Protein Chain Research Articles

Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.

Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dramatic advances were observed for the accurate prediction of single protein chains, driven by a surge of deep learning methodologies entering the prediction field. We review the mainscientific developments that enabled these recent breakthroughs and feature the important role of blind prediction experiments in building up and nurturing the structure prediction field. We discuss how the new wave of artificial intelligence-based methods is impacting the fields of computational and experimental structural biology and highlight areas in which deep learning methods are likely to lead to future developments, provided that major challenges are overcome.

Recording of cellular physiological histories along optically readable self-assembling protein chains

Observing cellular physiological histories is key to understanding normal and disease-related processes. Here we describe expression recording islands—a fully genetically encoded approach that enables both continual digital recording of biological information within cells and subsequent high-throughput readout in fixed cells. The information is stored in growing intracellular protein chains made of self-assembling subunits, human-designed filament-forming proteins bearing different epitope tags that each correspond to a different cellular state or function (for example, gene expression downstream of neural activity or pharmacological exposure), allowing the physiological history to be read out along the ordered subunits of protein chains with conventional optical microscopy. We use expression recording islands to record gene expression timecourse downstream of specific pharmacological and physiological stimuli in cultured neurons and in living mouse brain, with a time resolution of a fraction of a day, over periods of days to weeks.

Writing cellular history in protein chains.

Writing cellular history in protein chains.

Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase in Bifidobacterium pseudocatenulatum.

Aim: Dietary plant fibers affect gut microbiota composition; however, the underlying microbial degradation pathways are not fully understood. We previously discovered 3-O-α-D-galactosyl-α-L-arabinofuranosidase (GAfase), a glycoside hydrolase family 39 enzyme involved in the assimilation of side chains of arabinogalactan protein (AGP), from Bifidobacterium longum subsp. longum (B. longum) JCM7052. Although GAfase homologs are not highly prevalent in the Bifidobacterium genus, several Bifidobacterium strains possess the homologs. To explore the differences in substrate specificity among the homologs, a homolog of B. longum GAfase in Bifidobacterium pseudocatenulatum MCC10289 (MCC10289_0425) was characterized. Methods: Gum arabic, larch, wheat AGP, and sugar beet arabinan were used to determine the substrate specificity of the MCC10289_0425 protein. An amino acid replacement was introduced into GAfase to identify a critical residue that governs the differentiation of substrate specificity. The growth of several Bifidobacterium strains on β-L-arabinopyranosyl disaccharide and larch AGP was examined. Results: MCC10289_0425 was identified to be an unprecedented 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase (AAfase) with low GAfase activity. A single amino acid replacement (Asn119 to Tyr) at the catalytic site converted GAfase into AAfase. AAfase releases sugar source from AGP, thereby allowing B. pseudocatenulatum growth. Conclusion: Bifidobacteria have evolved several homologous enzymes with overlapping but distinct substrate specificities depending on the species. They have acquired different fitness abilities to respond to diverse plant polysaccharide structures.

De Novo Fibrinogen A Alpha Chain Amyloidosis in a Kidney Transplant Patient: Case Report and Literature Review

Rationale: De Novo transplant amyloidosis denotes the condition when a patient develops amyloidosis after transplantation but had not been diagnosed with the disease prior to transplantation. The incidence of de novo amyloidosis in kidney transplants is rare, but few published case reports have described the occurrence of de novo Amyloid A protein (AA) and Light Chain (AL) amyloidosis. However, de novo hereditary fibrinogen A alpha chain (AFib) has not been previously reported. Patient Presentation: We present a 72-year-old man, a kidney transplant recipient, who developed progressive rise in his creatinine about 3 years after transplantation. He has long-standing diabetes mellitus type 2, obesity, and hypertension, so he did not have a kidney biopsy of his native kidneys prior to transplantation. Diagnosis: A kidney transplant biopsy was done that showed amyloidosis. Mass spectrophotometry confirmed it as AFib amyloidosis. Genetic testing of the patient revealed that he has fibrinogen A alpha gene (FGA) point mutation with a p.E545V variant. Interventions: Cardiac evaluation showed normal transthoracic echocardiogram. Cardiac magnetic resonance imaging (MRI) showed no involvement by amyloidosis. A peripheral nerve biopsy showed diabetic neuropathy. Thus, the kidney was the only organ involved by the disease. The kidney transplant was managed conservatively with blood pressure and diabetes control in addition to his usual immunosuppression regimen which was not altered. He is being treated with diuretics, angiotensin receptor inhibitors, and sodium glucose transport 2 inhibitors. Outcomes: Kidney transplant function exhibited only slow progression over 18 months since the diagnosis was confirmed. This slow progression is likely because the p.E545V point mutation variant is less aggressive than other gene deletion mutations and because our patient was judged to have been diagnosed early in the course of his disease. Teaching Points: In this case report, we illustrate the findings and testing that confirmed the diagnosis of AFib amyloidosis. We summarize the clinical aspects, outcomes of the disease, and treatment options. We believe this case report is interesting because it is the first reported case of AFib amyloidosis in a kidney transplant recipient who was not known to have the disease prior to kidney transplantation.

