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Biochemistry Feb 2021The field of protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of... (Review)
Review
The field of protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.
Topics: Amino Acid Sequence; Circular Dichroism; Heme; Hemeproteins; Oxidation-Reduction; Peptides; Protein Conformation, beta-Strand; Protein Engineering; Protein Folding; Protein Structure, Secondary
PubMed: 33533248
DOI: 10.1021/acs.biochem.0c00662 -
Biomaterials Science Mar 2016Hydrogels have been widely studied in various biomedical applications, such as tissue engineering, cell culture, immunotherapy and vaccines, and drug delivery.... (Review)
Review
Hydrogels have been widely studied in various biomedical applications, such as tissue engineering, cell culture, immunotherapy and vaccines, and drug delivery. Peptide-based nanofibers represent a promising new strategy for current drug delivery approaches and cell carriers for tissue engineering. This review focuses on the recent advances in the use of self-assembling engineered β-sheet peptide assemblies for biomedical applications. The applications of peptide nanofibers in biomedical fields, such as drug delivery, tissue engineering, immunotherapy, and vaccines, are highlighted. The current challenges and future perspectives for self-assembling peptide nanofibers in biomedical applications are discussed.
Topics: Cell Culture Techniques; Drug Delivery Systems; Humans; Hydrogels; Immunotherapy; Nanofibers; Protein Conformation, beta-Strand; Tissue Engineering; Vaccines
PubMed: 26700207
DOI: 10.1039/c5bm00472a -
Chembiochem : a European Journal of... Apr 2024The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble... (Review)
Review
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
Topics: Protein Conformation, beta-Strand; Peptides; Proteins; Protein Folding; Temperature
PubMed: 38275210
DOI: 10.1002/cbic.202300745 -
ACS Synthetic Biology Jan 2022The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric...
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a p of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
Topics: Circular Dichroism; Peptides; Protein Conformation; Protein Conformation, beta-Strand; Proteins; Zinc
PubMed: 34935365
DOI: 10.1021/acssynbio.1c00396 -
The Journal of Physical Chemistry... Oct 2022The ability to detect and characterize multiple secondary structures or polymorphs within peptide and protein aggregates is crucial to treatment and prevention of...
The ability to detect and characterize multiple secondary structures or polymorphs within peptide and protein aggregates is crucial to treatment and prevention of amyloidogenic diseases, production of novel biomaterials, and many other applications. Here we report a label-free method to distinguish multiple β-sheet configurations within a single peptide aggregate using two-dimensional infrared spectroscopy. By calculating the transition dipole strength (TDS) spectrum from the ratio of linear and two-dimensional signals, we can extract maximum TDS values which provide higher sensitivity to vibrational coupling, and thus specifics of protein structure, than vibrational frequency alone. TDS spectra of AcKFE8 aggregates reveal two distinct β-sheet structures within fibers that appear homogeneous by other techniques. Furthermore, TDS spectra taken during early stages of aggregation show additional peaks that may indicate the presence of more weakly coupled β-sheet structures. These results demonstrate a unique and powerful spectroscopic method capable of distinguishing multiple oligomeric and polymorphic motifs throughout the aggregation using only native vibrational modes.
Topics: Biocompatible Materials; Peptides; Protein Aggregates; Protein Conformation, beta-Strand; Spectrophotometry, Infrared
PubMed: 36201012
DOI: 10.1021/acs.jpclett.2c02292 -
The Journal of Physical Chemistry. B Dec 2021Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional...
Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional biomaterials. Current efforts seek to design pairs of peptides, A and B, that form nanostructures (e.g., β-sheets with ABABA-type β-strand patterning) while resisting self-assembly (e.g., AAAAA-type or BBBBB-type β-sheets). To confer coassembly behavior, most existing designs have been based on highly charged variants of known self-assembling peptides; like-charge repulsion limits self-assembly while opposite-charge attraction promotes coassembly. Recent analyses using solid-state NMR and coarse-grained simulations reveal that preconceived notions of structure and molecular organization are not always correct. This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly.
Topics: Biocompatible Materials; Magnetic Resonance Spectroscopy; Nanostructures; Peptides; Protein Conformation, beta-Strand
PubMed: 34905370
DOI: 10.1021/acs.jpcb.1c04873 -
Nano Letters May 2022Amyloid peptide (AP) self-assembly is a hierarchical process. However, the mechanistic rule of guiding peptides to organize well-ordered nanostructure in a clear and...
Amyloid peptide (AP) self-assembly is a hierarchical process. However, the mechanistic rule of guiding peptides to organize well-ordered nanostructure in a clear and precise manner remains poorly understood. Herein we explored the molecular insight of AP motif aggregates underlying hierarchical process with helical fibrillar structure by atomic force microscope, cryo-electron microscopy (cryo-EM), and molecular dynamics simulation. AP assembly encompasses well-ordered twisted fibrils with uniform morphology, size, and periodicity. More importantly, a heterozipper β-sheet was identified in a protofilament of AP assembly determined by cryo-EM with a high resolution of 3.5 Å. Each peptide heterozipper was further composed of two antiparallel β strands and arranged by an alternative manner in a protofilament. The hydrophobic core and hydrophilic area in each zipper played the significant role for peptide assembling. This work proposed and verified the rule facilitating the basic building unit to form twisted fibrils and gave the explanation of peptide hierarchical assembling.
