The supramolecular chemistry of β-sheets

Uncovering Amyloid-β Interactions: Gray versus White Matter

Alzheimer's disease is characterized by the accumulation of amyloid plaques in the brain. Recent studies suggest that amyloid-β (Aβ) peptides interact with cell membranes, potentially catalyzing plaque formation. However, the effect of varying cell membrane compositions on this catalytic process requires further investigation. Using molecular dynamics simulations, we demonstrate that a model gray matter membrane significantly influences the secondary structure of β-amyloid peptides. Notably, residues Asp1 and Glu22 play crucial roles in the membrane interaction. Glutamic acid at position 22, located in the middle of the peptide chain, appears to promote the formation of β-hairpin conformations, which are critical for aggregation. Additionally, our simulations reveal that the model white matter membrane allows a spontaneous insertion of segments of the peptide into the membrane, suggesting that membrane interaction not only alters the peptide structure but may also compromise membrane integrity. Our results show that the different membrane compositions in the brain may play different roles when interacting with β-amyloid peptides.

Chiral helical scaffolds: Unlocking their potential in biomolecular interactions and biomedical applications

In nature, various molecules possess spiral geometry. Such helical structures are even prevalent within the human body, represented classically by DNA and three-dimensional (secondary structure) protein folding. In this review, we chose helicenes and helicene-like structures -synthetically accessible carbon-rich molecules- as a compelling example of helically chiral scaffolds. Helicene chemistry, traditionally anchored in materials science, has been a subject of increasing interest in the biomedical field due to the unique optical and chiral properties of these helical structures. This review explores the diverse applications of helicenes in biomedicine, focusing on their role in cell imaging, protective coatings for implants, drug delivery systems, biosensors, and drug discovery. We discuss the unique properties of helicenes and helicene-like structures, highlighting their ability to form complex interactions with various biomolecules and their potential in the development of candidates for therapeutic agents. Recent advances in helicene derivatives with enhanced circularly polarized luminescence and other photochemical properties are also reviewed, underlining their utility in precise bio-imaging and diagnostic techniques. The review consolidates the current literature and emphasizes the growing importance of helicenes in bridging chemistry, materials science, and biology for innovative technological and biomedical applications.

Skin Appendage Proteins of Tetrapods: Building Blocks of Claws, Feathers, Hair and Other Cornified Epithelial Structures

Reptiles, birds, mammals and amphibians, together forming the clade tetrapods, have a large diversity of cornified skin appendages, such as scales, feathers, hair and claws. The skin appendages consist of dead epithelial cells that are tightly packed with specific structural proteins. Here, we review the molecular diversity and expression patterns of major types of skin appendage proteins, namely keratin intermediate filament proteins, keratin-associated proteins (KRTAPs) and proteins encoded by genes of the epidermal differentiation complex (EDC), including corneous beta-proteins, also known as beta-keratins. We summarize the current knowledge about the components of skin appendages with a focus on keratins and EDC proteins that have recently been identified in reptiles and birds. We discuss gaps of knowledge and suggest directions of future research.

A Discrete Four-Stranded β-Sheet through Catenation of M2L2 Metal-Peptide Rings

Methods for precisely constructing a β-sheet assembly with number-defined strands in solution remains quite limited due to its intense aggregation property. Here, we report the precise construction of a four-stranded anti-parallel β-sheet by utilizing a non-covalent approach. This was achieved by folding and assembly of Ag+ and a pentapeptide (1) with the Ala-D3pa-Gly-3pa-Val (3pa: β-(3-pyridyl)-alanine) sequence, which was designed to form an interlocking Ag2(1)2 ring through metal cross-linking of the side chains. NMR analyses and X-ray crystallographic studies characterized the structure of the discrete β-sheet assembly as well as the remarkable structural selectivity in terms of strands' number, orientation and the sheet type.

Silk Sericin/Chitosan Supramolecular Multilayered Thin Films as Sustainable Cytocompatible Nanobiomaterials

Silk sericin (SS) has been widely discarded as a waste by the silk textile industry during the degumming process to obtain fibroin. However, in the past decade, an in-depth understanding of its properties and functions turned it into a high added-value biomaterial for biomedical applications. Herein, we report the molecular design and development of sustainable supramolecular multilayered nanobiomaterials encompassing SS and oppositely charged chitosan (CHT) through a combination of self-assembly and electrostatically driven layer-by-layer (LbL) assembly technology. The successful buildup of SS/CHT multilayered nanobiomaterials was demonstrated by the quartz crystal microbalance with dissipation monitoring and attenuated total reflectance-Fourier transform infrared spectroscopy, and the nanofilms' wettable properties and nanofibrillar-like topography were shown by water contact angle, atomic force microscopy, and scanning electron microscopy. In vitro assays demonstrated the cytocompatibility of the LbL nanofilms toward human primary dermal fibroblasts, holding great promise as biofunctional nanocoatings for drug/therapeutics/cell delivery, tissue engineering, and regenerative medicine.

From Double-Stranded Helicates to Abiotic Double Helical Supramolecular Assemblies

The folding of oligomeric strands is the method that nature has selected to generate ordered assemblies presenting spectacular functions. In the purpose to mimic these biomacromolecules and extend their properties and functions, chemists make important efforts to prepare artificial secondary, tertiary, and even quarternary structures based on folded abiotic backbones. A large variety of oligomers and polymers, encoded with chemical informations, were designed, synthesized and characterized, and the establishment of non-covalent interactions lead to complex and functional supramolecular architectures resulting from a spontaneous self-assembly process. The association of complementary molecular strands into double helical structures is a common structural pattern of nucleic acids and proteins, so the synthesis of bio-inspired double helices has emerged as an important subject. In recent years, a number of synthetic oligomers have been reported to form stable double helices and it was shown that the equilibrium between single and double helices can be controlled via different stimuli like the modification of the solvent or the temperature. This kind of structure presents highly interesting functions, such as molecular recognition within the cavity of double helices, and some other potential applications will emerge in the future.

