) over an extended timescale by using NMR spectroscopy and MD simulations. The location and extent of these motions indicates that the backbone flexibility of TTR is a cause of dissociation and destabilization, both of which are responsible for fibril formation. Importantly, approximately 10 % of wild‐type TTR exists in an intermediate state, which increased to up to 28 % for pathogenic TTR mutants, for which the formation of the intermediate state is shown to be energetically more favorable compared to the wild type. This result suggests an important role for the intermediates in TTR amyloidosis.     

Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

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).     

Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.     

Design, synthesis and in vitro cytotoxicity studies of novel pyrrolo [2,1][1,4] benzodiazepine-glycosylated pyrrole and imidazole polyamide conjugates

The design, synthesis and biological evaluation of novel pyrrolo [2,1][1,4] benzodiazepine-water insoluble 31-38 and water soluble 39-46 glycosylated pyrrole and imidazole polyamide conjugates are described that involved mercuric chloride mediated cyclization of the corresponding amino diethyl thioacetals. The compounds were prepared with varying numbers of pyrrole and imidazole containing polyamides and incorporating glucose moieties in order to improve the water solubility of PBD-polyamide conjugates and probe the structural requirements for optimal in vitro antitumor activity. These compounds were tested against a panel of 60 human cancer cells by the National Cancer Institute, and demonstrated that the water soluble PBD-polyamide compounds exhibited a higher level of cytotoxic activity than the existing natural and synthetic pyrrolo [2,1-c][1,4] benzodiazepines. The cytotoxic activities of these compounds dramatically increase after hydrolysis of their acetylated counterparts. The activity data summarized in Table 1 and Table 2 show that the solubility of the PBD-polyamides and also the type of heterocycle play important roles influencing the cytotoxic activity of the PBD-polyamide conjugates. The PBD-glycosylated polyamide (water soluble) conjugates 39-46 are highly cytotoxic against many human cancer cell lines in comparison with the PBD-polyamide (water insoluble version) conjugates.     

Synthetic Strategies for Artificial Lipidation of Functional Proteins

Biosynthesis of natural lipidated proteins is linked to important signal pathways, and therefore analyzing protein lipidation is crucial for understanding cellular functions. Artificial lipidation of proteins has attracted attention in recent decades as it allows modulation of the amphiphilic nature of the protein of interest, and is used in the design of drug-delivery systems containing antibodies anchored on a lipid bilayer carrier. However, the intrinsic hydrophobicity of lipids makes the synthesis of lipid–protein conjugates challenging with respect to the yield and selectivity of the lipidation. In this Minireview, the development of chemical and enzymatic synthetic strategies for the preparation of a range of lipid–protein conjugates that do not compromise the functions of the proteins are discussed as well as applications of the conjugates.     

Characterization of the Conjugation Pattern in Large Polysaccharide–Protein Conjugates by NMR Spectroscopy

Carbohydrate‐based vaccines are among the safest and most effective vaccines and represent potent tools for prevention of life‐threatening bacterial infectious diseases, like meningitis and pneumonia. The chemical conjugation of a weak antigen to protein as a source of T‐cell epitopes generates a glycoconjugate vaccine that results more immunogenic. Several methods have been used so far to characterize the resulting polysaccharide–protein conjugates. However, a reduced number of methodologies has been proposed for measuring the degree of saccharide conjugation at the possible protein sites. Here we show that detailed information on large proteins conjugated with large polysaccharides can be achieved by a combination of solution and solid‐state NMR spectroscopy. As a test case, a large protein assembly, l ‐asparaginase II, has been conjugated with Neisseria meningitidis serogroup C capsular polysaccharide and the pattern and degree of conjugation were determined.     

Effects of amino acid phi,psi propensities and secondary structure interactions in modulating H alpha chemical shifts in peptide and protein beta-sheet.

H alpha chemical shifts are often used as indicators of secondary structure formation in protein structural analysis and peptide folding studies. On the basis of NMR analysis of model beta-sheet and alpha-helical peptides, together with a statistical analysis of protein structures for which NMR data are available, we show that although the gross pattern of H alpha chemical shifts reflects backbone torsion angles, longer range effects from distant amino acids are the dominant factor determining experimental chemical shifts in beta-sheets of peptides and proteins. These show context-dependent variations that aid structural assignment and highlight anomalous shifts that may be of structural significance and provide insights into beta-sheet stability.     

