Peptide Bond Research Articles

Natural serine proteases and their applications in combating amyloid formation

Background and purpose: Amyloidosis is a group of diseases including diabetes type II and neurological disorders, such as Alzheimer’s disease, Parkinson’s disease, prion disease, etc., where a common trait is observed; accumulation of misfolded protein at different parts of the body, especially the brain which manifests the typical symptoms like dementia, movement disorders, etc. These misfolded proteins, named amyloids, are protease resistant and thus it becomes difficult to manage these diseases in vivo. Enzymes that catalyse the complete breakdown of proteins are known as proteases. The peptide bonds in proteins are degraded by these serine proteases, which cause amyloid disaggregation. Experimental approach: We have searched for related articles using the search engines Google Scholar, PubMed, and Scopus for the past 10 years, selected the relevant articles, and written the outcomes and benefits of protease using the medical topic “serine protease” and the following text phrases -keratinase, lumbrokinase, serratiopeptidase, nattokinase. Key results: Alkaline serine proteases exhibit activity within the neutral to alkaline pH range. They are most capable of degrading host complement proteins, cytokines, and host clotting factors mostly due to their serine centre or metallotype. Because of its potential usage in food, pharmaceutical, and other industrial domains, this category of enzymes has been extensively investigated. Specifically, serine proteases are a group of enzymes that can be consumed orally and are stable in our gastrointestinal tract. Conclusion: In this review, we discussed the role of different serine proteases in amyloid aggregate inhibition and their potential application in treating amyloidosis.

Protein structure alignment by reseek improves sensitivity to remote homologs.

Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opportunities and challenges to bioinformatics. Reseek is a novel protein structure alignment algorithm based on sequence alignment where each residue in the protein backbone is represented by a letter in a "mega-alphabet" of 85,899,345,920 (∼1011) distinct states. Reseek achieves substantially improved sensitivity to remote homologs compared to state-of-the-art methods including DALI, TMalign and Foldseek, with comparable speed to Foldseek, the fastest previous method. Scaling to large databases of AI-predicted folds is analyzed. Foldseek E-values are shown to be under-estimated by several orders of magnitude, while Reseek E-values are in good agreement with measured error rates. https://github.com/rcedgar/reseek. Supplementary data are available at Bioinformatics online.

Comprehensive Overview of the Amide Linker Modification in the Succinate Dehydrogenase Inhibitors.

Succinate dehydrogenase inhibitors (SDHIs) have become one of the most important classes of agrochemical fungicides. According to the data from FRAC, the resistance risk for SDHIs had reached up to medium and even to high. In general, the chemical structure of SDHIs mainly contained three fragments: an acid core, a hydrophobic tail, and an amide linker, corresponding to three modification directions for each fragment. Among them, amide linker modification (ALM) has become a research hotspot for the design of novel SDHIs fungicides in recent years. We presented here a detailed review on the ALM strategy in the past decade, and some of them had entered the market. According to their chemical structures, ALM strategy were classified into four parts: (1) linked aliphatic chain between amide bond and hydrophobic tail, (2) introducing substituents to replacing hydrogen atom in the amide bond, (3) reverse extending the amide linker, and (4) changed with other bioisosteres. Moreover, the structure-activity relationship and the interaction mechanism of ALM-SDHI with SDH were discussed. This review aims to provide a global perspective on research and development of novel SDHIs, as well as suggestions for food safety management.

The ribosome comes to life.

The ribosome, together with its tRNA substrates, links genotype to phenotype by translating the genetic information carried by mRNA into protein. During the past half-century, the structure and mechanisms of action of the ribosome have emerged from mystery and confusion. It is now evident that the ribosome is an ancient RNA-based molecular machine of staggering structural complexity and that it is fundamentally similar in all living organisms. The three central functions of protein synthesis-decoding, catalysis of peptide bond formation, and translocation of mRNA and tRNA-are based on elegant mechanisms that evolved from the properties of RNA, the founding macromolecule of life. Moreover, all three of these functions (and even life itself) seem to proceed in defiance of entropy. Protein synthesis thus appears to exploit both the energy of GTP hydrolysis and peptide bond formation to constrain the directionality and accuracy of events taking place on the ribosome.