Sequence-controlled divergent supramolecular assembly of polyproline helices into metallo-peptide nanoparticles

The field of peptide based supramolecular biomaterials is fast evolving. These types of constructs have been shown to find applications in the fields of bioimaging, drug delivery and scaffolds for chemical reactions. However, the community typically focuses on the use of two specific classes of structured peptides: α-helices and β-sheets, clearly neglecting a unique peptide secondary structure: the polyproline helix. Herein, we report the first design, synthesis and characterization of polyproline based metallo-peptide nanoparticles. We demonstrate that rationally engineered polyproline helices can assemble in a divergent manner, into two types of nanoparticles. We also demonstrate that the primary sequence of the functionalised polyproline peptide is crucial to ensure a controlled assembly. This work clearly demonstrates that polyproline helices can be a powerful tool to achieve supramolecular assemblies of complex and responsive bioinspired nanomaterials.

Unravelling the Complexity of Amyloid Peptide Core Interfaces

Amyloids, large intermolecular sandwiched β-sheet structures, underlie several protein misfolding diseases but have also been shown to have functional roles and can be a basis for designing smart and responsive nanomaterials. Short segments of proteins, called aggregation-prone regions (APRs), have been identified that nucleate amyloid formation. Here we present the database of 173 APR crystal structures currently available in the PDB, and a tool, ACW, for analyzing their topologies and the 267 inter-β-sheet interfaces of zipper regions assigned in these structures. We defined a new descriptor of zipper interfaces, the surface detail index (SDi), which quantifies the intertwining between the side chains of both β-sheets of the zipper, an important factor for the molecular recognition and self-assembly of these mesostructures. This allowed a comparative analysis of the zipper interfaces and identification of 6 clusters with different intertwining, steric fit, and size characteristics using three complementary descriptors, SDi, shape complementarity, and buried surface area. 60% of the APR structures are formed by parallel β-sheets, of which 52% belong to the topological class 1. This could be explained by the better fit and a deeper entanglement of the zipper regions of the parallel structures than of the antiparallel structures, as the analysis showed that both their shape complementarity (0.79 vs 0.70) and SDi (1.53 vs 1.32) were higher. The higher abundance of certain residues (Asn and Gln in parallel and Leu and Ala in antiparallel β-sheets) can be explained by their ability to form different ladder-like secondary interaction patterns within β-sheets. Analogous to the hierarchy of protein structure, we interpreted the primary, secondary, tertiary, and quaternary structure levels of APRs revealing different characteristics of the zipper regions for both parallel and antiparallel β-sheet structures, which may provide clues to the structural conditions of amyloid core formation and the rational design of amyloid polymorphs.

A Closer Look at Type I Left-Handed β-Helices Provides a Better Understanding in Their Sequence-Structure Relationship: Toward Their Rational Design

Understanding the sequence-structure relationship in protein is of fundamental interest, but has practical applications such as the rational design of peptides and proteins. This relationship in the Type I left-handed β-helix containing proteins is updated and revisited in this study. Analyzing the available experimental structures in the Protein Data Bank, we could describe, further in detail, the structural features that are important for the stability of this fold, as well as its nucleation and termination. This study is meant to complete previous work, as it provides a separate analysis of the N-terminal and C-terminal rungs of the helix. Particular sequence motifs of these rungs are described along with the structural element they form.

Crystallography Reveals Metal-Triggered Restructuring of β-Hairpins

Metal binding to β-sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo-β-sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β-sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ-helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12-residue β-sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X-ray diffraction (SC-XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher-order structures available to metallo-β-sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo-β-sheet peptides.

Recent Progress of pH-Responsive Peptides, Polypeptides, and Their Supramolecular Assemblies for Biomedical Applications

Peptides and polypeptides feature a variety of active functional groups on their side chains (including carboxylic acid, hydroxyl, amino, and thiol groups), enabling diverse chemical modifications. This versatility makes them highly valuable in stimuli-responsive systems. Notably, pH-responsive peptides and polypeptides, due to their ability to respond to pH changes, hold significant promise for applications in cellular pathology and tumor targeting. Extensive researches have highlighted the potentials of low pH insertion peptides (pHLIPs), peptide-drug conjugates (PDCs), and antibody-drug conjugates (ADCs) in biomedicine. Peptide self-assemblies, with their structural stability, ease of regulation, excellent biocompatibility, and biodegradability, offer immense potentials in the development of novel materials and biomedical applications. We also explore specific examples of their applications in drug delivery, tumor targeting, and tissue engineering, while discussing future challenges and potential advancements in the field of pH-responsive self-assembling peptide-based biomaterials.

Strategies for Making High-Performance Artificial Spider Silk Fibers

Artificial spider silk is an attractive material for many technical applications since it is a biobased fiber that can be produced under ambient conditions but still outcompetes synthetic fibers (e.g., Kevlar) in terms of toughness. Industrial use of this material requires bulk-scale production of recombinant spider silk proteins in heterologous host and replication of the pristine fiber's mechanical properties. High molecular weight spider silk proteins can be spun into fibers with impressive mechanical properties, but the production levels are too low to allow commercialization of the material. Small spider silk proteins, on the other hand, can be produced at yields that are compatible with industrial use, but the mechanical properties of such fibers need to be improved. Here, the literature on wet-spinning of artificial spider silk fibers is summarized and analyzed with a focus on mechanical performance. Furthermore, several strategies for how to improve the properties of such fibers, including optimized protein composition, smarter spinning setups, innovative protein engineering, chemical and physical crosslinking as well as the incorporation of nanomaterials in composite fibers, are outlined and discussed.