Antibody sequences assembly method based on weighted de Bruijn graph.

With the development of next-generation protein sequencing technologies, sequence assembly algorithm has become a key technology for de novo sequencing process. At present, the existing methods can address the assembly of an unknown single protein chain. However, for monoclonal antibodies with light and heavy chains, the assembly is still an unsolved question. To address this problem, we propose a new assembly method, DBAS, which integrates the quality scores and sequence alignment scores from de novo sequencing peptides into a weighted de Bruijn graph to assemble the final protein sequences. The established method is used to assembling sequences from two datasets with mixed light and heavy chains from antibodies. The results show that the DBAS can assemble long antibody sequences for both mixed light and heavy chains and single chains. In addition, DBAS is able to distinguish the light and heavy chains by using BLAST sequence alignment. The results show that the algorithm has good performance for both target sequence coverage and contig assembly accuracy.

Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose lineages were either ‘not classified’ or were ‘unclassifiable’ indicated the virus could still be evolving.

Non-covalent interactions reveal the protein chain δ conformation in a flexible single-residue model.

The δ conformation is a local secondary structure in proteins that implicates a πamide N-H⋯N interaction between a backbone N atom and the NH of the following residue. Small-molecule models thereof have been limited so far to rigid proline-type compounds. We show here that in derivatives of a cyclic amino acid with a sulphur atom in the γ-position, specific side-chain/backbone N-H⋯S interactions stabilize the δ conformation sufficiently to allow it to compete with classical C5 and C7 H-bonded conformers.

B-Cell Epitope Mapping of the Vibrio cholera Toxins A, B, and P and an ELISA Assay.

Oral immunization with the choleric toxin (CT) elicits a high level of protection against its enterotoxin activities and can control cholera in endemic settings. However, the complete B-cell epitope map of the CT that is responsible for protection remains to be clarified. A library of one-hundred, twenty-two 15-mer peptides covering the entire sequence of the three chains of the CT protein (CTP) was prepared by SPOT synthesis. The immunoreactivity of membrane-bound peptides with sera from mice vaccinated with an oral inactivated vaccine (Schankol™) allowed the mapping of continuous B-cell epitopes, topological studies, multi-antigen peptide (MAP) synthesis, and Enzyme-Linked Immunosorbent Assay (ELISA) development. Eighteen IgG epitopes were identified; eight in the CTA, three in the CTB, and seven in the protein P. Three V. cholera specific epitopes, Vc/TxA-3, Vc/TxB-11, and Vc/TxP-16, were synthesized as MAP4 and used to coat ELISA plates in order to screen immunized mouse sera. Sensitivities and specificities of 100% were obtained with the MAP4s of Vc/TxA-3 and Vc/TxB-11. The results revealed a set of peptides whose immunoreactivity reflects the immune response to vaccination. The array of peptide data can be applied to develop improved serological tests in order to detect cholera toxin exposure, as well as next generation vaccines to induce more specific antibodies against the cholera toxin.

