Protein Chain Research Articles

Bioengineering of Novel Non-Replicating mRNA (NRM) and Self-Amplifying mRNA (SAM) Vaccine Candidates Against SARS-CoV-2 Using Immunoinformatics Approach.

Presently, the world needs safe and effective vaccines to overcome the COVID-19 pandemic. Our work has focused on formulating two types of mRNA vaccines that differ in capacity to copy themselves inside the cell. These are non-amplifying mRNA (NRM) and self-amplifying mRNA (SAM) vaccines. Both the vaccine candidates encode an engineered viral replicon which can provoke an immune response. Hence we predicted and screened twelve epitopes from the spike glycoprotein of SARS-CoV-2. We used five CTL, four HTL, and three B-cell-activating epitopes to formulate each mRNA vaccine. Molecular docking revealed that these epitopes could combine with HLA molecules that are important for boosting immunogenicity. The B-cell epitopes were adjoined with GPGPG linkers, while CTL and HTL epitopes were linked with KK linkers. The entire protein chain was reverse translated to develop a specific NRM-based vaccine. We incorporate gene encoding replicase in the upstream region of CDS encoding antigen to design the SAM vaccine. Subsequently, signal sequences were added to human mRNA to formulate vaccines. Both vaccine formulations translated to produce the epitopes in host cells, initiate a protective immune cascade, and generate immunogenic memory, which can counter future SARS-CoV-2 viral exposures before the onset of infection.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12033-021-00432-6.

Specificity Analysis of Protein Methyltransferases and Discovery of Novel Substrates Using SPOT Peptide Arrays.

Posttranslational methylation of amino acid side chains in proteins mainly occurs on lysine, arginine, glutamine, and histidine residues. It is introduced by different protein methyltransferases (PMTs) and regulates many aspects of protein function including stability, activity, localization, and protein/protein interactions. Although the biological effects of PMTs are mediated by their methylation substrates, the full substrate spectrum of most PMTs is not known. For many PMTs, their activity on a particular potential substrate depends, among other factors, on the peptide sequence containing the target residue for methylation. In this protocol, we describe the application of SPOT peptide arrays to investigate the substrate specificity of PMTs and identify novel substrates. Methylation of SPOT peptide arrays makes it possible to study the methylation of many different peptides in one experiment at reasonable costs and thereby provides detailed information about the specificity of the PMT under investigation. In these experiments, a known substrate sequence is used as template to design a SPOT peptide array containing peptides with single amino acid exchanges at all positions of the sequence. Methylation of the array with the PMT provides detailed preferences for each amino acid at each position in the substratesequence, yielding a substrate sequencespecificity profile. This information can then be used to identify novel potential PMT substrates by in silico data basesearches. Methylation of novel substrate candidates can be validated in SPOT arrays at peptide level, followed by validation at protein level in vitro and in cells.

Valence-controlled protein conjugation on nanoparticles via re-arrangeable multivalent interactions of tandem repeat protein chains.

Precise control of the number of conjugated proteins on a nanoparticle surface has long been a highly challenging task. Here, we developed a one-pot, purification-free strategy for valency-controlled conjugation of tandem repeat protein chains on gold nanoparticles. Protein chains were designed to contain multiple, regularly spaced binding modules, which can multivalently interact with coating molecules on nanoparticle surfaces. We discovered that a slow increase of this interaction strength facilitates full participation of repeated binding modules on a protein chain for surface binding (as well as dynamic rearrangement) on a single nanoparticle, which resulted in stable protein chain wrapping around nanoparticles. By varying the protein chain length, a defined number of protein chains were conjugated on gold nanoparticles with difference sizes. Various high-order nanoparticle structures were accurately assembled with these valence-controlled protein–particle conjugates. The present strategy offers a highly dynamic but controlled protein coating approach on solid surfaces of diverse nanostructures. In addition, this work also provides a valuable clue to understand dynamic binding processes of multivalent repeat proteins.