Phosphoryl group wires stabilize pathological tau fibrils as revealed by multiple quantum spin counting NMR

Hyperphosphorylation of the protein tau is one of the biomarkers of neurodegenerative diseases in the category of tauopathies. However, the molecular level, mechanistic, role of this common post-translational modification (PTM) in enhancing or reducing the aggregation propensity of tau is unclear, especially considering that combinatorial phosphorylation of multiple sites can have complex, non-additive, effects on tau protein aggregation. Since tau proteins stack in register and parallel to elongate into pathological fibrils, phosphoryl groups from adjacent tau strands with 4.8 Å separation must find an energetically favorable spatial arrangement. At first glance, this appears to be an unfavorable configuration due to the proximity of negative charges between phosphate groups from adjacent neighboring tau fibrils. However, this study tests a counterhypothesis that phosphoryl groups within the fibril core-forming segments favorably assemble into highly ordered, hydrogen-bonded, one-dimensionally extended wires under biologically relevant conditions. We selected two phosphorylation sites associated with neurodegeneration, serine 305 (S305p) and tyrosine 310 (Y310p), on a model tau peptide jR2R3-P301L (tau295-313) spanning the R2/R3 splice junction of tau, that readily aggregate into a fibril with characteristics of a seed-competent mini prion. Using multiple quantum spin counting (MQ-SC) by 31P solid-state NMR of phosphorylated jR2R3-P301L tau peptide fibrils, enhanced by dynamic nuclear polarization, we find that at least six phosphorous spins must neatly arrange in 1D within fibrils or in 2D within a protofibril to yield the experimentally observed MQ-coherence orders of four. We found that S305p stabilizes the tau fibrils and leads to more seeding-competent fibrils compared to jR2R3 P301L or Y310p. This study introduces a new concept that phosphorylation of residues within a core forming tau segment can mechanically facilitate fibril registry and stability due a hitherto unrecognized role of phosphoryl groups to form highly ordered, extended, 1D wires that stabilize pathological tau fibrils.

Genes for laminarin degradation are dispersed in the genomes of particle-associated Maribacter species

Laminarin is a cytosolic storage polysaccharide of phytoplankton and macroalgae and accounts for over 10% of the world's annually fixed carbon dioxide. Algal disruption, for example, by viral lysis releases laminarin. The soluble sugar is rapidly utilized by free-living planktonic bacteria, in which sugar transporters and the degrading enzymes are frequently encoded in polysaccharide utilization loci. The annotation of flavobacterial genomes failed to identify canonical laminarin utilization loci in several particle-associated bacteria, in particular in strains of Maribacter. In this study, we report in vivo utilization of laminarin by Maribacter forsetii accompanied by additional cell growth and proliferation. Laminarin utilization coincided with the induction of an extracellular endo-laminarinase, SusC/D outer membrane oligosaccharide transporters, and a periplasmic glycosyl hydrolase family 3 protein. An ABC transport system and sugar kinases were expressed. Endo-laminarinase activity was also observed in Maribacter sp. MAR_2009_72, Maribacter sp. Hel_I_7, and Maribacter dokdonensis MAR_2009_60. Maribacter dokdonensis MAR_2009_71 lacked the large endo-laminarinase gene in the genome and had no endo-laminarinase activity. In all genomes, genes of induced proteins were scattered across the genome rather than clustered in a laminarin utilization locus. These observations revealed that the Maribacter strains investigated in this study participate in laminarin utilization, but in contrast to many free-living bacteria, there is no co-localization of genes encoding the enzymatic machinery for laminarin utilization.

An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2

DENV-2 strain is the most fatal and infectious of the five dengue virus serotypes. The non-structural protein NS1 encoded by its genome is the most significant protein required for viral pathogenesis and replication inside the host body. Thus, targeting the NS1 protein and designing an inhibitor to limit its stability and secretion is a propitious attempt in our fight against dengue. Four novel inhibitors are designed to target the conserved cysteine residues (C55, C313, C316, and C329) and glycosylation sites (N130 and N207) of the NS1 protein in an attempt to halt the spread of the dengue infection in the host body altogether. Numerous computer-aided drug designing techniques including molecular docking, molecular dynamics simulation, virtual screening, principal component analysis, and dynamic cross-correlation matrix were employed to determine the structural and functional activity of the NS1-inhibitor complexes. From our analysis, it was evident that the extent of structural and atomic level fluctuations of the ligand-bound protein exhibited a declining trend in contrast to unbound protein which was prominently noticeable through the RMSD, RMSF, Rg, and SASA graphs. The ADMET analysis of the four ligands revealed a promising pharmacokinetics and pharmacodynamic profile, along with good bioavailability and toxicity properties. The proposed drugs when bound to the targeted cavities resulted in stable conformations in comparison to their unbound state, implying they have good affinity promising effective drug action. Thus, they can be tested in vitro and used as potential anti-dengue drugs.Communicated by Ramaswamy H. Sarma.

Assembly-Driven Oxidative Degradation of Melarsomine Triggered by Cyanuric Acid

Molecular self-assembly can trigger or regulate specific chemical reactions that would otherwise be infeasible when molecules exist individually. Supramolecular structures can significantly affect the rate of chemical reactions; therefore, optimizing supramolecular structures by manipulating intermolecular interactions is crucial for achieving the desired reactivity. Melamine is known to form hydrogen bonds with cyanuric acid, resulting in the formation of a supramolecular network. Melarsomine, an effective medication for heartworm treatment in dogs, contains a melamine moiety. It has yet to be studied how the chemical stability of melarsomine is affected by its interaction with other molecules. Herein, we report the formation of a two-dimensional supramolecular network between melarsomine and cyanuric acid via hydrogen bonds. This network structure captures dissolved oxygen in an aqueous solution, accelerating the oxidative degradation of melarsomine.

Peptide hydrogen-bonded organic frameworks

Hydrogen-bonded porous frameworks (HPFs) are versatile porous crystalline frameworks with diverse applications. However, designing chiral assemblies or biocompatible materials poses significant challenges. Peptide-based hydrogen-bonded porous frameworks (P-HPFs) are an exciting alternative to conventional HPFs due to their intrinsic chirality, tunability, biocompatibility, and structural diversity. Flexible, ultra-short peptide-based P-HPFs (composed of 3 or fewer amino acids) exhibit adaptable porous topologies that can accommodate a variety of guest molecules and capture hazardous greenhouse gases. Longer, folded peptides present challenges and opportunities in designing P-HPFs. This review highlights recent developments in P-HPFs using ultra-short peptides, folded peptides, and foldamers, showcasing their utility for gas storage, chiral recognition, chiral separation, and medical applications. It also addresses design challenges and future directions in the field.

