B-factor Values Research Articles

Temperature-dependent structural changes in xylanase II from Trichoderma longibrachiatum

Endo-β-1,4-xylanases degrade heteroxylans that constitute the lignocellulosic plant cell wall. This enzyme is widely used in the food, paper, textile, and biorefinery industries. Temperature affects the optimum activity of xylanase and is an important factor in its application. Various structural analyses of xylanase have been performed, but its structural influence by temperature is not fully elucidated. To better understand the structural influence of xylanase due to temperature, the crystal structure of xylanase II from Trichoderma longibrachiatum (TloXynII) at room and cryogenic temperatures was determined at 2.1 and 1.9 Å resolution, respectively. The room-temperature structure of TloXynII (TloXynIIRT) showed a B-factor value 2.09 times higher than that of the cryogenic-temperature structure of TloXynII (TloXynIICryo). Subtle movement of the catalytic and substrate binding residues was observed between TloXynIIRT and TloXynIICryo. In TloXynIIRT, the thumb domain exhibited high flexibility, whereas in TloXynIICryo, the finger domain exhibited high flexibility. The substrate binding cleft of TloXynIIRT was narrower than that of TloXynIICryo, indicating a distinct finger domain conformation. Numerous water molecule networks were observed in the substrate binding cleft of TloXynIICryo, whereas only a few water molecules were observed in TloXynIIRT. These structural analyses expand our understanding of the temperature-dependent conformational changes in xylanase.

Surface plasmon resonance aptasensing and computational analysis of Staphylococcus aureus IsdA surface protein.

Staphylococcus aureus (S. aureus), a common foodborne pathogen, poses significant public health challenges due to its association with various infectious diseases. A key player in its pathogenicity, which is the IsdA protein, is an essential virulence factor in S. aureus infections. In this work, we present an integrated in-silico and experimental approach using MD simulations and surface plasmon resonance (SPR)-based aptasensing measurements to investigate S. aureus biorecognition via IsdA surface protein binding. SPR, a powerful real-time and label-free technique, was utilized to characterize interaction dynamics between the aptamer and IsdA protein, and MD simulations was used to characterize the stable and dynamic binding regions. By characterizing and optimizing pivotal parameters such as aptamer concentration and buffer conditions, we determined the aptamer's binding performance. Under optimal conditions of pH 7.4 and 150 mM NaCl concentration, the kinetic parameters were determined; ka = 3.789 × 104/Ms, kd = 1.798 × 103/s, and KD = 4.745 × 10-8 M. The simulations revealed regions of interest in the IsdA-aptamer complex. Region I, which includes interactions between amino acid residues H106 and R107 and nucleotide residues 9G, 10U, 11G and 12U of the aptamer, had the strongest interaction, based on ΔG and B-factor values, and hence contributed the most to the stability of the interaction. Region II, which covers residue 37A reflects the dynamic nature of the interaction due to frequent contacts. The approach presents a rigorous characterization of aptamer-IsdA binding behavior, supporting the potential application of the IsdA-binding aptamer system for S. aureus biosensing.

Abstract 5774: Are 19del and L858R really not the same disease entities

Abstract IntroductionThe similarities and differences between the two subtypes of common epidermal growth factor receptor (EGFR) mutations have been recognized by clinicians, but actual treatment strategies remain unchanged. The L858R mutation can be explained by the pharmacological conformational plasticity of the receptor protein and other co-occurring mutations, which may be subtypes of EGFR mutations or non-EGFR mutations, and differences in downstream signaling pathways. As long as we know that molecular differences lead to biological differences, it is a challenge for all of us that our treatment strategies must changeWe investigated the RWD, conformational structure and RNA expression profile about two types of common mutations in the mEGFR+ NSCLC patients.MethodWe collected the medical information for stage I-IIIA mEGFR+ NSCLC patients and explored the conformational structure by crystalized radiologic technique. And we performed RNA expression assay using multiplex IF and High-through-output Profiling. ResultOverall, the static structures of wild type (WT), L858R, and 19del (ΔL747-E749) EGFR did not show any significant differences. However, the difference in the static structure between WT-19del and L858R-19del was subtly greater than that of WT-L858R. In addition, further analyses demonstrated no significant structural differences in the phosphorylation sites. However, it should be noted that proteins do not exist as static structures in vivo, and they have a dynamic, flexible structure that changes over time, i.e., plasticity of proteins. Therefore, we investigated the X-ray B-factor value, which is an indicator of flexibility, dynamics, and plasticity of proteins. As expected, the loop or disordered regions mainly shows higher B-factor values, which indicates an active structure, highly changeable and dynamic. Together, the three types of the EGFR protein manifest wholly similar B-factor values, while several local regions present appreciably distinct B-factors. Physical properties such as the dynamic structure may affect intermolecular recognition of EGFR proteins and their function Recent biochemical and biophysical evidence suggests that oncogenic mutations have an impact on the conformational dynamics of enzymesConclusionIn conclusion, our results suggest that Patients with 19del and L858R mutations demonstrated a different clinical course. It is necessary to consider the dynamic structural characteristics and functional differences of EGFR membrane proteins. Citation Format: Yunseok Heo, Joo Ri Kim, Yeoun Eun Sung, Seoree Kim, Chan Kwon Jung, Jeong-Oh Kim, Jeong-yeon Shin, Guk Jin Lee, Sang hoon Chun, Seong Hyeon Bu, Young Ho Lee, Jin Hyoung Kang. Are 19del and L858R really not the same disease entities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5774.

Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach.

Escherichia fergusonii a gram-negative rod-shaped bacterium in the Enterobacteriaceae family, infect humans, causing serious illnesses such as urinary tract infection, cystitis, biliary tract infection, pneumonia, meningitis, hemolytic uremic syndrome, and death. Initially treatable with penicillin, antibiotic misuse led to evolving resistance, including resistance to colistin, a last-resort drug. With no licensed vaccine, the study aimed to design a multi-epitope vaccine against E. fergusonii. The study started with the retrieval of the complete proteome of all known strains and proceeded to filter the surface exposed virulent proteins. Seventeen virulent proteins (4 extracellular, 4 outer membranes, 9 periplasmic) with desirable physicochemical properties were identified from the complete proteome of known strains. Further, these proteins were processed for B-cell and T-cell epitope mapping. Obtained epitopes were evaluated for antigenicity, allergenicity, solubility, MHC-binding, and toxicity and the filtered epitopes were fused by specific linkers and an adjuvant into a vaccine construct. Structure of the vaccine candidate was predicted and refined resulting in 78.1% amino acids in allowed regions and VERIFY3D score of 81%. Vaccine construct was docked with TLR-4, MHC-I, and MHC-II, showing binding energies of -1040.8 kcal/mol, -871.4 kcal/mol, and -1154.6 kcal/mol and maximum interactions. Further, molecular dynamic simulation of the docked complexes was carried out resulting in a significant stable nature of the docked complexes (high B-factor and deformability values, lower Eigen and high variance values) in terms of intermolecular binding conformation and interactions. The vaccine was also reported to stimulate a variety of immunological pathways after administration. In short, the designed vaccine revealed promising predictions about its immune protective potential against E. fergusonii infections however experimental validation is needed to validate the results.

Radiation Damage on Selenomethionine-Substituted Single-Domain Substrate-Binding Protein

Radiation damage is an inherent challenge in macromolecular crystallography (MX). This diminishes the diffraction quality and also compromises the accuracy of the crystal structure. Investigating the impact of radiation damage on the crystal quality and structure can offer valuable insights into the structural interpretation and data collection strategy. Selenomethionine (SeMet, Mse) is an amino acid that exists in nature and contains a high-Z atom, i.e., selenium (Se), which is sensitive to radiation damage; however, little is known regarding the radiation damage of this amino acid. To better understand the radiation damage that affects SeMet, we investigated the radiation damage to a SeMet-substituted substrate-binding protein from Rhodothermus marinus. As the X-ray dose increased, the quality of the data statistics deteriorated. In particular, an increase in the X-ray dose increased the negative Fo-Fc electron density map near the Se atom of the Mse residue, while no negative Fo-Fc electron density map was observed in the other atoms (O, C, and N). Radiation damage increased the absolute B-factor value of the Se atom in the Mse residue, which was higher than that of the other atoms. This indicates that Se is more sensitive to radiation damage than other atoms. These results will contribute to advancing our knowledge of the radiation damage that can occur in MX.

N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE.

TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40-80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min-1⋅mmol-1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.

Improvement of the stability and catalytic efficiency of heparan sulfate N-sulfotransferase for preparing N-sulfated heparosan.