Multicomponent access to novel proline/cyclized cysteine tethered monastrol conjugates as potential anticancer agents

The versatility of multicomponent Biginelli’s reaction is exploited in the development of proline and cyclized cysteine tethered conjugates of monastrol, a kinesin Eg5 inhibitor. Ten new conjugates are synthesized focusing on structural replacement of the ester moiety (C-5 position) of the monastrol backbone with amino acid based amide moieties. On cytotoxic evaluation, conjugate 24 has shown promising in vitro cytotoxic activity against leukemia. Molecular docking studies revealed that the conjugates 19 and 24 exhibit better interaction at kinesin Eg5 receptor compared to monastrol. Moreover, computational calculations and predictions of important molecular properties suggest that these new amino acid based conjugates could be further improved to provide potential anticancer agents.     

Structural characterization of protein–polymer conjugates for biomedical applications with small-angle scattering

Protein–polymer conjugates, typically consisting of one or more polymers covalently attached to a protein, are an increasingly common component in biotechnology. Polymers can increase circulation time, alter immune responses, and influence the self-assembly of proteins to which they are attached. To understand and take full advantage of the benefits that protein–polymer conjugates provide, there is a strong need for structural characterization of both the conjugates and their self-assembled structures. Although X-ray crystallography is suitable for determining protein structure, protein–polymer conjugates do not generally crystallize, requiring the use of alternative techniques. Small-angle scattering, with neutrons in particular, is one such technique. In this article, we review recent work in the area of protein–polymer conjugates and highlight the important role that structure plays. We then highlight shape-dependent and shape-independent approaches for structural characterization of protein–polymer conjugates and future directions in small-angle scattering interpretation. We conclude by introducing a new model that we suggest may be useful in the future to acquire more detailed structural properties.     

Structural modifications of serum transthyretin in rats during protein-energy malnutrition

Transthyretin (TTR) is a sensitive marker of protein-energy malnutrition and changes in serum and expression levels during protein and energy deficiency are well described. However, little is known about structural modifications of TTR during protein and/or energy deprivation. Therefore, the aim of this study was to determine the effects of protein inadequacies on post-translational modifications of TTR. For this purpose, male Wistar rats were fed a diet with either casein or gelatine as sole protein source subsequent to a protein wash-out period. Changes in TTR serum levels as well as other markers of nutritional status as body weight, food consumption, total serum protein and serum RBP4 levels as well as antioxidative capacity were determined. Post-translational modifications of TTR were examined by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) analysis. The rats from the gelatine group revealed a marked change in the post-translational modification pattern of TTR which was reflected by a significant elevation of sulfonated TTR and which was inversely correlated to the antioxidative capacity. Additionally, the elevation of sulfonated TTR was accompanied by a decrease in body weight and food consumption, low antioxidative capacity as well as a deprivation of serum TTR, RBP4 and total serum protein levels in the animals of the gelatine group. Protein-energy malnutrition leads therefore next to changes in TTR serum concentration, also to changes in the post-translational modification pattern of TTR. Such changes are probably induced by protein-energy malnutrition-driven oxidative stress and might be linked to alterations in protein function and stability.     

Effects of oligonucleotide adsorption on the physicochemical characteristics of a nanoparticle-based model delivery system for antisense drugs

Cationic polystyrene nanoparticles, as a model drug carrier system for nucleic acids, are capable of binding negatively charged oligonucleotides by multiple electrostatic interactions. The effect of the adsorption of phosphorothioate oligonucleotides on the physicochemical properties of the carrier system was investigated for uncoated and sterically stabilized latex particles. Turbidity measurements and photon-correlation spectroscopy indicate that the colloidal stability of the nanoparticle-oligonucleotide conjugates is influenced by the number of oligonucleotides adsorbed on the carrier. Especially in the case of the uncoated material, a destabilizing effect has been observed up to oligonucleotide concentrations of 2.7 μmol/g polymer. Strikingly, at higher concentrations the latexes exhibit colloidal stability similar to the oligonucleotide-free samples. These results were correlated to zeta-potential measurements demonstrating a reversal from positive to negative values of the zeta potential with increasing oligonucleotide concentration. The points of zero charge of the particles are in the region of maximum coagulation. These findings were compared to adsorption studies and calculations based on the random sequential adsorption model. It appears that at first the colloidal stability of the carrier systems is diminished with increasing oligonucleotide adsorption, while higher surface coverages lead to a significant reduction in coagulation. At the saturation level the surface coverage can be considered as a monolayer of “side-on” adsorbed molecules and the conjugates exhibit colloidal stability similar to the bare particles without adsorbed molecules. Received: 20 April 1998 Accepted: 16 July 1998     