Crystal structure of LGR ligand α2/β5 from Caenorhabditis elegans with implications for the evolution of glycoprotein hormones

A family of leucine-rich-repeat-containing G-protein-coupled receptors (LGRs) mediate diverse physiological responses when complexed with their cognate ligands. LGRs are present in all metazoan animals. In humans, the LGR ligands include glycoprotein hormones (GPHs) chorionic gonadotropin (hCG), luteinizing hormone, follicle-stimulating hormone (hFSH), and thyroid-stimulating hormone (hTSH). These hormones are αβ heterodimers of cystine-knot protein chains. LGRs and their ligand chains have coevolved. Ancestral hormone homologs, present in both bilaterian animals and chordates, are identified as α2β5. We have used single-wavelength anomalous diffraction and molecular replacement to determine structures of the α2β5 hormone from Caenorhabditis elegans (Ceα2β5). Ceα2β5 is unglycosylated, as are many other α2β5 hormones. Both Hsα2β5, the human homolog of Ceα2β5, and hTSH activate the same receptor (hTSHR). Despite having little sequence similarity to vertebrate GPHs, apart from the cysteine patterns from core disulfide bridges, Ceα2β5 is generally similar in structure to these counterparts; however, its α2 and β5 subunits are more symmetric as compared with α and β of hCG and hFSH. This quasisymmetry suggests a hypothetical homodimeric antecedent of the α2β5 and αβ heterodimers. Known structures together with AlphaFold models from the sequences for other LGR ligands provide representatives for the molecular evolution of LGR ligands from early metazoans through the present-day GPHs. The experimental Ceα2β5 structure validates its AlphaFold model, and thus also that for Hsα2β5; and interfacial characteristics in a model for the Hsα2β5:hTSHR complex are similar to those found in an experimental hTSH:hTSHR structure.

PHOTOSENSITIVE EFFECT OF THE BIOCHEMICAL AND ECONOMIC TRAITS OF Bombyx mori L.

The silkworm is by nature very delicate and sensitive to environmental conditions. The ecological factors, chiefly temperature, humidity and light during rearing show significant effect on growth larvae and finally cocoon crop quality. Silkworms are photosensitive and they have a tendency to crawl towards dim light. They do not like either strong light or complete darkness. In this way, based on various exposures of light on the effect of biochemical content and economic traits of silkworm were recorded. Biochemical content such as protein is highly essential for insects. The intracellular transport of the silk protein is dependent on hydrophobicity or hydrophilicity of the amino acid residues of the heavy and light chain of the silk protein and the haemolymph is the only extracellular fluid of insects with diverse functions and serves as reservoir for the products required for every physiological activity of the insect body, thus changes in the composition of haemolymph reflect the physiological and biochemical transformations taking place in the insect tissue. In this way of study, effect of light on biochemical content such as protein and carbohydrate of haemolyph and silk gland are significantly increased. The protein content was high in the haemolymph (17.48%) when the larvae exposed to 5 watt light and silk gland (66.67%) in 3 watt exposure group but fat body (44.33 %) when the larvae exposed to 8 watt. The carbohydrate content of haemolymph (35.54 %), silk gland (12.85%) and fat body (57.26 %) were significantly increased in 3 watt exposure group. In this findings, biochemical content had direct relation to economic traits of B. mori. The cocoon characters such as cocoon weight (28.42 per cent), pupal weight (20.9 per cent), shell weight (71 per cent) and shell ratio (33.48 per cent) were significantly increased in the 3 watt exposed group.

Proposed Approach for Key Generation Based on the RNA

Due to fundamental role of random key in the design of cryptography algorithms, a new method is proposed for generating random key based on the bases of RNA translation to protein chain. The proposed method accept a key sequence size(9,18,27,…) byte and generate key sequence with extended length appropriate with plain message length. The security strength of generated key is acceptable according to the results of statistical tests of randomness

Proteomic Profiling of Major Peanut Allergens and Their Post-Translational Modifications Affected by Roasting.

Post-translational modifications (PTMs) are covalent changes occurring on amino acid side chains of proteins and yet are neglected structural and functional aspects of protein architecture. The objective was to detect differences in PTM profiles that take place after roasting using open PTM search. We conducted a bottom-up proteomic study to investigate the impact of peanut roasting on readily soluble allergens and their PTM profiles. Proteomic PTM profiling of certain modifications was confirmed by Western blotting with a series of PTM-specific antibodies. In addition to inducing protein aggregation and denaturation, roasting may facilitate change in their PTM pattern and relative profiling. We have shown that Ara h 1 is the most modified major allergen in both samples in terms of modification versatility and extent. The most frequent PTM was methionine oxidation, especially in roasted samples. PTMs uniquely found in roasted samples were hydroxylation (Trp), formylation (Arg/Lys), and oxidation or hydroxylation (Asn). Raw and roasted peanut extracts did not differ in the binding of IgE from the serum of peanut-sensitised individuals done by ELISA. This study provides a better understanding of how roasting impacts the PTM profile of major peanut allergens and provides a good foundation for further exploration of PTMs.