The chemo-enzymatic and enzymatic synthesis of heparan sulfate and heparin are considered as an attractive alternative to the extraction of heparin from animal tissues. Sulfation of the hydroxyl group at position 2 of the deacetylated glucosamine is a prerequisite for subsequent enzymatic modifications. In this study, multiple strategies, including truncation mutagenesis based on B-factor values, site-directed mutagenesis guided by multiple sequence alignment, and structural analysis were performed to improve the stability and activity of human N-sulfotransferase. Eventually, a combined variant Mut02 (MBP-hNST-NΔ599-602/S637P/S741P/E839P/L842P/K779N/R782V) was successfully constructed, whose half-life at 37°C and catalytic activity were increased by 105-fold and 1.35-fold, respectively. After efficient overexpression using the Escherichia coli expression system, the variant Mut02 was applied to N-sulfation of the chemically deacetylated heparosan. The N-sulfation content reached around 82.87% which was nearly 1.88-fold higher than that of the wild-type. The variant Mut02 with high stability and catalytic efficiency has great potential for heparin biomanufacturing.

Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming.

Alkaline pectate lyases have biotechnological applications in plant fiber processing, such as ramie degumming. Previously, we characterized an alkaline pectate lyase from Bacillus clausii S10, named BacPelA, which showed potential for enzymatic ramie degumming because of its high cleavage activity toward methylated pectins in alkaline conditions. However, BacPelA displayed poor thermo-alkaline stability. Here, we report the 1.78 Å resolution crystal structure of BacPelA in apo form. The enzyme has the characteristic right-handed β-helix fold of members of the polysaccharide lyase 1 family and shows overall structural similarity to them, but it displays some differences in the details of the secondary structure and Ca2+-binding site. On the basis of the structure, 10 sites located in flexible regions and showing high B-factor and positive ΔTm values were selected for mutation, aiming to improve the thermo-alkaline stability of the enzyme. Following site-directed saturation mutagenesis and screening, mutants A238C, R150G, and R216H showed an increase in the T5015 value at pH 10.0 of 3.0 °C, 6.5 °C, and 7.0 °C, respectively, compared with the wild-type enzyme, interestingly accompanied by a 24.5%, 46.6%, and 61.9% increase in activity. The combined mutant R150G/R216H/A238C showed an 8.5 °C increase in the T5015 value at pH 10.0, and an 86.1% increase in the specific activity at 60 °C, with approximately doubled catalytic efficiency, compared with the wild-type enzyme. Moreover, this mutant retained 86.2% activity after incubation in ramie degumming conditions (4 h, 60 °C, pH 10.0), compared with only 3.4% for wild-type BacPelA. The combined mutant increased the weight loss of ramie fibers in degumming by 30.2% compared with wild-type BacPelA. This work provides a thermo-alkaline stable, highly active pectate lyase with great potential for application in the textile industry, and also illustrates an effective strategy for rational design and improvement of pectate lyases.

Development of thermostable dextranase from Streptococcus mutans (SmdexTM) through in silico design employing B-factor and Cartesian-ΔΔG

The thermal stability of enzymes dramatically limits their application in the industrial field. Based on the crystal structure, we conducted a semi-rational design according to the B-factor and free energy values to improve the stability of dextranase from Streptococcus mutans (SmdexTM). The B-factor values of Asn102, Asn503, Asp501 and Asp500 were the highest predicted by B-FITTER. Then Rosetta was used to simulate the saturation mutations of Asn102, Asn503, Asp501 and Asp500. The mutated amino acid was designed according to the change of acG. The results showed that the thermal stability of N102P, N102C, D500G, and D500T was improved, and the half-lives of N102P/D500G and N102P/D500T at 45 °C were increased to 3.14 times and 2.44 times, respectively. Analyzing the interaction of amino acids by using Discovery Studio 4.5, it was observed that the thermal stability of dextranase was improved due to the increase in hydrophobicity and the number of hydrogen bonds of the mutant enzyme. The catalytic efficiency of N102P/D500T was increased. Compared with the hydrolyzed products of SmdexTM, the mutant enzymes do not change the specificity of hydrolysates.

Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke

The discovery of a novel drug for ischemic stroke is plagued by expensive and unsuccessful outcomes. FDA-approved drugs could be a viable repurposing strategy for stroke therapy. Emerging evidence suggests the regulating role of Glutathione peroxidase (GPX4) in stroke and attracts as a potential target. To overcome limited therapeutic interventions, a drug repurposing in silico investigation of FDA-approved drugs is proposed for the GPX4 receptor in distinctive species (Homo sapiens and Mus musculus). The GPX4 UniProt wild type ids, that is, P36969 (Homo sapiens), P36970 (Rattus norvegicus) and O70325 (Mus musculus) are Swiss modelled, and resultant templates are 2OBI and 6HN3 for Homo sapiens, and 5L71 for Mus musculus with a sequence identity of ∼88%. Enrichment analysis reveals high sensitivity and ranked actives with ROC and AUC values of 0.59 and 0.61, respectively. Virtual screening at extra precision resulted hit Acarbosum, is similar between 2OBI and 6HN3, demonstrating a multiple-target specificity and Iopromide, targeting 2OBI. MD simulation at 100 ns following trajectory analysis provides RMSD (∼1.2–1.8Å), RMSF (∼1.6–2.7Å), Rgyr (∼15–15.6Å) depicting stabilisation of receptor–ligand complexes. Furthermore, average B-factor value of 2OBI, 6HN3 and 5L71 is 25Å, 24Å and 60Å with a defined resolution of 1.55Å, 1.01Å and 1.80Å, respectively, depicting the thermodynamic stability of the protein structures. The dynamic cross-correlation and principal component analysis of residual fluctuations reveal more positive correlation, high atomic displacements and greater residual clustering of residues from atomic coordinates. Therefore, Acarbosum, an FDA-approved drug, could act as a potential repurposing drug with a multi-target approach translating from preclinical to clinical stages. Communicated by Ramaswamy H. Sarma

Diffusion-tensor magnetic resonance imaging of the growth plates: substantiation of the method and evaluation of its reproducibility

INTRODUCTION: In recent years there is an increasing interest in assessing the state of the physis among pediatric orthopedic traumatologists, due to the availability of surgical correction of conditions associated with impaired growth plate function. Application of these methods requires dynamic assessment of the state of the physis. The existing methods for assessing the functional state of the physis are few and imperfect. Magnetic resonance imaging (MRI), in particular diffusion tensor imaging (DTI), is promising for assessing the growth plates.OBJECTIVE: To assess the possibility of applying DTI technique to assess the state of the physis (growth plate).MATERIALS AND METHODS: The study was approved by the local ethical committee of the Institute of the Human Brain named after N.P. Bekhtereva of Russian Academy of Sciences, protocol No. 32, dated 21.12.2020. Informed consent was obtained from each legal representative. At the Turner National Medical Research Center for Сhildren’s Orthopedics and Trauma Surgery of the Ministry of Health of the Russian Federation a standard magnetic resonance examination of the knee joints was performed, additionally diffusion tensor tomography was performed in 75 patients aged 4.1 to 14.3 years (41 males, 34 females), both deemed healthy and with a known physeal pathology. The studies were performed using a Philips Ingenia ElitionX machine with a magnetic field strength of 3 Tesla, DTI was performed in the coronal plane, TE=71.2 ms, TR=4000 ms, b-factor value 600 s/mm2, 15 diffusion directions were used, slice thickness was 3 mm without gaps, the matrix size was 1.25×1.25 mm. The resulting images were processed using the DSI Studio software, including tract construction, estimation of the total volume and average length of the tracts. The reproducibility of the technique was assessed.RESULTS: Higher volumes and mean tract lengths were found in healthy males at puberty compared to other groups. When assessing reproducibility, the standard deviations were about 10% of the final value.DISCUSSION: Images of growth plate tracts were obtained. In individuals of pubertal age that were deemed healthy, the tract volume values and the average length of the tracts were higher than in individuals of prepubertal age and those with pathological conditions affecting the state of the growth plates. The average tract length turned out to be more reproducible than the total tract volume parameter.CONCLUSION: With the help of DTI, it is possible to evaluate the arrangement of the structures in the growth plates.

Improving the thermostability of alginate lyase FlAlyA with high expression by computer-aided rational design for industrial preparation of alginate oligosaccharides.