End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105–115) Amyloid Protofibrils

Pathological amyloid proteins are associated with degenerative and neurodegenerative diseases. These amyloid proteins develop as oligomer, fibrillar, and plaque forms, due to the denatured and unstable status of the amyloid monomers. Specifically, the development of fibrillar amyloid proteins has been investigated through several experimental studies. To understand the generation of amyloid fibrils, environmental factors such as point mutations, pH, and polymorphic characteristics have been considered. Recently, amyloid fibril studies related to end‐capping effects have been conducted to understand amyloid fibril development. However, atomic‐level studies to determine the stability and mechanical properties of amyloid fibrils based on end capping have not been undertaken. In this study, we show that end capping alters the structural characteristics and conformations of transthyretin (TTR) amyloid fibrils by using molecular dynamics (MD) simulations. Variation in the structural conformations and characteristics of the TTR fibrils through end capping are observed, due to the resulting electrostatic energies and hydrophobicity characteristics. Moreover, the end capping changes the mechanical properties of TTR fibrils. Our results shed light on amyloid fibril formation under end‐capping conditions.     

Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review

Protein therapeutics have emerged as a major class of biopharmaceuticals over the past several decades, a trend that has motivated the advancement of bioanalytical technologies for protein therapeutic characterization. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful and sensitive technique that can probe the higher order structure of proteins and has been used in the assessment and development of monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs) and biosimilar antibodies. It has also been used to quantify protein-ligand, protein-receptor and other protein-protein interactions involved in signaling pathways. In manufacturing and development, HDX-MS can validate storage formulations and manufacturing processes for various biotherapeutics. Currently, HDX-MS is being refined to provide additional coverage, sensitivity and structural specificity and implemented on the millisecond timescale to reveal residual structure and dynamics in disordered domains and intrinsically disordered proteins.     

CABS‐NMR—De novo tool for rapid global fold determination from chemical shifts,residual dipolar couplings and sparse methyl‐methyl noes

Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low‐cost global protein fold determination. Here, we present CABS‐NMR, an efficient protein modeling tool, which takes advantage of such structural restraints. The restraints are converted from original NMR data to fit the coarse grained protein representation of the C‐Alpha‐Beta‐Side‐group (CABS) algorithm. CABS is a Monte Carlo search algorithm that uses a knowledge‐based force field. Its versatile structure enables a variety of protein‐modeling protocols, including purely de novo folding, folding guided by restraints derived from template structures or, structure assembly based on experimental data. In particular, CABS‐NMR uses the distance and angular restraints set derived from various NMR experiments. This new modeling technique was successfully tested in structure determination of 10 globular proteins of size up to 216 residues, for which sparse NMR data were available. Additional detailed analysis was performed for a S100A1 protein. Namely, we successfully predicted Nuclear Overhauser Effect signals on the basis of low‐energy structures obtained from chemical shifts by CABS‐NMR. It has been observed that utility of chemical shifts and other types of experimental data (i.e. residual dipolar couplings and methyl‐methyl Nuclear Overhauser Effect signals) in the presented modeling pipeline depends mainly on size of a protein and complexity of its topology. In this work, we have provided tools for either post‐experiment processing of various kinds of NMR data or fast and low‐cost structural analysis in the still challenging field of new fold predictions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Characterization of Hapten-Protein Conjugates for Immunoassay of Polycyclic Aromatic Hydrocarbons（PAHs）

Preparation and characterization of the hapten-protein conjugates are fundamental to developing environmental immunoassays. As a hapten, 1-pyrenebutyric acid（PBA） was conjugated to the carrier protein of bovine serum albumin（BSA） or ovalbumin（OVA） by active ester method. Infrared spectra（IR） showed that PBA-BSA and PBA-OVA conjugates were successfully prepared. The number of the haptens conjugated to the carrier protein was determined by ultraviolet spectra（UV） and matrix-assisted laser desorption ionization time-of-flight mass spectrometry（MALDI-TOF-MS）. The calculated average binding ratios of PBA/BSA and PBA/OVA were 18：1 and 10：1 by UV, and 31：1 and 22：1 by MALDI-TOF-MS, respectively. Although there was a discrepancy between the results determined by the two methods, both of them were useful for the characterization of the hapten-protein conjugates. The antibody was produced against the antigen of PBA-BSA, and the affinity was tested by the double agar diffusion method The conjugates and the antibody could be used for developing a sensitive and selective immunoassay of polycyclic aromatic hydrocarbons（PAHs）.     

Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins

Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.     

Effect of Hydroxyl Groups Esterification with Fatty Acids on the Cytotoxicity and Antioxidant Activity of Flavones

Flavonoids and polyunsaturated fatty acids due to low cytotoxicity in vitro studies are suggested as potential substances in the prevention of diseases associated with oxidative stress. We examined novel 6-hydroxy-flavanone and 7-hydroxy-flavone conjugates with selected fatty acids (FA) of different length and saturation and examined their cytotoxic and antioxidant potential. Our findings indicate that the conjugation with FA affects the biological activity of both the original flavonoids. The conjugation of 6-hydroxy-flavanone increased its cytotoxicity towards prostate cancer PC3 cells. The most noticeable effect was found for oleate conjugate. A similar trend was observed for 7-hydroxy-flavone conjugates with the most evident effect for oleate and stearate. The cytotoxic potential of all tested conjugates was not specific towards PC3 because the viability of human keratinocytes HaCaT cells decreased after exposure to all conjugates. Additionally, we showed that esterification of the two flavonoids decreased their antioxidant activity compared to that of the original compounds. Of all the tested compounds, only 6-sorbic flavanone showed a slight increase in antioxidant potential compared to that of the original compound. Our data show that conjugated flavonoids are better absorbed and enhance cytotoxic effects, but the presence of FA lowered the antioxidant potential.     

Theoretical investigations of TTR derived aggregation-prone peptides’ potential to biochemically attenuate the amyloidogenic propensities of V30 M TTR amyloid fibrils

Transthyretin (TTR) is a cerebrospinal fluid and plasma prevalent protein implicated in heritable and sporadic amyloidosis. Numerous mutations and a wide range of phenotypes have been associated with TTR-mediated amyloidosis. Among these, V30 M is the most predominant point mutation, inculpated with familial amyloid polyneuropathy (FAP), a life-threatening autosomal dominant genetic disorder characterized by the deposition of amyloid fibrils in crucial areas. Hence, efficacious therapeutics against this detrimental disorder is warranted. Lately, several peptide-based analeptics, especially the ones that are aggregation-prone and the ones derived from aggregation hotspots of amyloidogenic proteins are being increasingly proffered against the amyloid fibrils. In the present study, as an effective precursor to in vitro investigations, we examined and assessed the therapeutic potentials of aggregation-prone peptides (APPs) derived from TTR, against V30 M TTR amyloid fibrils, computationally. Out of five experimentally corroborated APPs availed for this study, molecular dynamics simulation analysis endorses APP TAVVTN to be an effective beta-sheet breaker against V30 M TTR amyloid fibrils. Furthermore, consistent findings from various molecular trajectory analyses, residual frustration analysis and simulated thermal denaturation have indicated that APP TAVVTN could effectually relater the structural dynamics of V30 M TTR amyloid fibrils, to conformationally digress it away from its amyloidogenic propensities. Hence, based on consistent unvarying findings from numerous adept computational pipelines, APP TAVVTN could be an efficacious analeptic to therapeutically intervene and mitigate the amyloidogenic propensities of V30 M TTR amyloid fibrils, thereby ameliorating the pathological ramifications due to FAP.     

4D solid-state NMR for protein structure determination

Solid-state NMR offers the chance to extend structural studies to proteins that are otherwise difficult to study at atomic resolution, such as protein fibrils, membrane proteins or poorly diffracting crystals. As two-dimensional spatial correlation NMR spectra of proteins suffer from severe resonance overlap, we analyze in this perspective article the potential of higher-dimensional (3D and 4D) proton-detected experiments, which have an increased number of identifiable and assignable distance restraints for solid-state structural studies. We discuss practical considerations for the NMR measurements and the preparation of suitable protein samples and show results of structure calculations from 4D solid-state NMR spectra.