Polypeptide Structure Research Articles

Exploring the Fibrous Nature of Single-Stranded DNA-Collagen Complexes: Nanostructural Observations and Physicochemical Insights.

Nucleic acid-collagen complexes (NACCs) are a self-assembled biomimetic fibrillary platform arising from the spontaneous complexation of single-stranded DNA (ssDNA) oligonucleotides and collagen. NACCs merge the extracellular matrix functionality of collagen with the tunable bioactivity of ssDNA as aptamers for broad biomedical applications. We hypothesize that NACCs offer a hierarchical architecture across multiple length scales that significantly varies compared to native collagen. We investigate this using atomic force microscopy and electron microscopy (transmission electron microscopy and cryogenic electron microscopy). Results demonstrate key topographical differences induced by adding ssDNA oligonucleotides to collagen type I. NACCs form a dense network of intertwined collagen fiber bundles in the microscale and nanoscale while retaining their characteristic D-band periodicities (∼67 nm). Additionally, our exploration of thermodynamic parameters governing the interaction indicates an entropically favorable NACC formation driven by ssDNA. Thermal analysis demonstrates the preservation of collagen's triple helical domains and a more stabilized polypeptide structure at higher temperatures than native collagen. These findings offer important insights into our understanding of the ssDNA-induced complexation of collagen toward the further establishment of structure-property relationships in NACCs and their future development into practical biomaterials. They also provide pathways for manipulating and enhancing collagenous matrices' properties without requiring complex chemical modifications or fabrication procedures.

Nonionic Water-Soluble Oligo(ethylene glycol)-Modified Polypeptides with a β-Sheet Conformation.

The secondary structures of polypeptides, such as an α-helix and a β-sheet, often impart specific properties and functions, making the regulation of their secondary structures of great significance. Particularly, water-soluble polypeptides bearing a β-sheet conformation are rare and challenging to achieve. Here, a series of oligo(ethylene glycol)-modified lysine N-carboxylic anhydrides (EGmK-NCA, where m = 1-3) and the corresponding polymers EGmKn are synthesized, with urethane bonds as the linker between the side-chain EG and lysine. The secondary structure of EGmKn is delicately regulated by both m and n, the length (number of repeating units) of EG and the degree of polymerization (DP), respectively. Among them, EG2Kn adopts a β-sheet conformation with good water solubility at an appropriate DP and forms physically cross-linked hydrogels at a concentration as low as 1 wt %. The secondary structures of EG1Kn can be tuned by DP, exhibiting either a β-sheet or an α-helix, whereas EG3Kn appears to a adopt pure and stable α-helix with no dependence on DP. Compared to previous works reporting EG-modified lysine-derived polypeptides bearing exclusively an α-helix conformation, this work highlights the important and unexpected role of the urethane connecting unit and provides useful case studies for understanding the secondary structure of polypeptides.

Position Matters: Pyridine Regioisomers Influence Secondary Structure and Micelle Morphology in Polymer-Homopolypeptide Micelles.

Polymer-homopolypeptide block copolymers are a class of bioinspired materials that combine the processability and stability of synthetic polymers with the biocompatibility and unique secondary structures of peptides, such as α-helices and β-sheets. These properties make them ideal candidates for a wide variety of applications, for example, in the pharmaceutical field, where they are frequently explored as building blocks for polymeric micelle drug delivery systems. While homopolypeptide side chains can be furnished with an array of different moieties to impart the copolymers with desirable properties, such as stimulus responsivity, pyridine derivatives represent an underutilized functional group for this purpose. Additionally, the interplay between polypeptide side chain structure, secondary conformation, and micelle morphology is not yet well understood, particularly in the case of structural regioisomers. Therefore, in this work, a series of polymer-homopolypeptide copolymers were prepared from a poly(ethylene glycol)-b-poly(glutamic acid) (PEG-b-PGA) backbone, where the pendant carboxylic acid groups were covalently conjugated to a series of pyridine regioisomers by carbodiimide coupling. These pyridine regioisomers differed only in the position of the nitrogen heteroatom, ortho, meta or para, relative to the linking group, generating a series of PEG-b-poly(pyridinylmethyl glutamate) (PEG-b-PMG) copolymers. Following self-assembly of the copolymers in aqueous solutions, dynamic light scattering (DLS) revealed differences in micelle hydrodynamic diameter (Dh) (ranging from ∼60 to 120 nm), while transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) revealed distinctive morphologies ranging from ellipsoidal, to cylindrical, and disc-like, suggesting that subtle changes in positional isomers in the polypeptide block may influence the micelle structure. Analysis of the PEG-b-PMG copolymer micelles by circular dichroism (CD) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy revealed that differences in the morphology were associated with changes in polypeptide secondary structure, which in turn was influenced by the position of the pyridine heteroatom. Overall, these findings contribute to the broader understanding of the relationship between polypeptide structure and micelle morphology and serve as useful insight for the rational design of polymer-polypeptide nanoparticles.