Dissecting the Conformational Stability of a Glycan Hairpin

Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan-glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.

Metal-driven folding and assembly of a minimal β-sheet into a 3D-porous honeycomb framework

In contrast to short helical peptides, constrained peptides, and foldamers, the design and fabrication of crystalline 3D frameworks from the β-sheet peptides are rare because of their high self-aggregation propensity to form 1D architectures. Herein, we demonstrate the formation of a 3D porous honeycomb framework through the silver coordination of a minimal β-sheet forming a peptide having terminal metal coordinated 4- and 3-pyridyl ligands.

Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation

Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.

Structural Characterization and Properties of Modified Soybean Meal Protein via Solid-State Fermentation by Bacillus subtilis

Soybean meal (SBM) is a high-quality vegetable protein, whose application is greatly limited due to its high molecular weight and anti-nutritional properties. The aim of this study was to modify the protein of soybean meal via solid-state fermentation of Bacillus subtilis. The fermentation conditions were optimized as, finally, the best process parameters were obtained, namely fermentation temperature of 37 °C, inoculum amount of 12%, time of 47 h, and material-liquid ratio of 1:0.58, which improved the content of acid-soluble protein. To explore the utilization of modified SBM as a food ingredient, the protein structure and properties were investigated. Compared to SBM, the protein secondary structure of fermented soybean meal (FSBM) from the optimal process decreased by 8.3% for α-helix content, increased by 3.08% for β-sheet, increased by 2.71% for β-turn, and increased by 2.51% for random coil. SDS-PAGE patterns showed that its 25-250 KDa bands appeared to be significantly attenuated, with multiple newborn peptide bands smaller than 25 KDa. The analysis of particle size and zeta potential showed that fermentation reduced the average particle size and increased the absolute value of zeta potential. It was visualized by SEM and CLSM maps that the macromolecular proteins in FSBM were broken down into fragmented pieces with a folded and porous surface structure. Fermentation increased the solubility, decreased the hydrophobicity, increased the free sulfhydryl content, decreased the antigenicity, improved the protein properties of SBM, and promoted further processing and production of FSBM as a food ingredient.

Lipopeptides as tools in catalysis, supramolecular, materials and medicinal chemistry

Lipopeptides are amphiphilic peptides in which an aliphatic chain is attached to either the C or N terminus of peptides. Their self-assembly - into micelles, vesicles, nanotubes, fibres or nanobelts - leads to applications in nanotechnology, catalysis or medicinal chemistry. Self-organization of lipopeptides is dependent on both the length of the lipid tail and the amino acid sequence, in which the chirality of the peptide sequence can be transmitted into the supramolecular species. This Review describes the use of lipopeptides to design synthetic advanced dynamic supramolecular systems, nanostructured materials or self-responsive delivery systems in the area of medical biotechnology. We examine the influence of external stimuli, the ability of lipopeptide-derived structures to adapt over time and their application as medicinal agents with antibacterial, antifungal, antiviral or anticancer activities. Finally, we discuss the catalytic efficiency of lipopeptides, with the aim of building minimal synthetic enzymes, and recent efforts to incorporate metals into lipopeptide assemblies.

Hierarchical self-assembly of a reflectin-derived peptide

Reflectins are a family of intrinsically disordered proteins involved in cephalopod camouflage, making them an interesting source for bioinspired optical materials. Understanding reflectin assembly into higher-order structures by standard biophysical methods enables the rational design of new materials, but it is difficult due to their low solubility. To address this challenge, we aim to understand the molecular self-assembly mechanism of reflectin's basic unit-the protopeptide sequence YMDMSGYQ-as a means to understand reflectin's assembly phenomena. Protopeptide self-assembly was triggered by different environmental cues, yielding supramolecular hydrogels, and characterized by experimental and theoretical methods. Protopeptide films were also prepared to assess optical properties. Our results support the hypothesis for the protopeptide aggregation model at an atomistic level, led by hydrophilic and hydrophobic interactions mediated by tyrosine residues. Protopeptide-derived films were optically active, presenting diffuse reflectance in the visible region of the light spectrum. Hence, these results contribute to a better understanding of the protopeptide structural assembly, crucial for the design of peptide- and reflectin-based functional materials.

Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe

The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (V_L) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.

Electrostatic complementarity at the interface drives transient protein-protein interactions

Understanding the mechanisms driving bio-molecules binding and determining the resulting complexes' stability is fundamental for the prediction of binding regions, which is the starting point for drug-ability and design. Characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions, and the consequent shape complementarity between the interacting molecular surfaces are well established. However, no consensus has yet been reached on the role of electrostatic. Here, we perform extensive analyses on a large dataset of protein complexes for which both experimental binding affinity and pH data were available. Probing the amino acid composition, the disposition of the charges, and the electrostatic potential they generated on the protein molecular surfaces, we found that (i) although different classes of dimers do not present marked differences in the amino acid composition and charges disposition in the binding region, (ii) homodimers with identical binding region show higher electrostatic compatibility with respect to both homodimers with non-identical binding region and heterodimers. Interestingly, (iii) shape and electrostatic complementarity, for patches defined on short-range interactions, behave oppositely when one stratifies the complexes by their binding affinity: complexes with higher binding affinity present high values of shape complementarity (the role of the Lennard-Jones potential predominates) while electrostatic tends to be randomly distributed. Conversely, complexes with low values of binding affinity exploit Coulombic complementarity to acquire specificity, suggesting that electrostatic complementarity may play a greater role in transient (or less stable) complexes. In light of these results, (iv) we provide a novel, fast, and efficient method, based on the 2D Zernike polynomial formalism, to measure electrostatic complementarity without the need of knowing the complex structure. Expanding the electrostatic potential on a basis of 2D orthogonal polynomials, we can discriminate between transient and permanent protein complexes with an AUC of the ROC of [Formula: see text] 0.8. Ultimately, our work helps shedding light on the non-trivial relationship between the hydrophobic and electrostatic contributions in the binding interfaces, thus favoring the development of new predictive methods for binding affinity characterization.

