Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme

Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis

Developing effective amyloidosis inhibitors poses a significant challenge due to the dynamic nature of the protein structures, the complex interplay of interfaces in protein-protein interactions, and the irreversible nature of amyloid assembly. The interactions of amyloidogenic polypeptides with other peptides play a pivotal role in modulating amyloidosis and fibril formation. This study presents a novel approach for designing and synthesizing amyloid interaction surfaces using segments derived from the amyloid-promoting sequence of amyloid β-peptide [VF(Aβ(18-19)/FF(Aβ(19-20)/LVF(Aβ(17-19)/LVFF(Aβ(17-20)], where VF, FF, LVF and LVFF stands for valine phenylalanine dipeptide, phenylalanine phenylalanine dipeptide, leucine valine phenylalanine tripeptide and leucine valine phenylalanine phenylalanine tetrapeptide, respectively. These segments are conjugated with side-chain proline-based methacrylate polymers serving as potent lysozyme amyloidosis inhibitors and demonstrating reduced cytotoxicity of amyloid aggregations. Di-, tri-, and tetra-peptide conjugated chain transfer agents (CTAs) were synthesized and used for the reversible addition-fragmentation chain transfer polymerization of tert-butoxycarbonyl (Boc)-proline methacryloyloxyethyl ester (Boc-Pro-HEMA). Deprotection of Boc-groups from the side-chain proline pendants resulted in water-soluble polymers with defined peptide chain ends as peptide-polymer bioconjugates. Among them, the LVFF-conjugated polymer acted as a potent inhibitor with significantly suppressed lysozyme amyloidosis, a finding supported by comprehensive spectroscopic, microscopic, and computational analyses. These results unveil the synergistic effect between the segment-derived amyloid β-peptide and side-chain proline-based polymers, offering new prospects for targeting lysozyme amyloidosis.

The impact of modified polystyrene on lysozyme fibrillation studied by surface-enhanced Raman spectroscopy (SERS)

Nanoplastics could modulate the fibrillation of amyloid proteins. However, many chemical functional groups are adsorbed to change the interfacial chemistry of nanoplastics in the real world. Herein, this study aimed to investigate the effects of polystyrene (PS), carboxyl modified PS (PS-COOH), and amino modified PS (PS-NH₂) on the fibrillation of hen egg-white lysozyme (HEWL). Due to the differences in the interfacial chemistry, concentration was considered an essential factor. PS-NH₂ (10 μg/mL) could promote the fibrillation of HEWL similar to PS (50 μg/mL) and PS-COOH (50 μg/mL). Moreover, promoting the primary nucleation step of amyloid fibril formation was the primary reason. The differences in spatial conformation of HEWL were characterized by Fourier transform-infrared spectroscopy and surface enhanced Raman spectroscopy (SERS). Strikingly, a particular signal of SERS of HEWL incubated with PS-NH₂ at 1610 cm^-1 was found due to the interaction between amino group of PS-NH₂ and tryptophan (or tyrosine) of HEWL. Therefore, a new perspective was provided to understand the regulation of interfacial chemistry of nanoplastics on the fibrillation of amyloid proteins. Additionally, this study suggested that SERS could be a powerful method to investigate the interactions between proteins and nanoparticles.

Lysozyme amyloid fibril: Regulation, application, hazard analysis, and future perspectives

Self-assembly of misfolded proteins into ordered fibrillar aggregates known as amyloid results in various human diseases. However, more and more proteins, whether in human body or in food, have been found to be able to form amyloid fibrils with in-depth researches. As a model protein for amyloid research, lysozyme has always been the focus of research in various fields. Firstly, the formation mechanisms of amyloid fibrils are discussed concisely. Researches on the regulation of lysozyme amyloid fibrils are helpful to find suitable therapeutic drugs and unfriendly substances. And this review article summarizes a number of exogenous substances including small molecules, nanoparticles, macromolecules, and polymers. Small molecules are mainly connected to lysozyme through hydrophobic interaction, electrostatic interaction, π-π interaction, van der Waals force and hydrogen bond. Nanoparticles inhibit the formation of amyloid fibers by stabilizing lysozyme and fixing β-sheet. Besides, the applications of lysozyme amyloid fibrils in food-related fields are considered furtherly due to outstanding physical and mechanical properties. Nevertheless, the potential health threats are still worthy of our attention. Finally, we also give suggestions and opinions on the future research direction of lysozyme amyloid fibrils.

Modification with N-benzylisatin restricts stress-induced aggregation of hen egg white lysozyme: Anti-amyloidogenic property of isatin derivative with possible clinical implications

Hen egg white lysozyme (HEWL) is a structural homolog of human lysozyme and is widely used as a model protein to investigate protein aggregation. The effect of N-benzylisatin on stress-induced aggregation of HEWL has been investigated in the present study. Interaction of the isatin derivative with HEWL induced changes in protein secondary and tertiary structural conformation as evident from different biophysical and spectroscopic studies. In addition, modification with N-benzylisatin was found to increase the conformational stability of HEWL and afford considerable resistance to the protein to stress-induced aggregation as indicated from subsequent experimental studies, including thioflavin T fluorescence, microscopic imaging and dynamic light scattering analysis. Protein modification was analysed and confirmed by MALDI-TOF and ESI-MS studies. The results highlight possible clinical implications of isatin derivative in the treatment of protein misfolding and conformational disorders.