The First Reciprocal Activities of Chiral Peptide Pharmaceuticals: Thymogen and Thymodepressin, as Examples.

Peptides show high promise in the targeting and intracellular delivery of next-generation biotherapeutics. The main limitation is peptides' susceptibility to proteolysis in biological systems. Numerous strategies have been developed to overcome this challenge by chemically enhancing the resistance to proteolysis. In nature, amino acids, except glycine, are found in L- and D-enantiomers. The change from one form to the other will change the primary structure of polypeptides and proteins and may affect their function and biological activity. Given the inherent chiral nature of biological systems and their high enantiomeric selectivity, there is rising interest in manipulating the chirality of polypeptides to enhance their biomolecular interactions. In this review, we discuss the first examples of up-and-down homeostasis regulation by two enantiomeric drugs: immunostimulant Thymogen (L-Glu-L-Trp) and immunosuppressor Thymodepressin (D-Glu(D-Trp)). This study shows the perspective of exploring chirality to remove the chiral wall between L- and D-biomolecules. The selected clinical result will be discussed.

Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides.

Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.

Mechanistic evaluation of contrasting modulation in conformation and catalytic performance of urease by surface interaction of graphene oxide and amine- functionalized graphene oxide nanosheets

The increasing use of graphene-based nanomaterials raises concerns about their potential environmental impact as ecotoxicants. This article examines the interaction and effects of graphene oxide (GO) and its amine-derived (GONH2) 2-D nanosheets on urease dynamics, a crucial enzyme in soil nutrient cycling, through spectroscopic, microscopic, and computational analyses. The findings reveal the distinct interaction mechanisms: GO formed ground - and excited-state complexes with urease; thus, fluorescence quenching was static and dynamic via hydrophobic interaction. In contrast, GONH2 nanosheets formed a ground-state complex by static quenching involving Van der Waals and hydrogen bonding. These interactions were energetically favored and altered tryptophan (Trp) residues’ microenvironment more than tyrosine (Tyr). The average exciton lifetime of urease in the presence of GO have decreased from 4.34 ns to 3.647 ns at the mere concentration of 7.11 µM, while for GONH2, no discernable change (4.16 ns) was observed even at the concentration of 16.75 µM. Primarily, the strong interaction of GO leads to the rearrangement of polypeptide structure, reduced α-helices to 12 %, and increased β-sheets by six times. In contrast, with GONH2, α-helices were reduced to 79 %, and β-sheets were increased by 1.8 times at the similar concentration. Molecular docking revealed that neither GO nor GONH2 interacted with the active site of urease, and binding was primarily via hydrophobic, Van der Waals, and hydrogen bonding, concurrent with in-vitro incubation results. Positive total energy (3.85 kJ mol−1) during molecular docking analysis of urease-GO interaction and inhibition in enzyme activity to 62 %, altered Vmax value (0.04606 ± 0.001 mM/s), without affecting the Km (4.78045 ± 0.12 mM) suggested that inhibition was noncompetitive and steric clashes due to disruptive binding might drove the inhibition. Meanwhile, negative total internal energy (-3.97 kJ mol−1) during urease + GONH2 binding and enhanced enzymatic activity by 32 % in-vitro without altering Vmax (0.063091 ± 0.003 mM/s) and Km (4.953943 ± 0.2 mM) values suggested that urease's binding site was well-complemented by GONH2 nanosheets, serving as a redox-mediator and radical-quencher.

Structural evolution of the conformational ensembles in peptide fibrillar aggregates

Exploring the folding structures and intermolecular recognitions of proteins in their assemblies is essential for revealing the mechanisms of amyloid fibrillar aggregation. However, the molecular-level description of protein structural changes with aggregation progression is challenging due to the heterogeneity of assembled structures. Here we report the use of scanning tunneling microscopy (STM), which is competent in analyzing the highly heterogeneous structures with submolecular resolution, to probe the structures of human islet amyloid polypeptide (hIAPP) assemblies at the different time points of hIAPP fibrillation. The conformational substate ensembles of the β-strands formed by hIAPP as well as the interpeptide interactions are found to change with time in the growth and plateau phases. Detailed analyses of the distribution probability of interpeptide interactions at the different time points manifest that the enthalpic contribution to the structural conversions of β-sheet fibrillation becomes more significant. Our single-molecular level studies highlight the dynamic nature of protein structures within a β-sheet-assembled fibril.