Unique Peptides of Cathelicidin-1 in the Early Detection of Mastitis-In Silico Analysis

Based on the results of previously performed clinical studies, cathelicidin-1 has been proposed as a potential biomarker for the early diagnosis of mastitis in ewes. It has been hypothesized that the detection of unique peptides (defined as a peptide, irrespective of its length, that exists in only one protein of a proteome of interest) and core unique peptides (CUPs) (representing the shortest peptide that is unique) of cathelicidin-1 may potentially improve its identification and consequently the diagnosis of sheep mastitis. Peptides of sizes larger than those of the size of CUPs, which include consecutive or over-lapping CUPs, have been defined as 'composite core unique peptides' (CCUPs). The primary objective of the present study was the investigation of the sequence of cathelicidin-1 detected in ewes' milk in order to identify its unique peptides and core unique peptides, which would reveal potential targets for accurate detection of the protein. An additional objective was the detection of unique sequences among the tryptic digest peptides of cathelicidin-1, which would improve accuracy of identification of the protein when performing targeted MS-based proteomics. The potential uniqueness of each peptide of cathelicidin-1 was investigated using a bioinformatics tool built on a big data algorithm. A set of CUPs was created and CCUPs were also searched. Further, the unique sequences in the tryptic digest peptides of cathelicidin-1 were also detected. Finally, the 3D structure of the protein was analyzed from predicted models of proteins. In total, 59 CUPs and four CCUPs were detected in cathelicidin-1 of sheep origin. Among tryptic digest peptides, there were six peptides that were unique in that protein. After 3D structure analysis of the protein, 35 CUPs were found on the core of cathelicidin-1 of sheep origin and among them, 29 were located on amino acids in regions of the protein with 'very high' or 'confident' estimates of confidence of the structure. Ultimately, the following six CUPs: QLNEQ, NEQS, EQSSE, QSSEP, EDPD, DPDS, are proposed as potential antigenic targets for cathelicidin-1 of sheep. Moreover, another six unique peptides were detected in tryptic digests and offer novel mass tags to facilitate the detection of cathelicidin-1 during MS-based diagnostics.

Improving the generalizability of protein-ligand binding predictions with AI-Bind

Identifying novel drug-target interactions is a critical and rate-limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, here we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Here we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training to improve binding predictions for novel proteins and ligands. We validate AI-Bind predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. AI-Bind is a high-throughput approach to identify drug-target combinations with the potential of becoming a powerful tool in drug discovery.

The influence of pH on the structure and stability of the Grb2 dimer reveals changes in the inter-domain and molecular interaction: Could it be a modulation mechanism?

Cancer cells present an increased replicative potential as a hallmark. The increased replication leads to a higher intracellular pH. Grb2, an adapter protein, is mainly involved in several types of cancers due to its role in signaling pathways responsible for cell growth and proliferation. At pH 7, we observed a more compact structure, as seen by DLS and ¹H NMR relaxation experiments, with high cooperativity within domains. On the other hand, we observed an increase in disordered structures at pH 8, with relative independence between domains characterized by higher melting temperatures and enthalpy of unfolding. CD and DLS corroborate with these observations at pH 8, conferring more flexibility among the domains, followed by lower unfolding cooperativity and increased hydrodynamic diameter at higher pH. In addition, ¹⁵N-HSQC chemical shift perturbations experiments showed significant differences in the positions of several amino acids spread on the Grb2 structure when pH was changed, which agrees with the previous results. Finally, the molecular dynamic analysis demonstrates that Grb2 presents a movement pattern where both SH3 domains move toward the center of the protein at pH 7. On the contrary, the pattern changes its direction at pH 8, where domains move outside the center of the protein, conferring a more elongated structure at higher pH. So, Grb2 presents significant structural and dynamic changes modulated by pH. If considering the role of Grb2 in cell signaling upstream, these conformational changes could be a critical mechanistic behavior of this protein, preventing/disrupting the stability of the cell signaling pathways related to cancer.

Characterization of the Protein Corona of Three Chairside Hemoderivatives on Melt Electrowritten Polycaprolactone Scaffolds

In tissue engineering, the relationship between a biomaterial surface and the host's immune response during wound healing is crucial for tissue regeneration. Despite hemoderivative functionalization of biomaterials becoming a common tissue-engineering strategy for enhanced regeneration, the characteristics of the protein-biomaterial interface have not been fully elucidated. This study characterized the interface formed by the adsorbed proteins from various hemoderivatives with pristine and calcium phosphate (CaP)-coated polycaprolactone (PCL) melt electrowritten scaffolds. PCL scaffolds were fabricated by using melt electrospinning writing (MEW). Three hemoderivatives (pure platelet-rich plasma (P-PRP), leucocyte platelet-rich plasma (L-PRP) and injectable platelet-rich fibrin (i-PRF)) and total blood PLASMA (control) were prepared from ovine blood. Hemoderivatives were characterized via SEM/EDX, cross-linking assay, weight loss, pH and protein quantification. The interface between PCL/CaP and hemoderivative was examined via FTIR, XPS and electrophoresis. i-PRF/PCL-CaP (1653 cm^-1), PLASMA/PCL-CaP (1652 cm^-1) and i-PRF/PCL (1651 cm^-1) demonstrated a strong signal at the Amide I region. PLASMA and i-PRF presented similar N1s spectra, with most of the nitrogen involved in N-C=O bonds (≈400 eV). i-PRF resulted in higher adsorption of low molecular weight (LMW) proteins at 60 min, while PLASMA exhibited the lowest adsorption. L-PRP and P-PRP had a similar pattern of protein adsorption. The characteristics of biomaterial interfaces can be customized, thus creating a specific hemoderivative-defined layer on the PCL surface. i-PRF demonstrated a predominant adsorption of LMW proteins. Further investigation of hemoderivative functionalized biomaterials is required to identify the differential protein corona composition, and the resultant immune response and regenerative capacity.