Macromorphological characterization of filamentous fungi isolated from ripened cheese samples as potential protease producers

Proteases catalyze the hydrolysis of amide bonds of peptides and proteins, thereby playing crucial roles in the functioning of organisms, as well as having an important role in industrial processes. They are one of the three most widely commercially marketed enzymes. This study aimed to analyze the macromorphological characteristics of seventeen filamentous fungi and identify potential protease producers. The microorganisms were cultivated on a solid culture medium containing skim milk powder at 30 °C for seven days. After the incubation period, macroscopic morphological characteristics of the fungi were observed, and the strain diameters and the enzymatic halos around the colonies were measured. As a result, a wide variety of characteristics among the filamentous fungi was observed, highlighting the diversity of this group. Additionally, Potentials asprotease producers under the conditions presented were observed for eight filamentous fungi. These findings suggest that the these fungal strains might be valuable resources for the production of proteases with high biotechnological potentials.

Photochemical Deracemization of N‐Carboxyanhydrides En Route to Chiral α‐Amino Acid Derivatives

AbstractReadily accessible, racemic N‐carboxyanhydrides (NCAs) of α‐amino acids underwent a deracemization reaction upon irradiation at λ=366 nm in the presence of a chiral benzophenone catalyst. The enantioenriched NCAs (up to 98 % ee) serve as activated α‐amino acid surrogates and, due to their instability, they were directly converted into consecutive products. N‐Protected α‐amino acid esters were obtained after reaction with MeOH and N‐benzoylation (14 examples, 70 %‐quant., 82–96 % ee). Other consecutive reactions included amide (ten examples, 65 %‐quant., 90–98 % ee) and peptide (three examples, 75–89 %, d. r.=97/3 to 94/6) bond formation. Limitations of the method relate for some NCAs to issues with solubility, photooxidation, and high configurational lability.

Photochemical Deracemization of N-Carboxyanhydrides En Route to Chiral α-Amino Acid Derivatives.

Readily accessible, racemic N-carboxyanhydrides (NCAs) of α-amino acids underwent a deracemization reaction upon irradiation at λ=366 nm in the presence of a chiral benzophenone catalyst. The enantioenriched NCAs (up to 98 % ee) serve as activated α-amino acid surrogates and, due to their instability, they were directly converted into consecutive products. N-Protected α-amino acid esters were obtained after reaction with MeOH and N-benzoylation (14 examples, 70 %-quant., 82-96 % ee). Other consecutive reactions included amide (ten examples, 65 %-quant., 90-98 % ee) and peptide (three examples, 75-89 %, d. r.=97/3 to 94/6) bond formation. Limitations of the method relate for some NCAs to issues with solubility, photooxidation, and high configurational lability.

Site‐Selective Construction of N‐Linked Glycopeptides through Photoredox Catalysis

AbstractThe glycosylation of peptides and proteins can significantly impact their intrinsic properties, such as conformation, stability, antigenicity, and immunogenicity. Current methods for preparing N‐linked glycopeptides typically rely on amide bond formation, which can be limited by the presence of reactive functional groups like acids and amines. Late‐stage functionalization of peptides offers a promising approach to obtaining N‐linked glycopeptides. In this study, we demonstrate the preparation of N‐linked glycopeptides through a photoredox‐catalyzed site‐selective Giese addition between N‐glycosyl oxamic acid and peptides containing dehydroalanine (Dha) under visible light conditions. Unlike traditional methods that rely on the coupling of aspartic acid and glycosylamine, this approach utilizes the conjugation of N‐glycosylated carbamoyl radicals with Dha, facilitating the straightforward modification of complex peptides.

Upcycling of Polyamide Wastes to Tertiary Amines Using Mo Single Atoms and Rh Nanoparticles

AbstractThe pursuit of sustainable practices through the chemical recycling of polyamide wastes holds significant potential, particularly in enabling the recovery of a range of nitrogen‐containing compounds. Herein, we report a novel strategy to upcycle polyamide wastes to tertiary amines with the assistance of H2 in acetic acid under mild conditions (e.g., 180 °C), which is achieved over anatase TiO2 supported Mo single atoms and Rh nanoparticles. In this protocol, the polyamide is first converted into diacetamide intermediates via acidolysis, which are subsequently hydrogenated into corresponding carboxylic acid monomers and tertiary amines in 100 % selectivity. It is verified that Mo single atoms and Rh nanoparticles work together to activate both amide bonds of the diacetamide intermediate, and synergistically catalyze its hydrodeoxygenation to form tertiary amine, but this catalyst is ineffective for hydrogenation of carboxylic acid. This work presents an effective way to reconstruct various polyamide wastes into tertiary amines and carboxylic acids, which may have promising application potential.