FlAlyA, a PL7 alginate lyase with industrial potential, is widely applied in the preparation the alginate oligosaccharide because of its high activity of degradation the alginate. However, heat inactivation still limits the industrial application of FlAlyA. To further enhance its thermostability, a group of mutants were designed, according to evaluating the B-factor value and free energy change via computer-aided calculation. 25 single-point mutants and one double-points mutant were carried out by site-directed mutagenesis. The optimal two single-point mutants H176D and H71K showed 1.20 and 0.3°C increases in the values of T m, while 7.58 and 1.73 min increases in the values of half-life (t 1/2) at 50°C, respectively, compared with that of the wild-type enzyme. Interestingly, H71K exhibits the comprehensive improvement than WT, including expression level, thermal stability and specific activity. In addition, the mechanism of these two mutants is speculated by multiple sequence alignment, structural basis and molecular dynamics simulation, which is likely to be involved in the formation of new hydrogen bonds and decrease the SASA of the mutants. These results indicate that B-factor is an efficient approach to improves the thermostability of alginate lyase composed of β-sheet unit. Furthermore, the highest yield of the mutant reached about 650 mg/L, which was nearly 36 times that of previous studies. The high expression, excellent activity and good thermal stability make FlAlyA a potential candidate for the industrial production of alginate oligosaccharides.

Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition

In potato (Solanum tuberosum L.), 14-3-3 protein forms a protein complex with the FLOWERING LOCUS T (FT)-like protein StSP6A and the FD-like protein StFDL1 to activate potato tuber formation. Eleven 14-3-3 isoforms were reported in potato, designated as St14a-k. In this study, the crystal structure of the free form of St14f was determined at 2.5 Å resolution. Three chains were included in the asymmetric unit of the St14f free form crystal, and the structural deviation among the three chain structures was found on the C-terminal helix H and I. The St14f free form structure in solution was also investigated by nuclear magnetic resonance (NMR) residual dipolar coupling analysis, and the chain B in the crystal structure was consistent with NMR data. Compared to other crystal structures, St14f helix I exhibited a different conformation with larger B-factor values. Larger B-factor values on helix I were also found in the 14-3-3 free form structure with higher solvent contents. The mutation in St14f Helix I stabilized the complex with StFDL1. These data clearly showed that the flexibility of helix I of 14-3-3 protein plays an important role in the recognition of target protein.

Structure of thaumatin under acidic conditions: Structural insight into the conformations in lysine residues responsible for maintaining the sweetness after heat-treatment

Thaumatin is an intensely sweet-tasting protein. Its sweetness persists when heated under acidic conditions, but disappears when heated at a pH above 7.0. To clarify how the structural features of thaumatin resist insoluble aggregation during heating under acidic conditions, we analysed its crystal structure obtained at pH 4.0, 6.0, and 8.0. Simultaneously, the melting temperature (Tm) at these pH levels was determined using differential scanning fluorimetry. At pH 4.0, the Tm of thaumatin was substantially lower and the overall B-factor value of its structure was higher than those at pH 6.0. Interestingly, the relative B-factor values for most lysine residues decreased as the pH reduced. These results suggest that the overall structure at pH 4.0 becomes flexible but the relative flexibility of some regions is lower than that at pH 6.0. Thus, the reduction in relative flexibility might play an important role in preventing thermal aggregation, thereby maintaining the sweetness.

Quantifying and comparing radiation damage in the Protein Data Bank

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.

Diagnostic and prognostic value of a diffusion-weighted image of the liver with magnetic resonance imaging in patients with alcoholic liver disease

The aim of the study was to assess the diagnostic and prognostic value of a diffusion-weighted image of the liver with magnetic resonance imaging in patients with alcoholic liver disease.Material and methods. A total of 113 patients with alcoholic liver disease (ALD) were examined. Among them, 65 (57.5%) are men and 48 (42.5%) are women. The mean age of patients is 46.3 ± 5.2 years. The structure of the instrumental algorithm for examining patients was presented: ultrasound of the abdominal cavity organs with clinical elastography – 98 (86.7%) patients, MRI of the liver with the mandatory inclusion of the DWI liver sequence in the protocol (n = 113). The b-factor values of 100/600/1000 were used for the liver DWI sequence. Liver biopsy was chosen as the reference method in 65 (57.5%) patients.Results. The patients were monitored for 12 months. At the first stage, the qualitative characteristics of the liver DWI sequence were assessed: no or there is a diffusion limitation. At the second stage, the quantitative indicators of the DWI sequence were assessed in the form of calculating the measured diffusion index and coefficient. In order to standardize the technique of liver DWI on MRI in patients with ALD, the results were compared with the data of clinical elastography (p < 0.01) and liver biopsy (p < 0.05). Upon admission and monitoring of patients (after 1, 3, 6, 9 months), a high correlation was found in the assessment of comparing the quantitative indicators of DWI with clinical elastography (r = 0.873) and an average correlation with biopsy data (r = 0.715).Conclusions. There was a high correlation between the limitation of liver diffusion on MRI and negative clinical and laboratory dynamics (r = 0.889) and in the absence of limitation of diffusion in the liver and positive clinical and laboratory dynamics (r = 0.885). DWI of the liver on MRI in patients with ALD has a high diagnostic and prognostic value in assessing abnormal abstinence regimen (AUROC = 0.903 (95% CI 0.871–0.911)). Diagnostic and prognostic significance of the developed criteria for DWI of the liver at MRI in patients with ABD at admission: for a qualitative assessment AUROC = 0.844 (95% CI 0.801–0.869), quantitative – AUROC = 0.908 (95% CI 0.875–0.911); with dynamic observation: for a qualitative assessment AUROC = 0.939 (95% CI 0.901–0.955), quantitative – AUROC = 0.919 (95% CI 0.871–0.931).