The fabrication and characterisation of surimi gel modified by konjac glucomannan with the different hydrolysis degree

SummaryThe gel performance of surimi‐based products is indispensable technological attribute responsible for their high popularity. Here, surimi gels with tunable gel properties were successfully fabricated based on the double network theory. Konjac glucomannan (KGM) hydrolysed for various periods (0, 5, 15, 30, 60 and 90 min) was introduced into surimi systems. Corresponding structural characterisations including FTIR, XRD, SDS‐PAGE and grafting degree assessment, were conducted to confirm the presence of double crosslinking reactions. Furthermore, the gel strength, dynamic rheology, thermal stability and in vitro digestibility of the surimi gels were investigated. Red shifts in the amide A band and an increase in relative intensity indicated that hydrogen bonding existed in the complex systems, according to the FTIR spectra. The XRD patterns suggested that the crystalline structures were weakened by interfering with the protein chain arrangement due to the Maillard reaction. In addition, SDS‐PAGE and o‐phthalaldehyde (OPA) assays also confirmed that myofibrillar protein and hydrolysed KGM were partially linked by covalent bonding. The SK‐2 group showed the greatest mechanical strength and lowest digestibility amongst all groups due to its dense hierarchical structure. This work may provide inspiration for the design and development of surimi gels with improved gel properties via microarchitectural modulation.

Structure and features of amino acid sequences of Π-modules in OB-folds

Stereochemical analysis has been performed for П-modules from the large set of non-homologous protein structures containing the OB-fold. That module consists of two β-strands connected by a loop and placed in different sheets in such a way which looks as Greek letter П. Total 70 non-homologous proteins at resolution not less than 2.5Å have been selected for the analysis from 265 suitable structures belonging to sixteen OB-fold super families. We have disclosed two types of П-modules: the fist with the connecting loop containing α-helix, and second one without helix. Entrance of protein chain into second β-sheet is carried out by the same arch with conformation βββαLβp. In most cases, 85 % of total, α-positions are occupied by glycine residue, while at entrance in the loop such residues are absent. Occupancy frequency of П-modules has been obtained in dependence on the loop length. Spatial pathway of structures of all modules are superimposed very well. Structural alignment of amino acid for П-module sequences allows us to determine the key positions of the hydrophobic, hydrophilic, and glycine residues.

A novel fusion protein consisting of anti-ANGPTL3 antibody and interleukin-22 ameliorates diabetic nephropathy in mice.

The pathogenic mechanisms of diabetic nephropathy (DN) include podocyte injury, inflammatory responses and metabolic disorders. Although the antagonism of Angiopoietin-like protein 3 (ANGPTL3) can alleviate proteinuria symptoms by inhibiting the activation of integrin αvβ3 on the surface of podocytes, it can not impede other pathological processes, such as inflammatory responses and metabolic dysfunction of glucolipid. Interleukin-22 (IL-22) is considered to be a pivotal molecule involved in suppressing inflammatory responses, initiating regenerative repair, and regulating glucolipid metabolism. Genes encoding the mIL22IgG2aFc and two chains of anti-ANGPTL3 antibody and bifunctional protein were synthesized. Then, the DN mice were treated with intraperitoneal injection of normal saline, anti-ANGPTL3 (20 mg/kg), mIL22Fc (12 mg/kg) or anti-ANGPTL3 /IL22 (25.3 mg/kg) and irrigation of positive drug losartan (20mg/kg/d) twice a week for 8 weeks. In this research, a novel bifunctional fusion protein (anti-ANGPTL3/IL22) formed by the fusion of IL-22 with the C-terminus of anti-ANGPTL3 antibody exhibited favorable stability and maintained the biological activity of anti-ANGPTL3 and IL-22, respectively. The fusion protein showed a more pronounced attenuation of proteinuria and improved dysfunction of glucolipid metabolism compared with mIL22Fc or anti-ANGPTL3. Our results also indicated that anti-ANGPTL3/IL22 intervention significantly alleviated renal fibrosis via inhibiting the expression of the inflammatory response-related protein nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) p65 and NOD-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome. Moreover, transcriptome analysis revealed the downregulation of signaling pathways associated with injury and dysfunction of the renal parenchymal cell indicating the possible protective mechanisms of anti-ANGPTL3/IL22 in DN. Collectively, anti-ANGPTL3/IL22 bifunctional fusion protein can be a promising novel therapeutic strategy for DN by reducing podocyte injury, ameliorating inflammatory response, and enhancing renal tissue recovery.