Aza-Residue Modulation of Cyclic d,l-α-Peptide Nanotube Assembly with Enhanced Anti-Amyloidogenic Activity

Transient soluble oligomers of amyloid-β (Aβ) are considered among the most toxic species in Alzheimer's disease (AD). Soluble Aβ oligomers accumulate early prior to insoluble plaque formation and cognitive impairment. The cyclic d,l-α-peptide CP-2 (1) self-assembles into nanotubes and demonstrates promising anti-amyloidogenic activity likely by a mechanism involving engagement of soluble oligomers. Systematic replacement of the residues in peptide 1 with aza-amino acid counterparts was performed to explore the effects of hydrogen bonding on propensity to mitigate Aβ aggregation and toxicity. Certain azapeptides exhibited improved ability to engage, alter the secondary structure, and inhibit aggregation of Aβ. Moreover, certain azapeptides disassembled preformed Aβ fibrils and protected cells from Aβ-mediated toxicity. Substitution of the l-norleucine³ and d-serine⁶ residues in peptide 1 with aza-norleucine and aza-homoserine provided, respectively, nontoxic [azaNle³]-1 (4) and [azaHse⁶]-1 (7), that significantly abated symptoms in a transgenic Caenorhabditis elegans AD model by decreasing Aβ oligomer levels.

Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons

Human induced pluripotent stem cell (hiPSC) technologies offer a unique resource for modeling neurological diseases. However, iPSC models are fraught with technical limitations including abnormal aggregation and inefficient maturation of differentiated neurons. These problems are in part due to the absence of synergistic cues of the native extracellular matrix (ECM). We report on the use of three artificial ECMs based on peptide amphiphile (PA) supramolecular nanofibers. All nanofibers display the laminin-derived IKVAV signal on their surface but differ in the nature of their non-bioactive domains. We find that nanofibers with greater intensity of internal supramolecular motion have enhanced bioactivity toward hiPSC-derived motor and cortical neurons. Proteomic, biochemical, and functional assays reveal that highly mobile PA scaffolds caused enhanced β1-integrin pathway activation, reduced aggregation, increased arborization, and matured electrophysiological activity of neurons. Our work highlights the importance of designing biomimetic ECMs to study the development, function, and dysfunction of human neurons.

Tailored Cross-β Assemblies Establish Peptide "Dominos" Structures for Anchoring Undruggable Pharmacophores

β-sheets have the ability to hierarchically stack into assemblies, and much effort has been spent on designing different peptides to regulate their assembly behaviors. Although the progress is remarkable, it remains challenging to manipulate them in a controllable way for achieving both tailored structures and specific functions. In this study, we obtained bola-like peptides using de novo design and combinatorial chemical screening. By regulating the solvent-accessible surface area of the peptide chain, a series of assemblies with different tilt angles and active sites of the β-sheet were obtained, resembling collapsed dominos. The structure-activity relationship of the optimized peptide NQ40 system was established and its ability to target the PD-L1 was demonstrated. This study successfully established the structure-function relationship of β-sheets assemblies and has positive implications on the rational design of peptide assemblies that possess recognition abilities.

Early diagnosis and treatment of Alzheimer's disease by targeting toxic soluble Aβ oligomers

Transient soluble oligomers of amyloid-β (Aβ) are toxic and accumulate early prior to insoluble plaque formation and cognitive impairment in Alzheimer's disease (AD). Synthetic cyclic D,L-α-peptides (e.g., 1) self-assemble into cross β-sheet nanotubes, react with early Aβ species (1-3 mers), and inhibit Aβ aggregation and toxicity in stoichiometric concentrations, in vitro. Employing a semicarbazide as an aza-glycine residue with an extra hydrogen-bond donor to tune nanotube assembly and amyloid engagement, [azaGly⁶]-1 inhibited Aβ aggregation and toxicity at substoichiometric concentrations. High-resolution NMR studies revealed dynamic interactions between [azaGly⁶]-1 and Aβ42 residues F19 and F20, which are pivotal for early dimerization and aggregation. In an AD mouse model, brain positron emission tomography (PET) imaging using stable ⁶⁴Cu-labeled (aza)peptide tracers gave unprecedented early amyloid detection in 44-d presymptomatic animals. No tracer accumulation was detected in the cortex and hippocampus of 44-d-old 5xFAD mice; instead, intense PET signal was observed in the thalamus, from where Aβ oligomers may spread to other brain parts with disease progression. Compared with standard ¹¹C-labeled Pittsburgh compound-B (¹¹C-PIB), which binds specifically fibrillar Aβ plaques, ⁶⁴Cu-labeled (aza)peptide gave superior contrast and uptake in young mouse brain correlating with Aβ oligomer levels. Effectively crossing the blood-brain barrier (BBB), peptide 1 and [azaGly⁶]-1 reduced Aβ oligomer levels, prolonged lifespan of AD transgenic Caenorhabditis elegans, and abated memory and behavioral deficits in nematode and murine AD models. Cyclic (aza)peptides offer novel promise for early AD diagnosis and therapy.

Benchmarking supramolecular adhesive behavior of nanocelluloses, cellulose derivatives and proteins

One of the key steps towards a broader implementation of renewable materials is the development of biodegradable adhesives that can be attained at scale and utilized safely. Recently, cellulose nanocrystals (CNCs) were demonstrated to have remarkable adhesive properties. Herein, we study three classes of naturally synthesized biopolymers as adhesives, namely nanocelluloses (CNFs), cellulose derivatives, and proteins by themselves and when used as additives with CNCs. Among the samples evaluated, the adhesion strength was the highest for bovine serum albumin and hydroxypropyl cellulose (beyond 10 MPa). These were followed by carboxymethylcellulose and CNCs (ca. 5 MPa) and mechanically fibrillated CNFs (ca. 2 MPa), and finally by tempo-oxidized CNFs (0.2 MPa) and lysozyme (1.5 MPa). Remarkably, we find that the anisotropy of adhesion (in plane vs out of plane) falls within a narrow range across the bio-based adhesives studied. Collectively, this study benchmarks bio-based non-covalent adhesives aiming towards their improvement and implementation.