Oferta e demanda de milho para a cadeia da proteína animal no Rio Grande do Sul

ABSTRACT: The animal production system has been affected in the Rio Grande do Sul State by low maize production, mainly non-ruminants. The total demand is not well known and official data are inaccurate and underestimated. This research characterized and analyzed the maize grain demand and supply for animal feed in the last 15 years at the Rio Grande do Sul State. The state supply was obtained from governmental harvests measurement. The demand was obtained by the total animals (swine, poultry and dairy and beef cattle), while the total state demand was obtained using the relative national consumption from these segments in relation to the total. The current maize grain demand was at the order of 6 million tons for the feeding of swine, poultry and cattle, while total demand was between 9 to 12 million tons in the Rio Grande do Sul State. The state maize production supplied near half of the total demand for the animal protein chain, characterizing a significant deficit for this sector, providing instability and making this productive chain economically unfeasible in the state.

Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases

The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analyzed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.

Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis.

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.

Immunohistochemical and Transcriptional Analysis of SARS-CoV-2 Entry Factors and Renin-Angiotensin-Aldosterone System Components in Lethal COVID-19

Introduction: Since angiotensin converting enzyme-2 (ACE2) was discovered as an essential entry factor of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), there has been conflicting evidence regarding the role of renin-angiotensin-aldosterone system (RAAS) in COVID-19. This study elucidates pulmonary expression patterns SARS-CoV-2 entry factors (ACE2 and transmembrane protease serine subtype 2, TMPRSS2) and RAAS components in lethal COVID-19. Methods: Lung tissue from COVID-19 autopsies (n = 27) and controls (n = 23) underwent immunohistochemical staining for RAAS components (angiotensin receptors 1 and 2, ACE2 and Mas-receptor) and bradykinin receptors 1 and 2. Staining of individual cellular populations (alveolar pneumocytes [ALV], desquamated cells [DES] and endothelium [END]) was measured by a binary scale (positive/negative). SARS-CoV-2 was detected using immunohistochemistry against nucleocapsid protein, in-situ hybridization and quantitative reverse transcriptase polymerase chain reaction. Gene expression profiling for ACE2, ACE and TMPRSS2 was performed. Results: Subtle differences were observed when comparing COVID-19 patients and controls not reaching statistical significance, such as a higher incidence of ACE2-positivity in END (52% vs. 39%) but lower positivity in ALVs (63% vs. 70%) and an overall downregulation of ACE2 gene expression (0.25 vs. 0.55). However, COVID-19 patients with RAAS inhibitor (RAASi) intake had significantly shorter hospitalization times (5 vs. 12 days), higher viral loads (57,517 vs. 15,980/10⁶ RNase P-gene copies) and decreased ACE/ACE2-expression ratios (4.58 vs. 11.07) than patients without. TMPRSS2 expression was significantly (1.76-fold) higher in COVID-19 patients than controls. Conclusion: Our study delineates the heterogeneous expression patterns of RAAS components in the lungs, which vary amongst cellular populations, and implies that COVID-19 patients with RAASi-intake present with a more rapid disease progression, although this requires further investigation.

Risk factors and genetic characterization of bovine respiratory syncytial virus in the inner Aegean Region, Turkey