Structural Flexibility of Proteins Dramatically Alters Membrane Stability─A Novel Aspect of Lipid-Protein Interaction.

Protein isoforms are structural variants with changes in the overall flexibility predominantly at the tertiary level. For membrane associated proteins, such structural flexibility or rigidity affects membrane stability by playing modulatory roles in lipid-protein interaction. Herein, we investigate the protein chain flexibility mediated changes in the mechanistic behavior of phospholipid model membranes in the presence of two well-known isoforms, erythroid (ER) and nonerythroid (NER) spectrin. We show dramatic alterations of membrane elasticity and stability induced by spectrin in the Langmuir monolayers of phosphatidylocholine (PC) and phosphatidylethanolamine (PE) by a combination of isobaric relaxation, surface pressure-area isotherm, X-ray scattering, and microscopy measurements. The NER spectrin drives all monolayers to possess an approximately equal stability, and that required 25-fold increase and 5-fold decrease of stability in PC and PE monolayers, respectively. The untilting transition of the PC membrane in the presence of NER spectrin observed in X-ray measurements can explain better membrane packing and stability.

Protein cysteine S-glycosylation: oxidative hydrolysis of protein S-glycosidic bonds in aqueous alkaline environments

Some glycoproteins contain carbohydrates S-linked to cysteine (Cys) residues. However, relatively few S-glycosylated proteins have been detected, due to the lack of an effective research methodology. This work outlines a general concept for the detection of S-glycosylation sites in proteins. The approach was verified by exploratory experiments on a model mixture of β-S-glucosylated polypeptides obtained by the chemical transformation of lysozyme P00698. The model underwent two processes: (1) oxidative hydrolysis of S-glycosidic bonds under alkaline conditions to expose the thiol group of Cys residues; (2) thiol S-alkylation leading to thiol S-adduct formation at the former S-glycosylation sites. Oxidative hydrolysis was conducted in aqueous urea, dimethyl sulfoxide, or trifluoroethanol, with silver nitrate as the reaction promoter, in the presence of triethylamine and/or pyridine. The concurrent formation of stable protein silver thiolates, gluconic acid, and silver nanoclusters was observed. The essential de-metalation of protein silver thiolates using dithiothreitol preceded the S-labeling of Cys residues with 4-vinyl pyridine or a fluorescent reagent. The S-labeled model was sequenced by tandem mass spectrometry to obtain data on the modifications and their distribution over the protein chains. This enabled the efficiency of both S-glycosidic bonds hydrolysis and S-glycosylation site labeling to be evaluated. Suggestions are also given for testing this novel strategy on real proteomic samples.

RNA codons govern the mechanism of protein folding through the shape memory effect

The complex protein folding mechanism had been researched during the past half-century, given its potential to offer cures for illnesses caused by viruses and protein misfolding. However, to date, the work remains inadequately successful and mastered, provoking the question of whether researchers are looking at the wrong place for the answer. Specifically, can RNA codons define the protein folding mechanism? This review will first present existing mechanisms for protein folding and their limitations. Then, the logic and evidence supporting the use of a protein folding mechanism governed by RNA codons will be presented. This paper explains protein folding as a shape-memory phenomenon wherein the protein chain memorises the native folded structure. Under the right chemical environment, the protein chain will fold back into its native memorised structure. The RNA codon is the imprint for the natively folded protein shape memory, responsible for programming the native folded structure shape memory onto the protein chain.

De novo design of obligate ABC-type heterotrimeric proteins

The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.