Antibody Interfaces Revealed Through Structural Mining

Antibodies are fundamental effectors of humoral immunity, and have become a highly successful class of therapeutics. There is increasing evidence that antibodies utilize transient homotypic interactions to enhance function, and elucidation of such interactions can provide insights into their biology and new opportunities for their optimization as drugs. Yet the transitory nature of weak interactions makes them difficult to investigate. Capitalizing on their rich structural data and high conservation, we have characterized all the ways that antibody fragment antigen-binding (Fab) regions interact crystallographically. This approach led to the discovery of previously unrealized interfaces between antibodies. While diverse interactions exist, β-sheet dimers and variable-constant elbow dimers are recurrent motifs. Disulfide engineering enabled interactions to be trapped and investigated structurally and functionally, providing experimental validation of the interfaces and illustrating their potential for optimization. This work provides first insight into previously undiscovered oligomeric interactions between antibodies, and enables new opportunities for their biotherapeutic optimization.

Fragment Localized Molecular Orbitals

We introduce the concept of fragment localized molecular orbitals (FLMOs), which are Hartree-Fock molecular orbitals localized in specific fragments constituting a molecular system. In physical terms, we minimize the local electronic energies of the different fragments, at the cost of maximizing the repulsion between them. To showcase the approach, we rationalize the main interactions occurring in large biological systems in terms of interactions between the fragments of the system. In particular, we study an anticancer drug intercalated within DNA and retinal in anabaena sensory rhodopsin as prototypes of molecular systems embedded in biological matrixes. Finally, the FLMOs are exploited to rationalize the formation of two oligomers, prototypes of amyloid diseases, such as Parkinson and Alzheimer.

Single-crystal-to-single-crystal translation of a helical supramolecular polymer to a helical covalent polymer

Polymers possessing helical conformation in the solid state are in high demand. We report a helical peptide-polymer via the topochemical ene-azide cycloaddition (TEAC) polymerization. The molecules of the designed Gly-Phe-based dipeptide, decorated with ene and azide, assemble in its crystals as β-sheets and as supramolecular helices in two mutually perpendicular directions. While the NH…O H-bonding facilitates β-sheet-like stacking along one direction, weak CH…N H-bonding between the azide-nitrogen and vinylic-hydrogen of molecules belonging to the adjacent stacks arranges them in a head-to-tail manner as supramolecular helices. In the crystal lattice, the azide and alkene of adjacent molecules in the supramolecular helix are suitably preorganized for their TEAC reaction. The dipeptide underwent regio- and stereospecific polymerization upon mild heating in a single-crystal-to-single-crystal fashion, yielding a triazoline-linked helical covalent polymer that could be characterized by single-crystal X-ray diffraction studies. Upon heating, the triazoline-linked polymer undergoes denitrogenation to aziridine-linked polymer, as evidenced by differential scanning calorimetry, thermogravimetric analysis, and solid-state NMR analyses.

Protein Based Biomaterials for Therapeutic and Diagnostic Applications

Proteins are some of the most versatile and studied macromolecules with extensive biomedical applications. The natural and biological origin of proteins offer such materials several advantages over their synthetic counterparts, such as innate bioactivity, recognition by cells and reduced immunogenic potential. Furthermore, proteins can be easily functionalized by altering their primary amino acid sequence and can often be further self-assembled into higher order structures either spontaneously or under specific environmental conditions. This review will feature the recent advances in protein-based biomaterials in the delivery of therapeutic cargo such as small molecules, genetic material, proteins, and cells. First, we will discuss the ways in which secondary structural motifs, the building blocks of more complex proteins, have unique properties that enable them to be useful for therapeutic delivery. Next, supramolecular assemblies, such as fibers, nanoparticles, and hydrogels, made from these building blocks that are engineered to behave in a cohesive manner, are discussed. Finally, we will cover additional modifications to protein materials that impart environmental responsiveness to materials. This includes the emerging field of protein molecular robots, and relatedly, protein-based theranostic materials that combine therapeutic potential with modern imaging modalities, including near-infrared fluorescence spectroscopy (NIRF), single-photo emission computed tomography/computed tomography (SPECT/CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and ultrasound/photoacoustic imaging (US/PAI).

Microcrystalline solid–solid transformations of conformationally-responsive solvates, desolvates and a salt of N,N′-(1,4-phenylene)dioxalamic acid: the energetics of hydrogen bonding and n/π → π* interactions

The supramolecular structures of H2pOx·2S (S = DMSO, DMF, ⅓(MeOH·2W), W) solvates were stablished. The energetics of amide N–H⋯O and n/π → π* interactions maintain the crystal network and the reversibility between polymorphs.

A new two-dimensional folding sheet-like coordination polymer assembled from cadmium(II) and (S)-2-(benzylamino)succinic acid: synthesis, structure and properties

A new two-dimensional (2D) coordination polymer, namely, poly[[diaqua[μ₃-(S)-2-(benzylamino)succinato-κ⁴N,O¹:O^1':O⁴]cadmium(II)] monohydrate], {[Cd(C₁₁H₁₁NO₄)(H₂O)₂]·H₂O}_n, has been synthesized by the solvothermal reaction of Cd(CH₃COO)₂·2H₂O with the synthesized ligand (S)-2-(benzylamino)succinic acid (H₂L). The title compound has been structurally characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction analysis. In the crystal structure, each Cd^II cation binds to three carboxylate groups from three symmetry-related L^2- dianions. The tetradentate L^2- ligand links three symmetry-related Cd^II cations into a 2D folding sheet, which can be simplified as a uninodal (3,3)-connected hcb net with the point symbol (6³). In the lattice, all the folding sheets are arranged in an interdigitated fashion and aggregate into zipper-like arrays through interlayer π-π interactions. The large and nonpolar side chain may play an important role in the formation and aggregation of the 2D sheet. The thermal stability and photoluminescence properties of the title compound were investigated, and it exhibits a blue emission with a quantum yield of 8%.

Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide

The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH₂, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.

Identification of key stabilizing interactions of amyloid-β oligomers based on fragment molecular orbital calculations on macrocyclic β-hairpin peptides

Analyzing the electronic states and inter-/intra-molecular interactions of amyloid oligomers expand our understanding of the molecular basis of Alzheimer's disease and other amyloid diseases. In the current study, several high-resolution crystal structures of oligomeric assemblies of Aβ-derived peptides have been studied by the ab initio fragment molecular orbital (FMO) method. The FMO method provides comprehensive details of the molecular interactions between the residues of the amyloid oligomers at the quantum mechanical level. Based on the calculations, two sequential aromatic residues (F19 and F20) and negatively charged E22 on the central region of Aβ have been identified as key residues in oligomer stabilization and potential interesting pharmacophores for preventing oligomer formation.

Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers

The capsids of RNA viruses such as MS2 are great models for studying protein self-assembly because they are made almost entirely of multiple copies of a single coat protein (CP). Although CP is the minimal repeating unit of the capsid, previous studies have shown that CP exists as a homodimer (CP2) even in an acid-disassembled system, indicating that CP2 is an obligate dimer. Here, we investigate the molecular basis of this obligate dimerization using coarse-grained structure-based models and molecular dynamics simulations. We find that, unlike monomeric proteins of similar size, CP populates a single partially folded ensemble whose "foldedness" is sensitive to denaturing conditions. In contrast, CP2 folds similarly to single-domain proteins populating only the folded and the unfolded ensembles, separated by a prominent folding free energy barrier. Several intramonomer contacts form early, but the CP2 folding barrier is crossed only when the intermonomer contacts are made. A dissection of the structure of CP2 through mutant folding simulations shows that the folding barrier arises both from the topology of CP and the interface contacts of CP2. Together, our results show that CP2 is an obligate dimer because of kinetic stability, that is, dimerization induces a folding barrier and that makes it difficult for proteins in the dimer minimum to partially unfold and access the monomeric state without completely unfolding. We discuss the advantages of this obligate dimerization in the context of dimer design and virus stability.

Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain

The native structure of a protein is stabilized by a number of interactions such as main-chain hydrogen bonds and side-chain hydrophobic contacts. However, it has been challenging to determine how these interactions contribute to protein stability at single amino acid resolution. Here, we quantified site-specific thermodynamic stability at the molecular level to extend our understanding of the stabilizing forces in protein folding. We derived the free energy components of individual amino acid residues separately for the folding of the human Pin WW domain based on simulated structures. A further decomposition of the thermodynamic properties into contributions from backbone and side-chain groups enabled us to identify the critical residues in the secondary structure and hydrophobic core formation, without introducing physical modifications to the system as in site-directed mutagenesis methods. By relating the structural and thermodynamic changes upon folding for each residue, we find that the simultaneous formation of the backbone hydrogen bonds and side-chain contacts cooperatively stabilizes the folded structure. The identification of stabilizing interactions in a folding protein at atomic resolution will provide molecular insights into understanding the origin of the protein structure and into engineering a more stable protein.

Optimal Protein Sequence Design Mitigates Mechanical Failure in Silk β-Sheet Nanocrystals

The excellent mechanical strength and toughness of spider silk are well characterized experimentally and understood atomistically using computational simulations. However, little attention has been focused on understanding whether the amino acid sequence of β-sheet nanocrystals, which is the key to rendering strength to silk fiber, is optimally chosen to mitigate molecular-scale failure mechanisms. To investigate this, we modeled β-sheet nanocrystals of various representative small/polar/hydrophobic amino acid repeats for determining the sequence motif having superior nanomechanical tensile strength and toughness. The constant velocity pulling of the central β-strand in the nanocrystal, using steered molecular dynamics, showed that homopolymers of small amino acid (alanine/alanine-glycine) sequence motifs, occurring in natural silk fibroin, have better nanomechanical properties than other modeled structures. Further, we analyzed the hydrogen bond (HB) and β-strand pull dynamics of modeled nanocrystals to understand the variation in their rupture mechanisms and explore sequence-dependent mitigating factors contributing to their superior mechanical properties. Surprisingly, the enhanced side-chain interactions in homopoly-polar/hydrophobic amino acid models are unable to augment backbone HB cooperativity to increase mechanical strength. Our analyses suggest that nanocrystals of pristine silk sequences most likely achieve superior mechanical strength by optimizing side-chain interaction, packing, and main-chain HB interactions. Thus, this study suggests that the nanocrystal β-sheet sequence plays a crucial role in determining the nanomechanical properties of silk, and the evolutionary process has optimized it in natural silk. This study provides insight into the molecular design principle of silk with implications in the genetically modified artificial synthesis of silk-like biomaterials.

Higher-order interfiber interactions in the self-assembly of benzene-1,3,5-tricarboxamide-based peptides in water

Mimicking the complexity of biological systems with synthetic supramolecular materials requires a deep understanding of the relationship between the structure of the molecule and its self-assembly pattern. Herein, we report a series of water-soluble benzene-1,3,5-tricarboxamide-based di- and tripeptide derivatives modified with small non-bulky terminal amine salt to induce self-assembly into twisted one-dimensional higher-order nanofibers. The morphology of nanofibers strongly depends on the nature, order, and quantity of amino acids in the short peptide fragments and vary from simple cylindrical to complex helical. From observations of several fiber-splitting events, we detected interfiber interactions that always occur in a pairwise manner, which implies that the C3 symmetry of benzene-1,3,5-tricarboxamide-based molecules in higher-order fibers becomes gradually distorted, thus facilitating hydrophobic contact interactions between fibrils. The proposed mechanism of self-assembly through hydrophobic contact allowed the successful design of a compound with pH-responsive morphology, and may find use in the future development of complex hierarchical architectures with controlled functionality.