Peptides - Science topic

Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. We...

Antibodies raised in peptide-immunized rabbits have been used in biological research for decades. Although there has been wide implementation of this approach, specific proteins are occasionally difficult to target for multiple reasons. One consideration that was noted in mice is that humoral responses may preferentially target the carboxyl terminu...

Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. Whilst this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chem...

Background: The occurrence of accidental nerve damage during surgery and the increasing application of image guidance during head-and-neck surgery have highlighted the need for molecular targeted nerve-sparing interventions. The implementation of such interventions relies on the availability of nerve-specific tracers. In this paper, we describe the...

Monitoring protein structure before and after perturbations can give insights into the role and function of proteins. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry (MS) allows monitoring of structural rearrangements by exposing proteins to OH radicals that oxidize solvent accessible residues, indicating protein regi...

We previously identified a lipopeptide, EK1C4, by linking cholesterol to EK1, a pan-CoV fusion inhibitory peptide via a polyethylene glycol (PEG) linker, which showed potent pan-CoV fusion inhibitory activity. However, PEG can elicit antibodies to PEG in vivo, which will attenuate its antiviral activity. Therefore, we designed and synthesized a deP...

Reversible protein S-nitrosylation regulates a wide range of biological functions and physiological activities in plants. However, it is challenging to quantitively determine the S-nitrosylation targets and dynamics in vivo. In this study, we develop a highly sensitive and efficient fluorous affinity tag-switch (FAT-switch) chemical proteomics appr...

A bstract Deep learning can create accurate predictive models by exploiting existing large-scale experimental data, and guide the design of molecules. However, a major barrier is the requirement of both positive and negative examples in the classical supervised learning frameworks. Notably, most peptide databases come with missing information and l...

Cytokines are a collection of proteins, peptides, or glycoproteins synthesized by immunity system cells. They are often act as signaling molecules and have a function of immunity, inflammation, and haematopoiesis initiation and regulation. In general, the cytokines are subdivided into two subgroups pro-inflammatory and anti-inflammatory cytokine.

Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also than...

Sulfation widely exists in the eukaryotic proteome. However, understanding of the biological functions of sulfation in peptides and proteins has been hampered by the lack of methods to control its spatial or temporal distribution in the proteome. Herein, we report that fluorosulfotyrosine can serve as a latent precursor of sulfotyrosine in peptides...

Adropin is a peptide that was suggested to have a role in cirrhosis. The present study aimed to determine the ability to use serum adropin levels to improve their prediction accuracy as an adjunct to the current scores. In a single-center, proof-of-concept study, serum adropin levels were determined in thirty-three cirrhotic patients. The data were...

Machine learning models provide an informed and efficient strategy to create novel peptide and protein sequences with the desired profiles. Nevertheless, they are primarily trained on sequences where the tridimensional structures of peptides and proteins are often overlooked. We need a fast and reliable approach to estimate the structural diversity...

Quantum numbers identify and differentiate between quantum states of a quantum system. The azimuthal or orbital angular momentum quantum numbers characterize wave functions that are invariant under discrete rotations. For a chiral system with screw symmetry, the rotational invariance is broken and the Bloch orbital angular momentum is generally not...

Neurodegenerative diseases are often characterized by the formation of aggregates of amyloidogenic peptides and proteins, facilitating the formation of neurofibrillary plaques. In this study, we investigate a series of Ru-complexes sharing three-legged piano-stool structures based on the arene ring and glucosylated carbene ligands. The ability of t...

Objectives The importance of thioesterase domains on bacillomycin D synthesis and the ability of different thioesterase domains to selectively recognize and catalyze peptide chain hydrolysis and cyclization were studied by deleting and substituting thioesterase domains. Results No bacillomycin D analogs were found in the thioesterase-deleted strai...

The prevalence of metabolic-related disorders, such as non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (DM2), has been increasing. Therefore, developing improved methods for the prevention, treatment, and detection of these two conditions is also necessary. In this study, our primary focus was on examining the role of chronic...

Cell-penetrating peptides (CPPs) play a significant role in the delivery of cargos into human cells for a wide range of therapeutic and diagnostic applications. We disclose the first CPPs based on peptide–bismuth bicycles, which can be readily obtained from commercially available peptide precursors, making them highly accessible for a wide range of...

The concept of molecular mimicry describes situations in which antigen sharing between parasites and hosts could benefit pathogen evasion from host immune responses. However, antigen sharing can generate host responses to parasite-derived self-like peptides, triggering autoimmunity. Since its conception, molecular mimicry and the consequent potenti...

In the modern scientific landscape, natriuretic peptides are a complex and interesting network of molecules playing pleiotropic effects on many organs and tissues, ensuring the maintenance of homeostasis mainly in the cardiovascular system and regulating the water–salt balance. The characterization of their receptors, the understanding of the molec...

Despite its clinical importance, biomarkers of disease activity in aortic stenosis (AS) are lacking. We investigated the association between anti-cyclic citrullinated peptide (CCP) antibodies and AS. All 678 patients who underwent echocardiography and anti-CCP antibody testing were analysed. Anti-CCP antibody status was categorized as negative, low...