Photocontrol of the β-Hairpin Polypeptide Structure through an Optimized Azobenzene-Based Amino Acid Analogue.

A family of neurodegenerative diseases, including Huntington's disease (HD) and spinocerebellar ataxias, are associated with an abnormal polyglutamine (polyQ) expansion in mutant proteins that become prone to form amyloid-like aggregates. Prior studies have suggested a key role for β-hairpin formation as a driver of nucleation and aggregation, but direct experimental studies have been challenging. Toward such research, we set out to enable spatiotemporal control over β-hairpin formation by the introduction of a photosensitive β-turn mimic in the polypeptide backbone, consisting of a newly designed azobenzene derivative. The reported derivative overcomes the limitations of prior approaches associated with poor photochemical properties and imperfect structural compatibility with the desired β-turn structure. A new azobenzene-based β-turn mimic was designed, synthesized, and found to display improved photochemical properties, both prior and after incorporation into the backbone of a polyQ polypeptide. The two isomers of the azobenzene-polyQ peptide showed different aggregate structures of the polyQ peptide fibrils, as demonstrated by electron microscopy and solid-state NMR (ssNMR). Notably, only peptides in which the β-turn structure was stabilized (azobenzene in the cis configuration) closely reproduced the spectral fingerprints of toxic, β-hairpin-containing fibrils formed by mutant huntingtin protein fragments implicated in HD. These approaches and findings will enable better deciphering of the roles of β-hairpin structures in protein aggregation processes in HD and other amyloid-related neurodegenerative diseases.

Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials.

In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.

Kvantitativno određivanje insulin asparta u rastvoru pomoću Ramanove spektroskopije zasnovano na PLS metodi

The complex structure of medicines containing polypeptide active substances requires the implementation of challenging analytical approaches, based on physicochemical methods, and, where necessary, biological assays for quality control, as well as for the detection of substandard and falsified products. Vibrational spectroscopic techniques, including Raman spectroscopy, are fast, powerful, and non-destructive techniques which, when combined with multivariate chemometric modelling, can provide specific identification, quantitative determination, and insight into the secondary structure of proteins and peptides. The aim of this study was to investigate the possibility of using Raman spectroscopy as a screening method for quantification of pharmaceutical products containing active substances with polypeptide structures. For that purpose, a model based on partial least square (PLS) analysis for quantitative determination of insulin aspart in solution was developed using Raman spectroscopy. The proposed model enables the establishment of a rapid approach for screening of the quality of formulations containing active substances with polypeptide structure, providing the selection of suspected samples that should be further analysed using routine techniques, which are time-consuming and costly.

Production and Applications of Keratinases in Industry

Keratin is an insoluble protein with fibrous structure. It is mainly found in hair,feathers,nail,wool and horn of various animals. These animal accessories can be utilized as animals feed, amino-acids and fertilizers. This insoluble protein is very difficult to degrade and has extreme stability because it has disulfide bonds, hydrogen and hydrophobic interaction present in it. But keratin can be easily digested by keratinase enzyme. Keratinase is an extracellular enzyme. It also degrades keratin in prokaryotic organisms. Microorganisms that produce keratinase are species of Bacillus, Actinobacteria and fungi. It can also be obtained from Streptomyces, Aspergillus, Fervidobacterium, Xanthomonas, Chryseobacteriumand Vibrio. Keratinases produced by microbes arevery diverse due to their chemical as well as physical properties. It is a vigorous enzyme that can survive broad pH and temperature. Their optimum pH range is neutral to alkaline and their optimum temperature reported is 40°C to 60°C. And thermophiles have also been reported for stable microbial activity. Microbial keratinases are cheaply available as compared to conventional producers for keratinases production. They have gained great significance in biotechnology by acting on strong, inflexible cross linked polypeptide structure of keratin instead of ordinary proteolytic enzyme papain, trypsin or pepsin. They are mostly extracted by degrading keratin as substrate. Keratin substrates include feather, hair, wool,horn and nails. This degradation process is helpful in converting keratinous wastes in to fertilizer and poultry feed. Other renowned biotechnological implementations include removing hair from leather by using keratinase, development of bio-polymer from keratinous fiber, delivering drug, hydrolysis of prion proteins and detergent industry. They are also used in converting biomass in to biofuel that significantly boosts power preservation and recycling. The main problem for producing enzymes on large scale is their costly production procedures. This hurdle is overcome by utilizing keratin waste eg feathers of chicken as fermentation substrate on industrial scale. The benefit of utilizing this left over is extremely cost effective fermentation process of keratinase and the effluents are environmental friendly. Keratinase enzyme has become popular and provided newly effective and efficient way for managing waste products by using them on industrial scales as substrates which gives rise to environmental friendly industries for nonstop development.