Bovine respiratory syncytial virus (BRSV) is one of the causative viral agents of the bovine respiratory disease complex. This study was conducted to determine the seropositivity and risk factors associated with BRSV infection and to evaluate the phylogenetic relatedness of the BRSVs in the inner Aegean region of Turkey. In this cross-sectional study, serum samples (n = 557) and nasal swabs (n = 21) were collected from cattle herds (n = 43) between February 2018 and March 2019. A commercial indirect-ELISA kit was used for the detection of antibodies in the sera samples. Reverse-transcriptase PCR was used to detect viral RNA in nasal swabs. Nasal samples were also examined for the detection of bovine parainfluenza-3, bovine viral diarrhoea virus, and bovine herpesvirus 1 by molecular detection methods. Genetic characterization of the local BRSV field isolates was conducted by sequencing attachment glycoprotein (G) gene segment. Epidemiological data on potential risk factors were collected from each sampled herd during blood collection. All herds had at least one seropositive animal. After adjustment for assay sensitivity and specificity, the overall true seropositivity was 58.48% (95% CI: 53.32–63.47). BRSV RNA was detected in 2 of the 21 nasal swabs, whereas other infectious agents were not detected in the investigated samples. Phylogenetic analysis showed that the field isolates of BRSV obtained in this study belonged to subgroup III, but they were located on separate branch from previously characterised Turkish subgroup III isolates. BRSV field strains from this study displayed 3 new amino acid substitutions (P89S, D115G, and S165L) in the G protein chains compared to other main reference BRSV isolates, demonstrating that BRSV is still evolving. Generalised estimating equation model showed that there were positive associations between BRSV infection, age (OR = 2.36, p = 0.001), herd size (OR = 10.32, p < 0.001), herd type (OR = 8.97, p < 0.001), a past history of respiratory disease (OR = 4.06, p < 0.001). The results of this study revealed that BRSV infection is common among cattle herds in the inner Aegean region of Turkey. The obtained epidemiological and genetic data on BRSV infection from this study could be beneficial for designing effective biosecurity practices and vaccination strategies.

Random sampling of the Protein Data Bank: RaSPDB

A novel and simple procedure (RaSPDB) for Protein Data Bank mining is described. 10 PDB subsets, each containing 7000 randomly selected protein chains, are built and used to make 10 estimations of the average value of a generic feature F—the length of the protein chain, the amino acid composition, the crystallographic resolution, and the secondary structure composition. These 10 estimations are then used to compute an average estimation of F together with its standard error. It is heuristically verified that the dimension of these 10 subsets—7000 protein chains—is sufficiently small to avoid redundancy within each subset and sufficiently large to guarantee stable estimations amongst different subsets. RaSPDB has two major advantages over classical procedures aimed to build a single, non-redundant PDB subset: a larger fraction of the information stored in the PDB is used and an estimation of the standard error of F is possible.

Plasma glial fibrillary acidic protein and neurofilament light chain for the diagnostic and prognostic evaluation of frontotemporal dementia

BackgroundAstrocytes play an essential role in neuroinflammation and are involved in the pathogenesis of neurodenegerative diseases. Studies of glial fibrillary acidic protein (GFAP), an astrocytic damage marker, may help advance our understanding of different neurodegenerative diseases. In this study, we investigated the diagnostic performance of plasma GFAP (pGFAP), plasma neurofilament light chain (pNfL) and their combination for frontotemporal dementia (FTD) and Alzheimer’s disease (AD) and their clinical utility in predicting disease progression.MethodspGFAP and pNfL concentrations were measured in 72 FTD, 56 AD and 83 cognitively normal (CN) participants using the Single Molecule Array technology. Of the 211 participants, 199 underwent cerebrospinal (CSF) analysis and 122 had magnetic resonance imaging. We compared cross-sectional biomarker levels between groups, studied their diagnostic performance and assessed correlation between CSF biomarkers, cognitive performance and cortical thickness. The prognostic performance was investigated, analyzing cognitive decline through group comparisons by tertile.ResultsUnlike pNfL, which was increased similarly in both clinical groups, pGFAP was increased in FTD but lower than in AD (all P < 0.01). Combination of both plasma markers improved the diagnostic performance to discriminate FTD from AD (area under the curve [AUC]: combination 0.78; pGFAP 0.7; pNfL 0.61, all P < 0.05). In FTD, pGFAP correlated with cognition, CSF and plasma NfL, and cortical thickness (all P < 0.05). The higher tertile of pGFAP was associated with greater change in MMSE score and poor cognitive outcome during follow-up both in FTD (1.40 points annually, hazard ratio [HR] 3.82, P < 0.005) and in AD (1.20 points annually, HR 2.26, P < 0.005).ConclusionspGFAP and pNfL levels differ in FTD and AD, and their combination is useful for distinguishing between the two diseases. pGFAP could also be used to track disease severity and predict greater cognitive decline during follow-up in patients with FTD.