Site-Selective Construction of N-Linked Glycopeptides through Photoredox Catalysis.

The glycosylation of peptides and proteins can significantly impact their intrinsic properties, such as conformation, stability, antigenicity, and immunogenicity. Current methods for preparing N-linked glycopeptides typically rely on amide bond formation, which can be limited by the presence of reactive functional groups like acids and amines. Late-stage functionalization of peptides offers a promising approach to obtaining N-linked glycopeptides. In this study, we demonstrate the preparation of N-linked glycopeptides through a photoredox-catalyzed site-selective Giese addition between N-glycosyl oxamic acid and peptides containing dehydroalanine (Dha) under visible light conditions. Unlike traditional methods that rely on the coupling of aspartic acid and glycosylamine, this approach utilizes the conjugation of N-glycosylated carbamoyl radicals with Dha, facilitating the straightforward modification of complex peptides.

Structural, biophysical, and biochemical insights into C–S bond cleavage by dimethylsulfone monooxygenase

Sulfur is an essential element for life. Bacteria can obtain sulfur from inorganic sulfate; but in the sulfur starvation-induced response, Pseudomonads employ two-component flavin-dependent monooxygenases (TC-FMOs) from the msu and sfn operons to assimilate sulfur from environmental compounds including alkanesulfonates and dialkylsulfones. Here, we report binding studies of oxidized FMN to enzymes involved within the P. fluorescens enzymatic pathway responsible for converting dimethylsulfone (DMSO2) to sulfite. In this catabolic pathway, SfnG serves as the initial TC-FMO for sulfur assimilation, which is investigated in detail by solving the 2.6-Å resolution crystal structure of unliganded SfnG and the 1.75-Å resolution crystal structure of the SfnG ternary complex containing FMN and DMSO2. We find that SfnG adopts a (β/α)8 barrel fold with a distinct quaternary configuration from other tetrameric class C TC-FMOs. To probe the unexpected tetramer arrangement, structural heterogeneity is assessed by chromatography and light scattering to confirm ligand binding correlates with a tetramer. Binding of FMN and DMSO2 accompanies ordering of the active site, with DMSO2 bound on the si-face of the flavin. A previously unobserved protein backbone conformation is found within the oxygen-binding site on the re-face of the flavin. Functional assays and the positioning of ligands with respect to the oxygen-binding site are consistent with use of an N5-(hydro)peroxyflavin pathway. Biochemical endpoint assays and docking studies reveal SfnG breaks the C-S bond of a range of dialkylsulfones.

UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.

Chemical shifts are a readily obtainable NMR observable that can be measured with high accuracy, and because they are sensitive to conformational averages and the local molecular environment, they yield detailed information about protein structure in solution. To predict chemical shifts of protein structures, we introduced the UCBShift method that uniquely fuses a transfer prediction module, which employs sequence and structure alignments to select reference chemical shifts from an experimental database, with a machine learning model that uses carefully curated and physics-inspired features derived from X-ray crystal structures to predict backbone chemical shifts for proteins. In this work, we extend the UCBShift 1.0 method to side chain chemical shift prediction to perform whole protein analysis, which, when validated against well-defined test data shows higher accuracy and better reliability compared to the popular SHIFTX2 method. With the greater abundance of cleaned protein shift-structure data and the modularity of the general UCBShift algorithms, users can gain insight into different features important for residue-specific stabilizing interactions for protein backbone and side chain chemical shift prediction. We suggest several backward and forward applications of UCBShift 2.0 that can help validate AlphaFold structures and probe protein dynamics.