Topics: Amyloid; Amyloidosis; Cryoelectron Microscopy; Humans; Molecular Dynamics Simulation; Peptides; Protein Conformation, beta-Strand
PubMed: 35467349
DOI: 10.1021/acs.nanolett.2c00596 -
Biomacromolecules Feb 2023Intrinsically disordered proteins (IDPs) play an important role in molecular biology and medicine because their induced folding can lead to so-called conformational...
Intrinsically disordered proteins (IDPs) play an important role in molecular biology and medicine because their induced folding can lead to so-called conformational diseases, where β-amyloids play an important role. Still, the molecular folding process into the different substructures, such as parallel/antiparallel or extended β-sheet/crossed β-sheet is not fully understood. The recombinant spider silk protein eADF4(Cx) consisting of repeating modules C, which are composed of a crystalline (pep-c) and an amorphous peptide sequence (pep-a), can be used as a model system for IDP since it can assemble into similar structures. In this work, blend films of the pep-c and pep-a sequences were investigated to modulate the β-sheet formation by varying the molar fraction of pep-c and pep-a. Dichroic Fourier-transform infrared spectroscopy (FTIR), circular dichroism, spectroscopic ellipsometry, atomic force microscopy, and IR nanospectroscopy were used to examine the secondary structure, the formation of parallel and antiparallel β-sheets, their orientation, and the microscopic roughness and phase formation within peptide blend films upon methanol post-treatment. New insights into the formation of filament-like structures in these silk blend films were obtained. Filament-like structures could be locally assigned to β-sheet-rich structures. Further, the antiparallel or parallel character and the orientation of the formed β-sheets could be clearly determined. Finally, the ideal ratio of pep-a and pep-c sequences found in the fibroin 4 of the major ampullate silk of spiders could also be rationalized by comparing the blend and spider silk protein systems.
Topics: Animals; Silk; Protein Conformation, beta-Strand; Peptides; Fibroins; Protein Structure, Secondary; Recombinant Proteins; Spiders
PubMed: 36632028
DOI: 10.1021/acs.biomac.2c01266 -
The Journal of Physical Chemistry. B May 2021Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain...
Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain peptides or proteins responsible for different neurodegenerative diseases were studied to understand whether they can mimic the property and function of native peptides or not. It was reported that such a kind of peptide adopts a β-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a β-sheet conformation. In this article, we are first time reporting the crystal structure of two tetrapeptides: Boc-GAII-OMe (Peptide 1) and Boc-GGVV-OMe (Peptide 2), composed of aliphatic amino acids, and the sequences are similar to the Aβ-peptide fragments Aβ and Aβ , respectively. In the solid-state, they are self-assembled in an antiparallel β-sheet fashion. The peptide units are connected by the strong amide hydrogen-bonding (N-H···O) interactions. Apart from that, other noncovalent interactions are also present, which help to stabilize the cross-β-sheet arrangement. Interestingly, in the crystal structure of Peptide 1, noncovalent C···C interaction between the electron-deficient carbonyl carbon, and the electron-rich sp-carbon atom is observed, which is quite rare in the literature. The calculated torsion angles for these peptides are lying in the β-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel β-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly β-sheet-like conformation in the aqueous solution. Under cross-polarized light, Congo Red stained both peptides showed green-gold color due to birefringence indicating their amyloidogenic nature. This result indicates that the short peptide composed of aliphatic amino acid is capable of forming a β-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.
Topics: Amyloid; Circular Dichroism; Peptides; Protein Conformation, beta-Strand; Spectroscopy, Fourier Transform Infrared
PubMed: 33886330
DOI: 10.1021/acs.jpcb.0c10920 -
Current Opinion in Chemical Biology Oct 2019Protein-protein interactions involving β-sheet secondary structures have been questioned in many fatal human diseases such as cancer, autoimmune and neurodegenerative... (Review)
Review
Protein-protein interactions involving β-sheet secondary structures have been questioned in many fatal human diseases such as cancer, autoimmune and neurodegenerative diseases. Small selective peptide derivatives and analogues are promising drug candidates for inhibiting this poorly known class of PPIs. In this review, we will highlight the main strategies developed for designing linear and cyclic peptide and peptidomimetic inhibitors of PPIs involving β-sheet structures. These compounds either do not adopt preferred conformations or can mimic protein secondary structures such as β-strands, β-hairpins or α-helices.
Topics: Antibodies; Humans; Macrocyclic Compounds; Optical Tweezers; Peptides; Peptides, Cyclic; Peptidomimetics; Protein Binding; Protein Conformation, beta-Strand; Protein Structure, Secondary; Proteins
PubMed: 31590141
DOI: 10.1016/j.cbpa.2019.07.008