Comparison of plasma neurofilament light and total tau as neurodegeneration markers: associations with cognitive and neuroimaging outcomes

BackgroundTotal tau protein (T-Tau) and neurofilament light chain (NfL) have emerged as candidate plasma biomarkers of neurodegeneration, but studies have not compared how these biomarkers cross-sectionally or longitudinally associate with cognitive and neuroimaging measures. We therefore compared plasma T-Tau and NfL as cross-sectional and longitudinal markers of (1) global and domain-specific cognitive decline and (2) neuroimaging markers of cortical thickness, hippocampal volume, white matter integrity, and white matter hyperintensity volume.MethodsWe included 995 participants without dementia who were enrolled in the Mayo Clinic Study of Aging cohort. All had concurrent plasma NfL and T-tau, cognitive status, and neuroimaging data. Follow-up was repeated approximately every 15 months for a median of 6.2 years. Plasma NfL and T-tau were measured on the Simoa-HD1 Platform. Linear mixed effects models adjusted for age, sex, and education examined associations between baseline z-scored plasma NfL or T-tau and cognitive or neuroimaging outcomes. Analyses were replicated in Alzheimer’s Disease Neuroimaging Initiative (ADNI) among 387 participants without dementia followed for a median of 3.0 years.ResultsAt baseline, plasma NfL was more strongly associated with all cognitive and neuroimaging outcomes. The combination of having both elevated NfL and T-tau at baseline, compared to elevated levels of either alone, was more strongly associated at cross-section with worse global cognition and memory, and with neuroimaging measures including temporal cortex thickness and increased number of infarcts. In longitudinal analyses, baseline plasma T-tau did not add to the prognostic value of baseline plasma NfL. Results using ADNI data were similar.ConclusionsOur results indicate plasma NfL had better utility as a prognostic marker of cognitive decline and neuroimaging changes. Plasma T-tau added cross-sectional value to NfL in specific contexts.Trial registrationNot applicable

Mechanism of ultrasound and tea polyphenol assisted ultrasound modification of egg white protein gel

In order to improve the characteristics of egg white protein gel and the stability of egg white protein gel products. In this work, the changes of the texture, physicochemical properties, secondary structure and microstructure of ultrasound modified egg white protein gel (UEP) and tea polyphenols (TP) assisted ultrasound modification of egg white protein gel (TUEP) with different ultrasonic power (0–360 W) were studied. With the increase of ultrasonic power, soluble protein, surface hydrophobicity and disulfide bonds of TUEP and UEP showed an increasing trend. In particular, with the increase of ultrasonic power, the content of intramolecular β-sheets and α-helices of TUEP showed an increasing trend, and significantly improved the relaxation time and microstructure, thus enhancing TUEP gel stability. In addition, the hardness and water holding capacity (WHC) of TUEP and UEP can be increased by ultrasonic treatment, and when the ultrasonic power reached 120 W, the hardness and WHC reached the maximum. The hardness and WHC of TUEP were significantly better than that of UEP. SDS-PAGE results showed that the peptide chain of protein without being broken under ultrasonic treatment. Ultrasonic treatment can improve the gel strength of egg white protein by promoting the cross-linking of proteins to form a dense gel structure, and egg white protein gel form more disulfide bonds and a more stable gel conformation under TP assisted ultrasound. In conclusion, ultrasound and TP assisted ultrasound modification of egg white protein gel is a reliable technique, which can improve the value of egg white protein in food processing.

Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications.

Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.