Innovative biopolymers composite based thin film for wound healing applications

Efficient wound and burn healing is crucial for minimising complications, preventing infections, and enhancing overall well-being, necessitating the development of innovative strategies. This study aimed to formulate a novel thin film combining chitosan, carboxymethyl cellulose, tannic acid, and beeswax for improved wound healing applications. Several formulations, incorporating chitosan, carboxymethyl cellulose, tannic acid, and beeswax in various percentages, were utilized to deposit thin films via the solvent evaporation technique, Mechanical properties, morphology, antioxidant activity, antibacterial efficacy, and wound healing potential were evaluated. The optimized thin film (M4), composed of 2% chitosan, 2% carboxymethyl cellulose, and 1% tannic acid, along with 0.2% glycerol and 0.2% tween80, exhibited a thickness of 39.0 ± 1.14 μm and a tensile strength of 0.275 ± 0.003 MPa. It demonstrated a swelling degree of 283.0 ± 2.0% and a drug release capacity of 89.4% within 24 h. The film also showed a low contact angle of 40.5° and a water vapour transmission rate of 1912.25 ± 13.10 g m−2 0.24 h−1. FT-IR spectroscopy indicated that chitosan and carboxymethyl cellulose were cross-linked through amide linkages, with tannic acid occupying the interstitial spaces and hydrogen bonding stabilizing the structure. Microscopy of M4 revealed a uniform morphology. The film exhibited strong antioxidant activity of (95.17 ± 0.02%) and antibacterial efficiency (80.8%) against S. aureus. In a rabbit model, the film significantly enhanced burn and excision wound recovery, with 90.0 ± 3.3% healing for burns and 88.85 ± 1.7% for infected wounds by day 7. Complete skin regeneration was observed within 10–12 days. The M4 thin film demonstrated exceptional mechanical properties and bioactivity, offering protection against pathogens and promoting efficient wound healing. These findings suggest its potential for further investigation in treating various infections and its role in developing novel therapeutic interventions.

Design, preclinical evaluation, and first-in-human PET study of [68Ga]Ga-PSFA-01: a PSMA/FAP heterobivalent tracer.

Prostate cancer (PCa), characterized by tumor heterogeneity, may exhibit low or absent prostate-specific membrane antigen (PSMA) expression in cancerous lesions, limiting the detection sensitivity of monospecific probes. Given that fibroblast activation protein (FAP) is frequently overexpressed in the tumor microenvironment (TME), we developed a PSMA/FAP dual-targeting tracer to address this limitation. The precursor (PSFA-01) was synthesized by coupling a quinolone-based FAP-targeting scaffold and EuK with HBED-CC via amide bonds. The dual-receptor-binding affinity and cell uptake of PSFA-01 and [natGa]Ga-PSFA-01 was evaluated in vitro. Micro-PET/CT imaging was performed on 22Rv1 and U87MG tumor-bearing mice. The feasibility of [68Ga]Ga-PSFA-01 PET/CT in a clinical setting was evaluated in a metastatic prostate cancer patient, and the results were compared with those of [68Ga]Ga-FAPI-04 and [68Ga]Ga-PSMA-11 PET/CT. PSFA-01 and [natGa]Ga-PSFA-01 showed high affinity for both FAP and PSMA proteins (Ki = 0.14-1.02 nM). On micro-PET/CT imaging, the 22Rv1 tumor uptake of [68Ga]Ga-PSFA-01 (SUVmax = 3.89 ± 0.47) was higher than that of [68Ga]Ga-PSMA-11 (SUVmax = 2.96 ± 0.48). The U87MG tumor uptake of [68Ga]Ga-PSFA-01 was significantly higher (SUVmax = 7.29 ± 1.13) than [68Ga]Ga-FAPI-04 (SUVmax = 0.28 ± 0.12), showing tumor to muscle ratio as 12.68 ± 1.93 at 1h p.i. On clinical trial, the primary tumor and metastatic lesions were distinctly identified by [68Ga]Ga-PSFA-01 (21 lesions), demonstrating superior performance compared to [68Ga]Ga-FAPI-04 (3 lesions) and [68Ga]Ga-PSMA-11 (13 lesions) in terms of lesion count and specificity. [68Ga]Ga-PSFA-01 exhibited satisfactory PSMA and FAP dual-receptor-targeting properties both in vitro and in vivo. This study highlights the clinical feasibility of [68Ga]Ga-PSFA-01 PET/CT for detecting metastatic tumors of prostate cancer more sensitively compared to monomeric [68Ga]Ga-PSMA-11 and [68Ga]Ga-FAPI-04, which also suggests that a PSMA/FAP dual-targeted radionuclide therapy could potentially overcome challenges related to tumor heterogeneity and insufficient PSMA expression in PCa. Clinical trial registry NCT06387381, Registered 1 May 2024.