Colorectal cancer (CRC) is one of the most lethal malignancies worldwide, so the attempts to find novel therapeutic approaches are necessary. The aim of our study was to analyze how chemical modifications influence physical, chemical, and biological properties of the two peptides, namely, bradykinin (BK) and neurotensin (NT). For this purpose, we u...

We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide complexes are limited, making it difficult to accurately predict interactions between proteins and peptides. To...

Soluble secretory proteins with a signal peptide reach the extracellular space through the endoplasmic reticulum-Golgi conventional pathway. During translation, the signal peptide is recognised by the secretory recognition particle and results in a co-translational translocation to the endoplasmic reticulum to continue the secretory pathway. Howeve...

Lanthipeptide synthetases are present in all domains of life. They catalyze a crucial step during lanthipeptide biosynthesis by introducing thioether linkages during posttranslational peptide modification. Lanthipeptides have a wide range of functions, including antimicrobial and morphogenetic activities. Intriguingly, several Clostridium species c...

Macrocyclic peptides are an emerging therapeutic modality, yet computational approaches for accurately sampling their diverse 3D ensembles remain challenging due to their conformational diversity and geometric constraints. Here, we introduce RINGER, a diffusion-based transformer model for sequence-conditioned generation of macrocycle structures bas...

Investigation of the folding pathways of protein molecules plays a key role in studying diseases such as Alzheimer’s and designing viral drugs at the molecular level. Despite recent advances in visualization techniques, effective sonification (i.e., non-speech auditory representation) of large datasets associated with protein folding pathways is st...

The pathological aggregation of α-synuclein (αS) into amyloid fibrils is the hallmark of Parkinson's disease (PD). The self-assembly and membrane interactions of αS are mainly governed by the seven imperfect 11-residue repeats of the XKTKEGVXXXX motif around residues 1-95. However, the particular role of each repeat in αS fibrillization remains unc...

Since conventional therapy faces limitations in the field of different cancers as well as gastrointestinal cancers, that decrease the survival rate of patients, there is an urgent need to find new effective therapeutic approaches without the adverse effects of the traditional agents. Antimicrobial peptides (AMPs) attract much attention and are well...

Antibacterial peptides can be a potential game changer in the fight against antibiotic resistance. In order for these peptides to become successful antibiotic alternatives, it is essential that they possess high efficacy in addition to just being antibacterial. In this study, we have developed a two-level SVM-based binary classification approach to...

Over the past decades, peptides and proteins have been increasingly important in the treatment of various human diseases and conditions owing to their specificity, potency, and minimized off-target toxicity. However, the existence of the practically impermeable blood brain barrier (BBB) limits the entry of macromolecular therapeutics into the centr...

Public proteomics data is rapidly increasing, creating a computational challenge for large-scale reanalysis. Here, we introduce quantms, an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 56 of the largest datasets, comprising 26801 instrument files from 9502 human samples, to quantify...

Because organic molecules and materials are generally insensitive or weakly sensitive to magnetic fields, a certain means to enhance their magnetic responsiveness needs to be exploited. Here we show a strategy to amplify the magnetic responsiveness of self-assembled peptide nanostructures by synergistically combining the concepts of perfect α-helix...

Biosensors show promising prospects in the assays of various targets due to their advantages of high sensitivity, good selectivity and rapid response. Molecular recognition is a key event of biosensors, which usually involves the interaction of antigen–antibody, aptamer–target, lectin–sugar, boronic acid–diol, metal chelation and DNA hybridization....

A short peptide, FHHF-11, was designed to change stiffness as a function of pH due to changing degree of protonation of histidines. As pH changes in the physiologically relevant range, G′ was measured at 0 Pa (pH 6) and 50,000 Pa (pH 8). This peptide-based hydrogel is antimicrobial and cytocompatible with skin cells (fibroblasts). It was demonstrat...

Despite the increasing availability of modern treatments, including personalized therapies, there is a strong need to search for new drugs that will be effective in the fight against cancer. The chemotherapeutics currently available to oncologists do not always yield satisfactory outcomes when used in systemic treatments, and patients experience bu...

In this randomized, double-blind, placebo-controlled study, we investigated the effects of collagen peptides (CP) containing high concentrations of prolyl-hydroxyproline and hydroxyprolyl-glycine on the advanced glycation end products (AGEs) levels in the skin and subcutaneous blood vessel walls. Thirty-one individuals aged 47–87 years were randoml...

Orthoflavivirus encephalitidis, formerly tick-borne encephalitis virus (TBEV), belongs to the Orthoflavivirus genus. TBEV is transmitted by tick bites and infection with TBEV can lead to serious disorders of the central nervous system. In this study, a new protective monoclonal mouse antibody (mAb) FVN-32, with high binding activity to glycoprotein...

Conventional cancer therapies cause severe side effects. Peptide-based therapy as a complementary option in cancer treatment reports promising results due to its multifunctionality, selectivity, and safety. The aim of this study was to describe the multiple roles peptides have acquired in cancer therapy, the engineering approaches utilized to enhan...