Protein secondary structure prediction using a lightweight convolutional network and label distribution aware margin loss

Protein secondary structure prediction (PSSP) is an important task in computational molecular biology. Recently, deep neural networks have demonstrated great potential in improving the performance of eight-class PSSP. However, the existing deep predictors usually have higher model complexity and ignore the class imbalance of eight-class secondary structure data in training. In addition, the current methods cannot guarantee that the features corresponding to the padded residue positions are always zero during the forward propagation of the network, which will cause the prediction results of the same protein chain to be different under varied zero-padding numbers. To this end, we propose a novel lightweight convolutional network ShuffleNet_SS, which adopts modified 1-dimensional batch normalization to eliminate the impact of padded residue positions on nonpadded residue positions and uses the label distribution aware margin loss to enhance the network’s ability to learn rare classes. In particular, in order to enable ShuffleNet_SS to fully achieve cross-group information exchange, we further improve the standard channel shuffle operation. Experimental results on the benchmark datasets including CASP10, CASP11, CASP12, CASP13, CASP14 and CB513 show that the proposed method achieves state-of-the-art performance with much lower parameters compared to the five existing deep predictors.

Bioinformatically Prediction of the miRNAs Targeting BCL9,FRMD6 Genes in Colorectal Cancer

CRC is a malignancy with no significant symptoms such as bleeding or abdominal pain, and the condition is usually diagnosed when the tumor growth makes the treatment difficult. The survival of CRC patients depends on the disease progression. Most of the CRCs begin with an unbalanced and noncancerous growth of a polyp. CRC may be prevented if the polyps are removed from the colon. Screening reduces the incidence and mortality of CRC. As the miRNAs play a significant role in the regulation of the cellular procedures, this study aims to predict the miRNAs, targeting the BCL9,FRMD6 genes , using bioinformatics tools. After getting the BCL9,FRMD6 protein chain from the NCBI database, the miRNAs targeting the genes were predicted using TargetScan, miRDB, DIANA and miRWalk databases using different algorithms. Based on the scoring system of the bioinformatics software and considering the best targeting scores, (hsa-miR-30e-5p , hsa-miR-30d-5p) and (hsa-miR-106b-5p , hsa-miR-106a-5p) are suggested as the potential miRNAs, targeting the BCL9,FRMD6 genes for future researches. Considering the significant role of the BCL9,FRMD6 genes on Colorectal cancer, the predicted miRNAs can be used as the molecular biomarkers for the early detection of Colorectal cancer patients.

The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.

We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. The resulting prefiltered data typically contain the entire core of each chain, in quite long continuous fragments. Each reference file is a single protein chain, and the total set of files were selected for low redundancy, high resolution, good MolProbity score, and other chain-level criteria. Then each residue was critically tested for adequate local map quality to firmly support its conformation, which must also be free of serious clashes or covalent-geometry outliers. The resulting Top2018 prefiltered datasets have been released on the Zenodo online web service and are freely available for all uses under a Creative Commons license. Currently, one dataset is residue filtered on main chain plus Cβ atoms, and a second dataset is full-residue filtered; each is available at four different sequence-identity levels. Here, we illustrate both statistics and examples that show the beneficial consequences of residue-level filtering. That process is necessary because even the best of structures contain a few highly disordered local regions with poor density and low-confidence conformations that should not be included in reference data. Therefore, the open distribution of these very large, prefiltered reference datasets constitutes a notable advance for structural bioinformatics and the fields that depend upon it.

Functionalized surfaces created by perturbation in luminescent polymer nanocomposites: Materials for forensic and security ink applications

Europium ions doped pearl white dispersed effectively in PVA binder using Bovine Serum Albumin (BSA) as a stabilizer. Nano-powders (NPs) were synthesized by using propellant chemistry approach. Further, these NPs were incorporated into the polymer binder matrix by solvent casting approach to obtain nanocomposites (NCs). BSA stabilizer made any avenue for the perturbation to the secondary protein chains leading to functionalized surfaces. This helped in obtaining the uniform dispersion of the filler added. Different proportions of (2–10 wt%) functionalized BiOCl-Y2O3:Eu3+ NPs were loaded into PVA matrix. X-ray diffraction profile shows the effective incorporation of the NPs into the polymer. Upon exciting at 398 nm near UV light, the NC shows strong red emission at 612 nm along with other three peaks were due to the transition from 5D0 to 7Fj (j = 1, 2, 3 and 4). The highest PL intensity was registered for 8 wt% NPs in PVA matrix. The optimized NCPs were further utilized for various technological applications namely solid-state lighting, forensic and security ink preparation. The latent fingerprints developed on commonly encountered objects were investigated from the functionalized BiOCl-Y2O3:Eu3+ NCPs by powder dusting method. The results undoubtedly revealed all the Type – I – III ridge details irrespective of surfaces. Anti – counterfeiting ink has been developed and testified on various surfaces. The overall results clearly revealed that surface functionalized NCs were quite suitable for multifunctional applications.