Aminolipids in bacterial membranes and the natural environment.

Our comprehension of membrane function has predominantly advanced through research on glycerophospholipids, also known as phosphoglycerides, which are glycerol phosphate-based lipids found across all three domains of life. However, in bacteria, a perplexing group of lipids distinct from glycerol phosphate-based ones also exists. These are amino acid-containing lipids that form an amide bond between an amino acid and a fatty acid. Subsequently, a second fatty acid becomes linked, often via the 3-hydroxy group on the first fatty acid. These amide-linked aminolipids have, as of now, been exclusively identified in bacteria. Several hydrophilic head groups have been discovered in these aminolipids including ornithine, glutamine, glycine, lysine, and more recently, a sulfur-containing non-proteinogenic amino acid cysteinolic acid. Here, we aim to review current advances in the genetics, biochemistry and function of these aminolipids as well as giving an ecological perspective. We provide evidence for their potential significance in the ecophysiology of all major microbiomes i.e. gut, soil and aquatic as well as highlighting their important roles in influencing biological interactions.

Molecular-scale dissipative chemistry drives the formation of nanoscale assemblies and their macroscale transport.

Fuelled chemical systems have considerable functional potential that remains largely unexplored. Here we report an approach to transient amide bond formation and use it to harness chemical energy and convert it to mechanical motion by integrating dissipative self-assembly and the Marangoni effect in a source-sink system. Droplets are formed through dissipative self-assembly following the reaction of octylamine with 2,3-dimethylmaleic anhydride. The resulting amides are hydrolytically labile, making the droplets transient, which enables them to act as a source of octylamine. A sink for octylamine was created by placing a drop of oleic acid at the air-water interface. This source-sink system sets up a gradient in surface tension, which gives rise to a macroscopic Marangoni flow that can transport the droplets in solution with tunable speed. Carbodiimides can fuel this motion by converting diacid waste back to anhydride. This study shows how fuelling at the molecular level can, via assembly at the supramolecular level, lead to liquid flow at the macroscopic level.

Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation.

HNTX-XXI, a peptide toxin derived from the venom of the spider Ornithoctonus hainana, comprises a 64-amino-acid protein architecture that notably incorporates eight cysteine residues positioned at positions 2, 10, 14, 16, 17, 23, 36, and 63. The close spatial proximity of Cys16 and Cys17 poses a challenge in resolving their disulfide bridge configurations using standard methodologies. In this study, we introduce an innovative and highly efficient approach for delineating disulfide pairings in peptides containing adjacent cysteines. Our methodology integrates a two-step proteolytic digestion strategy utilizing trypsin and Glu-specific staphylococcal V8 protease coupled with a subsequent round of Edman degradation. This multifaceted approach enables the precise characterization of the disulfide bonds within the peptide. Specifically, targeted proteolysis by trypsin and V8, followed by reversed-phase HPLC separation of the resulting peptides, facilitated the unambiguous identification of disulfide linkages between Cys10-Cys23 and Cys14-Cys63. For the fragment containing the four remaining cysteines, a single cycle of Edman degradation was employed, strategically breaking the peptide bond between the adjacent cysteines. This pivotal step enabled the isolation and analysis of the resulting fragments. Subsequently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was utilized, revealing the presence of two additional disulfide bonds: Cys2-Cys17 and Cys16-Cys36. Collectively, these findings allow for the definitive assignment of the four disulfide linkages in HNTX-XXI as Cys2-Cys17, Cys10-Cys23, Cys14-Cys63, and Cys16-Cys36. This rapid and sensitive methodology represents a significant advancement in the structural characterization of peptide toxins with complex disulfide bond patterns, underscoring its potential for broad application in the field of venom peptide research.