Methylglyoxal modification reduces the sensitivity of hen egg white lysozyme to stress-induced aggregation: Insight into the anti-amyloidogenic property of α-dicarbonyl compound

The reactive α-oxoaldehyde, methylglyoxal reacts with different proteins to form Advanced Glycation End Products (AGEs) through Maillard reaction. Its level increases significantly in diabetic condition. Here, we have investigated the effect of different concentrations of methylglyoxal (200-400 µM) on the monomeric protein, hen egg white lysozyme (HEWL) following incubation for 3 weeks. Reaction of methylglyoxal with HEWL induced considerable changes in tertiary structure of the protein, but no significant alteration in secondary structure, as evident from different spectroscopic and biophysical studies. Interestingly, methylglyoxal modification was found to enhance the thermal stability of the protein and reduce its sensitivity to stress-induced aggregation. Finally, peptide mass fingerprinting revealed modification of arginine (Arg-45, Arg-14, Arg-68 or Arg-72) and lysine (Lys-116) residues of the protein to AGE adducts, namely, hydroimidazolone, tetrahydropyrimidine, and carboxyethyllysine. Methylglyoxal-derived AGE adducts (MAGE) appear to be responsible for the observed changes in protein. As demonstrated in the present study, the findings may highlight a possible therapeutic potential of the α-oxoaldehyde against protein misfolding and conformational disorder.Communicated by Ramaswamy H. Sarma.

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space

Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.

Application of circular dichroism and magnetic circular dichroism for assessing biopharmaceuticals formulations photo-stability and small ligands binding properties

Synchrotron radiation circular dichroism (SRCD) is a powerful tool for photo-stability assessment of proteins. Recently our research has been interested in applying SRCD to develop screening methodologies for accelerated photo-stability assessment of monoclonal antibody formulations. Despite it was proven to be reliable and applicable within a wide range of salts and excipients containing solutions, the presence of far-UV (<260nm) strong absorbing species (e.g., sodium chloride, histidine, arginine) in common formulations completely prevent the analysis. Herein, we propose a new method based on CD coupled with magnetic CD (MCD) to address the problem and offer an additional versatile tool for monitoring the photo-stability. This is done by assessing the stability of the samples by looking at the near-UV band, as well as giving insights in the denaturation mechanism. We applied this method to four mAbs formulations and correlated the results with dynamic light scattering data. Finally, we applied MCD in ligand interaction to key proteins such as lysozyme, comparing the human with the hen enzyme in the binding of N,N',N''-triacetylchitotriose.

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and average solvation free energies of model compounds which are more consistent with experiment. Most importantly, we show that this scaling is small enough not to affect adversely the stability of the folded state, with only a modest effect on the stability of model peptides forming α-helix and β-sheet structures. The proposed adjustment opens the way to more accurate atomistic simulations of proteins, particularly for intrinsically disordered proteins, protein-protein association, and crowded cellular environments.

Solution NMR of MPS-1 reveals a random coil cytosolic domain structure

Caenorhabditis elegans MPS1 is a single transmembrane helical auxiliary subunit that co-localizes with the voltage-gated potassium channel KVS1 in the nematode nervous system. MPS-1 shares high homology with KCNE (potassium voltage-gated channel subfamily E member) auxiliary subunits, and its cytosolic domain was reported to have a serine/threonine kinase activity that modulates KVS1 channel function via phosphorylation. In this study, NMR spectroscopy indicated that the full length and truncated MPS-1 cytosolic domain (134–256) in the presence or absence of n-dodecylphosphocholine detergent micelles adopted a highly flexible random coil secondary structure. In contrast, protein kinases usually adopt a stable folded conformation in order to implement substrate recognition and phosphoryl transfer. The highly flexible random coil secondary structure suggests that MPS-1 in the free state is unstructured but may require a substrate or binding partner to adopt stable structure required for serine/threonine kinase activity.

A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis

We report here the detailed characterisation of a non-naturally occurring variant of human lysozyme, I59T, which possesses a destabilising point mutation at the interface of the alpha- and beta-domains. Although more stable in its native structure than the naturally occurring variants that give rise to a familial form of systemic amyloidosis, I59T possesses many attributes that are similar to these disease-associated species. In particular, under physiologically relevant conditions, I59T populates transiently an intermediate in which a region of the structure unfolds cooperatively; this loss of global cooperativity has been suggested to be a critical feature underlying the amyloidogenic nature of the disease-associated lysozyme variants. In the present study, we have utilised this variant to provide direct evidence for the generic nature of the conformational transition that precedes the ready formation of the fibrils responsible for lysozyme-associated amyloid disease. This non-natural variant can be expressed at higher levels than the natural amyloidogenic variants, enabling, for example, singly isotopically labelled protein to be generated much more easily for detailed structural studies by multidimensional NMR spectroscopy. Moreover, we demonstrate that the I59T variant can readily form fibrils in vitro, similar in nature to those of the amyloidogenic I56T variant, under significantly milder conditions than are needed for the wild-type protein.