Enhanced Cellular Uptake of H-Chain Human Ferritin Containing Gold Nanoparticles.

Gold nanoparticles (AuNP) capped with biocompatible layers have functional optical, chemical, and biological properties as theranostic agents in biomedicine. The ferritin protein containing in situ synthesized AuNPs has been successfully used as an effective and completely biocompatible nanocarrier for AuNPs in human cell lines and animal experiments in vivo. Ferritin can be uptaken by different cell types through receptor-mediated endocytosis. Despite these advantages, few efforts have been made to evaluate the toxicity and cellular internalization of AuNP-containing ferritin nanocages. In this work, we study the potential of human heavy-chain (H) and light-chain (L) ferritin homopolymers as nanoreactors to synthesize AuNPs and their cytotoxicity and cellular uptake in different cell lines. The results show very low toxicity of ferritin-encapsulated AuNPs on different human cell lines and demonstrate that efficient cellular ferritin uptake depends on the specific H or L protein chains forming the ferritin protein cage and the presence or absence of metallic cargo. Cargo-devoid apoferritin is poorly internalized in all cell lines, and the highest ferritin uptake was achieved with AuNP-loaded H-ferritin homopolymers in transferrin-receptor-rich cell lines, showing more than seven times more uptake than apoferritin.

Deubiquitylating enzymes: potential target in autoimmune diseases.

The ubiquitin-proteasome pathway is responsible for the turnover of different cellular proteins, such as transport proteins, presentation of antigens to the immune system, control of the cell cycle, and activities that promote cancer. The enzymes which remove ubiquitin, deubiquitylating enzymes (DUBs), play a critical role in central and peripheral immune tolerance to prevent the development of autoimmune diseases and thus present a potential therapeutic target for the treatment of autoimmune diseases. DUBs function by removing ubiquitin(s) from target protein and block ubiquitin chain elongation. The addition and removal of ubiquitin molecules have a significant impact on immune responses. DUBs and E3 ligases both specifically cleave target protein and modulate protein activity and expression. The balance between ubiquitylation and deubiquitylation modulates protein levels and also protein interactions. Dysregulation of the ubiquitin-proteasome pathway results in the development of various autoimmune diseases such as inflammatory bowel diseases (IBD), psoriasis, multiple sclerosis (MS), systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). This review summarizes the current understanding of ubiquitination in autoimmune diseases and focuses on various DUBs responsible for the progression of autoimmune diseases.

Hindered Rotations of Protein Asparagine/Glutamine Side-Chain NH2 Groups: Impact of Hydrogen Bonding with DNA

Hindered rotation about an sp2 C-N bond is known to occur in arginine (Arg), asparagine (Asn), and glutamine (Gln) side chains of proteins. However, very little is known about the rotational dynamics of Asn and Gln side-chain NH2 groups. Here, using a unique NMR method, we quantitatively characterized the hindered rotations of protein Asn/Gln side-chain NH2 groups. This NMR method yields simple NH2-selective spectra that allow for an accurate determination of the kinetic rate constants for the hindered rotations. Through the NMR measurements at different temperatures, we investigated the energy barriers that restrict the C-N bond rotations of protein side-chain NH2 groups. Through a comparison of the kinetic data for the free and DNA-bound states of the Antp homeodomain, we also examined the impact of hydrogen bonding on the hindered rotations of the side-chain NH2 groups. Our data suggest that the hydrogen bonding increases the energy barriers by 1-6 kJ/mol.