Parameterized hypercomplex convolutional network for accurate protein backbone torsion angle prediction

Predicting the backbone torsion angles corresponding to each residue of a protein from its amino acid sequence alone is a challenging problem in computational biology. Existing torsion angle predictors mainly use profile features, which are generated by performing time-consuming multiple sequence alignments, for torsion angle prediction. Compared with traditional profile features, embedding features from pretrained protein language models have significant advantages in prediction performance and computational speed. However, embedding features usually have higher dimensions and different embedding features have significantly different dimensions. To this end, we design a novel parameter-efficient deep torsion angle predictor, PHAngle, specifically for embedding features. PHAngle is a parameterized hypercomplex convolutional network consisting of parameterized hypercomplex linear and convolutional layers whose weight parameters can be characterized as the sum of Kronecker products. Experimental results on six benchmark test sets including TEST2016, TEST2018, TEST2020_HQ, CASP12, CASP13 and CASP-FM demonstrate that PHAngle achieves the state-of-the-art torsion angle performance with the fewest parameters compared to the nine existing methods. The source code and datasets are available at https://github.com/fengtuan/PHAngle.

Solvation phenomena in ternary system tetramethylurea-methylacetamide-water: Insights from volumetric, compressibility and FTIR analysis

The properties of the ternary systems N,N,N',N'-tetramethylurea - N-methylacetamide - water were investigated using Fourier-transform infrared spectroscopy (FTIR), volumetric and compression measurements. Densities and sound velocities were determined in order to obtain the apparent molar volumes (VΦ) and apparent molar isentropic compressions (▪S,Φ). These values were then extrapolated to infinite dilution. Additionally, interaction parameters were calculated from the McMillan-Mayer theory. The studies were conducted at 288.15, 298.15, and 308.15 K, at atmospheric pressure (0.1 MPa). The concentration ranges of N-methylacetamide were 2, 4, 6, and 8 moles per kilogram of pure water, and for N,N,N',N'-tetramethylurea from 0 to around 0.35 moles per kilogram of solvent. Discrete changes in isentropic compression were observed. This is the result of the alignment of plots of ▪S,Φ0 as a function of NMA concentration. The results for N,N,N',N'-tetramethylurea were compared with analogous data for the system containing n-butylurea, which is an isomeric compound but exhibits different hydration behaviour. Additionally, large volumetric interaction coefficients were observed, indicating strong interactions between urea derivatives and NMA. This suggests the possibility of strong interactions between protein destabilizers and the protein backbone, differing from those observed for protein structure stabilizers. The observation contributes to understanding the mechanism of osmolyte action and their influence on protein stability.

Conformational Switching of a Nano-Size Urea-Bridged Zn(II)Porphyrin Dimer by External Stimuli.

For the first time, explicit stabilization of all the three conformers, viz. (cis,cis), (cis,trans) and (trans,trans), of a 'nano-sized' highly-flexible urea-bridged Zn(II)porphyrin dimer have been achieved via careful manipulations of external stimuli such as solvent dielectrics, temperature, anionic interactions, axial ligation and surface-induced stabilization. The conformers differ widely in their structures, chemical and photophysical properties and thus have vast potential applicability. X-ray structural characterizations have been reported for the (cis,cis) and (cis,trans)-conformers. While (cis,cis) conformer stabilized exclusively in dichloromethane, more polar solvents resulted in the stabilization of (cis,trans) and (trans,trans)-conformers. Low temperature promotes the stabilization of (cis,trans)-conformer while rise in temperature facilitates flipping to the (cis,cis) one. Significantly, exclusive stabilization of the (trans,trans)-isomer has been illustrated using acetate anion which facilitates H-bonding with the two amide linkages of the urea spacer. Remarkably, HOPG surface facilitates stabilization of the energetically challenging (trans,trans)-conformer via CH⋅⋅⋅π and π⋅⋅⋅π interactions with the solid surface to the porphyrinic cores. DFT calculations demonstrate that the relative stability of the conformers can be modulated upon slight external perturbations as also observed in the experiment. Several factors contributing towards the conformational landscape for the highly flexible urea-bridged porphyrin dimers have been mapped.