Analysis of internal motions of RNase T1 complexed with a productive substrate involving 15N NMR relaxation measurements

The backbone dynamics of RNase T1 in the presence of exo-guanosine 2',3'-cyclophosphorothioate (exo-cGPS isomer), which is a productive substrate, and in the presence of 3'-guanylic acid (3'GMP), which is an nonproductive substrate, were examined using (15)N nuclear magnetic resonance. Although the X-ray crystal structure suggests that the modes of binding of these substrates to the active-site cleft are very similar, the order parameters in a number of regions in RNase T1 complexed with exo-cGPS isomer were different from those with 3'GMP. Moreover, the chemical exchange in line width observed for RNase T1 complexed with exo-cGPS isomer was also different from that observed for RNase T1 complexed with 3'GMP. From these results, we concluded that the internal motions in RNase T1 complexed with a productive substrate were not always identical to those in RNase T1 complexed with a nonproductive substrate.

Rationalising Lysozyme Amyloidosis: Insights from the Structure and Solution Dynamics of T70N Lysozyme

T70N human lysozyme is the only known naturally occurring destabilised lysozyme variant that has not been detected in amyloid deposits in human patients. Its study and a comparison of its properties with those of the amyloidogenic variants of lysozyme is therefore important for understanding the determinants of amyloid disease. We report here the X-ray crystal structure and the solution dynamics of T70N lysozyme, as monitored by hydrogen/deuterium exchange and NMR relaxation experiments. The X-ray crystal structure shows that a substantial structural rearrangement results from the amino acid substitution, involving residues 45-51 and 68-75 in particular, and gives rise to a concomitant separation of these two loops of up to 6.5A. A marked decrease in the magnitudes of the generalised order parameter (S2) values of the amide nitrogen atom, for residues 70-74, shows that the T70N substitution increases the flexibility of the peptide backbone around the site of mutation. Hydrogen/deuterium exchange protection factors measured by NMR spectroscopy were calculated for the T70N variant and the wild-type protein. The protection factors for many of backbone amide groups in the beta-domain of the T70N variant are decreased relative to those in the wild-type protein, whereas those in the alpha-domain display wild-type-like values. In pulse-labelled hydrogen/deuterium exchange experiments monitored by mass spectrometry, transient but locally cooperative unfolding of the beta-domain of the T70N variant and the wild-type protein was observed, but at higher temperatures than for the amyloidogenic variants I56T and D67H. These findings reveal that such partial unfolding is an intrinsic property of the human lysozyme structure, and suggest that the readiness with which it occurs is a critical feature determining whether or not amyloid deposition occurs in vivo.

B-cell repertoire specific for an unfolded self-determinant of mouse lysozyme escape tolerance and dominantly participate in the autoantibody response

We previously found that autoantibodies against mouse lysozyme (ML) were strongly induced in normal BALB/c mice when immunized with mutant ML that has triple mutations rendering the dominant T-cell epitope of hen egg lysozyme (HEL), HEL 107-116. As T cells specific for HEL 107-116 were primed in these mice, the anti-ML immunoglobulin G (IgG) responses would be the result of collaborations between autoreactive B cells specific for ML and T cells specific for HEL 107-116. Serum IgG responses against ML were dominantly focused on the ML 14-69 region, indicating that B cells responding to the epitope escape tolerance. In the present study, we prepared several monoclonal antibodies (mAbs) specific for ML 14-69 and examined their antigen specificities in detail, to characterize the nature of the remaining B-cell repertoire specific for ML. mAbs specific for ML 14-69 interacted weakly with soluble, native ML, but the interactions were strengthened by denaturation of ML. The apparent affinity constants between these mAbs and ML showed an increase, ranging from six- to 80-fold, by denaturation of ML. Therefore, these mAbs were more specific for the denatured determinant than for the determinant in the native structure. These results indicate that a substantial number of autoreactive B cells, specific for the unfolded conformation of ML, escape tolerance and are dominantly involved in the autoantibody response to ML. Our finding provides important information to understand the naturally occurring autoreactive B-cell repertoire in normal mice.

[Foundation of the bases for protein research and its application to the pharmaceutical science field]

This paper reviews the results of basic research conducted by the author's group to determine appropriate methods to develop protein-based drugs. These include production strategies, elucidation of physiologic function, improving existing pharmaceuticals, de novo design, and protein reconstruction. The antigenicity of modified proteins and methods to induce antigenic protein tolerance are also described.