Rearrangement of the Conformations of Polyampholitic Macromolecules on the Surface of a Charged Spherical Metal Nanoparticle in an Alternating Electric Field: Molecular Dynamic Simulation

The rearrangement of the conformational structure of polyampholytic polypeptides on the surface of a charged spherical gold nanoparticle with its polarity intermittently changing over time was studied using molecular dynamics modeling. The angular distributions of the polypeptide atoms, as well as the radial distributions of the macrochain atomic density in the equatorial region of the nanoparticle with differentiation according to the types of links, were calculated. The polyampholyte shell acquired an annular shape, and the resulting macromolecular ring was located around the charged nanoparticle perpendicularly to the vector of the external electric field strength. With an increase in the charge of the nanoparticle, the ring belt was ordered according to the types of macrochain links, forming concentric annular layers. The diameter of the macromolecular ring depended on the law of distribution of charged units in the macrochain. At elevated temperatures the annular macromolecular ring was deformed at the moments of the highest polarization of the nanoparticle.

Investigation of peanut allergen-procyanidin non-covalent interactions: Impact on protein structure and in vitro allergenicity

Interactions between plant polyphenols and food allergens may be a new way to alleviate food allergies. The non-covalent interactions between the major allergen from peanut (Ara h 2) with procyanidin dimer (PA2) were therefore characterized using spectroscopic, thermodynamic, and molecular simulation analyses. The main interaction between the Ara h 2 and PA2 was hydrogen bonding. PA2 statically quenched the intrinsic fluorescence intensity and altered the conformation of the Ara h 2, leading to a more disordered polypeptide structure with a lower surface hydrophobicity. In addition, the in vitro allergenicity of the Ara h 2-PA2 complex was investigated using enzyme-linked immunosorbent assay (ELISA) kits. The immunoglobulin E (IgE) binding capacity of Ara h 2, as well as the release of allergenic cytokines, decreased after interacting with PA2. When the ratio of Ara h 2-to-PA2 was 1:50, the IgE binding capacity was reduced by around 43 %. This study provides valuable insights into the non-covalent interactions between Ara h 2 and PA2, as well as the potential mechanism of action of the anti-allergic reaction caused by binding of the polyphenols to the allergens.

Determination of Sulfuric Acid Effects on Degradation and Structural Changes of Gelatin Using Fourier-Transform Infrared Spectroscopy and Peak Deconvolution Analysis

The present research was aimed to investigate the effects of sulfuric acid on the structures of gelatin polypeptides. Gelatin samples were immersed in 0.5 M sulfuric acid solution for different periods of 15, 30, 60, 120, 240, 480, 960, and 1920 s, with possible structural changes analyzed by Fourier-transform infrared spectroscopy (FT-IR). Spectra at amide I and II regions were scrutinized using the Gaussian deconvolution method for the resulting changes in the protein secondary structure. The hydrolysis process initially led to a decrease in the α-helix chain and an increase in random coil and β-sheet structures. An equilibrium was formed in degradation and these structures were sequentially turned on each other. Results revealed a correlation between the peak intensity changes of these conformations, so that the degradation process could be observed in the conversion of α-helix to random coil and β-sheet structures and vice versa, indicating the oxidation and expansion of protein structure at the onset of the degradation process.

Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy.

Characterization of the secondary structures of two model polypeptides, poly-l-lysine and poly-l-glutamic acid in aqueous solutions has been demonstrated by hyper-Raman (HR) spectroscopy for the first time. Complementary to infrared (IR) and visible Raman spectroscopy, HR spectroscopy gives the amide I, II, and III bands originating from the polypeptide backbones and the CCH3 symmetric bending mode, enabling us to distinguish different conformations. The α-helix gives the broad and weak amide III band, while the β-sheet and the random coil show similar spectral patterns with different relative intensities between the amide I and II bands. HR spectra from aqueous solutions of the α-helix and the random coil of poly-l-ornithine also possess these spectral features. The HR spectra are analogous to UV resonance Raman (UVRR) spectra, indicating the signal enhancement due to the electronic resonance effect via the π-π* transition. In contrast, the vibrational frequencies of the amide I band in the HR spectra are much higher than those in the IR, visible Raman, and UVRR spectra, suggesting the non-coincidence between HR, IR, and Raman bands. Our finding suggests that HR spectroscopy is promising to provide complementary information on the secondary structures of polypeptides in aqueous solutions as a spectral approach differing from existing vibrational spectroscopic methods.

Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?

We propose a mechanism for α-helix folding of polyalanine in aqueous urea that reconciles experimental and simulation studies. Over 15 μs long, all-atom simulations reveal that, upon dehydrating the protein's first solvation shell, a delicate balance between localized urea-residue dipole interactions and hydrogen bonds dictates polypeptide solvation properties and structure. Our work clarifies the experimentally observed tendency of these alanine-rich systems to form secondary structures at low and intermediate urea concentrations. Moreover, it is consistent with the commonly accepted hydrogen-bond-induced helix unfolding, dominant at high urea concentrations. These results establish a structure-property relationship highlighting the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

Secondary Structure-Governed Phase Separation Behavior in Glutamate-Based Polypeptides.

The phase separation behavior of biomacromolecules plays a key role in the fields of biology and medicine. In this work, we gain a deep insight into how the primary and secondary structures govern and regulate the phase separation behavior of polypeptides. To this end, we synthesized a series of polypeptides with tailorable hydroxyl-containing side chains. The secondary structure of polypeptides can be modulated by the local chemical environment and content of side chains. Interestingly, these polypeptides with different helical contents exhibited upper critical solution temperature behavior with marked differences in the cloud point temperature (Tcp) and the width of hysteresis. The phase transition temperature is highly relevant to the content of secondary structure and interchain interactions of polypeptides. The aggregation/deaggregation and the transition of secondary structure are completely reversible during heating-cooling cycles. Much to our surprise, the recovery rate of the α-helical structure governs the width of hysteresis. This work establishes the structure-property relationship between the secondary structure and phase separation behavior of the polypeptide and delivers new insight into the rational design of peptide-based materials with tailor-made phase separation behavior.

Intrinsic mechanisms for the inhibition effect of graphene oxide on the catalysis activity of alpha amylase

Comprehending the interactions between graphene oxide (GO) and enzymes is critical for understanding the toxicities of GO. In this study, the inherent interactions of GO with α-amylase as a typical enzyme, and the impacts of GO on the conformation and biological activities of α-amylase were systematically investigated. The results reveal that GO formed ground-state complex with α-amylase primarily via hydrogen bonding and van der Waals interactions, thus quenching the intrinsic fluorescence of the protein statically. Particularly, the strong interactions altered the microenvironment of tyrosine and tryptophan residues, caused rearrangement of polypeptide structure, and reduced the contents of α-helices and β-sheets, thus changing the conformational structure of α-amylase. According to molecular docking results, GO binds with the amino acid residues (i.e., His299, Asp300, and His305) of α-amylase mainly through hydrogen bonding, which is in accordance with in vitro incubation experiments. As a consequence, the ability of α-amylase to catalyze starch hydrolysis into glucose was depressed by GO, suggesting that GO might cause dysfunction of α-amylase. This study discloses the intrinsic binding mechanisms of GO with α-amylase and provides novel insights into the adverse effects of GO as it enters organisms.

Molecular Dynamics Simulation of the Conformational Structure of Polyampholyte Polypeptides at the Surface of a Charged Gold Nanoparticle in External Electric Field

Molecular Dynamics Simulation of the Conformational Structure of Polyampholyte Polypeptides at the Surface of a Charged Gold Nanoparticle in External Electric Field

Computational and Functional Insights of Protein Misfolding in Neurodegeneration.

Protein folding is the process by which a polypeptide chain self-assembles into the correct three-dimensional structure, so that it ends up in the biologically active, native state. Under conditions of proteotoxic stress, mutations, or cellular aging, proteins can begin to aggregate into non-native structures such as ordered amyloid fibrils and plaques. Many neurodegenerative diseases involve the misfolding and aggregation of specific proteins into abnormal, toxic species. Experimental approaches including crystallography and AFM (atomic force microscopy)-based force spectroscopy are used to exploit the folding and structural characterization of protein molecules. At the same time, computational techniques through molecular dynamics, fold recognition, and structure prediction are widely applied in this direction. Benchmarking analysis for combining and comparing computational methodologies with functional studies can decisively unravel robust interactions between the side groups of the amino acid sequence and monitor alterations in intrinsic protein dynamics with high precision as well as adequately determine potent conformations of the folded patterns formed in the polypeptide structure.