Background Plasma amyloid-β (Aβ) peptides and tau proteins are promising biomarkers of Alzheimer’s disease (AD), not only for predicting Aβ and tau pathology but also for differentiating AD from other neurodegenerative diseases. However, reference intervals for plasma biomarkers of AD in healthy elderly Chinese individuals have not yet been establi...

It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino acids in the association. We have recently demonstrated...

Non-ribosomal peptide synthetases are mega-enzyme assembly lines that synthesize many clinically useful compounds. As a gatekeeper, they have an adenylation (A)-domain that controls substrate specificity and plays an important role in product structural diversity. This review summarizes the natural distribution, catalytic mechanism, substrate predi...

Objective: To investigate the associations of disease duration and anti-cyclic citrullinated peptide antibody (ACPA) status with the effectiveness of abatacept in biologic-naïve patients with rheumatoid arthritis (RA). Methods: We performed post-hoc analyses of the ORIGAMI study of biologic-naïve RA patients aged ≥20 years with moderate disease...

Several insects are known as vectors of a wide range of animal and human pathogens causing various diseases. However, they are also a source of different substances, such as the Antimicrobial Peptides (AMPs), which can be employed in the development of natural bioactive compounds for medical, veterinary and agricultural applications. It is well kno...

A palladium-catalyzed enantioselective three-component reaction of glyoxylic acid, sulfonamides and aryltrifluoroborates is described. This process provides modular access to the important α-arylglycine motif in moderate to good yields and enantioselectivies. The formed α-arylglycine products constitute useful building blocks for the synthesis of p...

SuFEx click chemistry has established itself as a formidable tool to rapidly and effectively link chemical structures. Despite tremendous advancements in the field in recent years, the installment of the crucial -SO2F handle still requires the use of purposely designed, expensive, and non-atom economical reagents. However, the use of the most obvio...

Here, we combined unsupervised machine learning (ML), non-natural amino acids, and affinity-selection mass-spectrometry (AS-MS) for the discovery of ultra-high affinity peptidomimetics that bind to a protein target. Peptides and peptidomimetics were discovered using AS-MS, encoded using diverse representations, and decomposed into two-dimensional “...

The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. There are specific amino acids invol...

Background Early and accurate diagnosis of infection-induced osteomyelitis, which often involves increased PD-L1 expression, is crucial for better treatment outcomes. Radiolabeled anti-PD-L1 nuclear imaging allows for sensitive and non-invasive whole-body assessments of PD-L1 expression. This study aimed to compare the efficacy of ¹⁸ F-FDG and an ¹...

Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer’s disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers...

Stings of certain ant species (Hymenoptera: Formicidae) can cause intense, long-lasting nociception. Here we show that the major contributors to these symptoms are venom peptides that modulate the activity of voltage-gated sodium (NaV) channels, reducing their voltage threshold for activation and inhibiting channel inactivation. These peptide toxin...

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering meth...

Three-dimensional (3D) cell cultures, including organ-on-a-chip (OOC) devices, offer the possibility to mimic human physiology conditions better than 2D models. The organ-on-a-chip devices have a wide range of applications, including mechanical studies, functional validation, and toxicology investigations. Despite many advances in this field, the m...

The proteins of extracellular vesicles (EVs) provide proteomic signatures that reflect molecular features of EV-producing cells, including cancer cells. Detection of cancer cell EV proteins is of great interest due to the development of novel predictive diagnostic approaches. Using targeted mass spectrometry with stable-isotope-labeled peptide stan...

Motivation With the great number of peptide sequences produced in the postgenomic era, it is highly desirable to identify the various functions of therapeutic peptides quickly. Furthermore, it is a great challenge to predict accurate multi-functional therapeutic peptides (MFTP) via sequence-based computational tools. Results Here we propose a nove...

Simple Summary Evidence indicates that angiotensin (Ang)-related peptides, also known as hypertensive peptides, are involved in pain regulation. Ang-related peptides exhibit various physiological effects via their receptors expressed throughout the body, and changes in the expression of Ang system components at the site of a lesion affect the local...

Parkinson's disease is a neurodegenerative disorder that affects millions of people worldwide, posing significant challenges for diagnosis and treatment. This study presents a machine learning pipeline for identifying candidate biomarker proteins and peptides from cerebrospinal fluid mass spectrometry (CSF-MS) tests in Parkinson's disease patients....

Mass spectrometry is a powerful technique for the structural and functional characterization of biomolecules. However, it remains challenging to accurately gauge the gas-phase structure of biomolecular ions and assess to what extent native-like structures are maintained. Here we propose a synergistic approach which utilizes Förster resonance energy...

Targeted radionuclide therapy is become increasingly prominent as a nuclear medicine subspe-cialty. For many decades, treatment with radionuclides has been mainly restricted to the use of iodine-131 in thyroid disorders. Currently, radiopharmaceuticals, consisting of a radionuclide coupled to a vector that binds to a desired biological target with...

De novo genes are often mistaken for ORFs belonging to genes that were formerly coding (i.e pseudogenes). Experimental research has actually indicated that the structural elements contained in these sequences are showing up when they are translated back into peptides.