Engineered Stable 5-Hydroxymethylfurfural Oxidase (HMFO) from 8BxHMFO Variant of Methylovorus sp. MP688 through B-Factor Analysis

What is known as Furan-2,5-dicarboxylic acid (FDCA) is an attractive compound since it has similar properties to terephthalic acid. Further, 5-hydroxymethylfurfural oxidase (HMFO) is an enzyme, which could convert HMF to FDCA directly. Most wild types of HMFO have low activity on the oxidation of HMF to FDCA. The variant of 8BxHFMO from Methylovorus sp. MP688 was the only reported enzyme that was able to perform FDCA production. However, the stabilization of 8BxHMFO is still not that satisfactory, and further improvement is necessary for the industrial application of the enzyme. In this work, stability-enhanced HMFO from 8BxHFMO was engineered through employing B-factor analysis. The mutation libraries were created based on the NNK degeneracy of residues with the top ten highest B-factor value, and two of the effective mutants were screened out through the high throughput selection with the horseradish peroxidase (HRP)-Tyr assay. The mutants Q319K and N44G show a significantly increased yield of FDCA in the reaction temperature range of 30 to 40 °C. The mutant Q319K shows the best performance at 35 °C with a FDCA yield of 98% (the original 8BxHMFO was only 85%), and a half-life exceeding 72 h. Moreover, molecular dynamic simulation indicates that more hydrogen bonds are formed in the mutants, which improves the stability of the protein structure. The method could enhance the design of more stable biocatalysts; and provides potential for the further optimization and utilization of HMFO in biotechnological processes.

Structure of Blood Coagulation Factor VIII in Complex With an Anti-C2 Domain Non-Classical, Pathogenic Antibody Inhibitor.

Factor VIII (fVIII) is a procoagulant protein that binds to activated factor IX (fIXa) on platelet surfaces to form the intrinsic tenase complex. Due to the high immunogenicity of fVIII, generation of antibody inhibitors is a common occurrence in patients during hemophilia A treatment and spontaneously occurs in acquired hemophilia A patients. Non-classical antibody inhibitors, which block fVIII activation by thrombin and formation of the tenase complex, are the most common anti-C2 domain pathogenic inhibitors in hemophilia A murine models and have been identified in patient plasmas. In this study, we report on the X-ray crystal structure of a B domain-deleted bioengineered fVIII bound to the non-classical antibody inhibitor, G99. While binding to G99 does not disrupt the overall domain architecture of fVIII, the C2 domain undergoes an ~8 Å translocation that is concomitant with breaking multiple domain-domain interactions. Analysis of normalized B-factor values revealed several solvent-exposed loops in the C1 and C2 domains which experience a decrease in thermal motion in the presence of inhibitory antibodies. These results enhance our understanding on the structural nature of binding non-classical inhibitors and provide a structural dynamics-based rationale for cooperativity between anti-C1 and anti-C2 domain inhibitors.

Designing multi-epitope subunit vaccine for ocular trachoma infection using Chlamydia trachomatis polymorphic membrane proteins G

Chlamydia trachomatis serovars A, B, Ba and C are bacteria serovars responsible for the blinding disease trachoma, the infection affects the upper tarsal conjunctiva of the eye. Repeated infection occurs among people in endemic areas throughout childhood which may later lead to blindness at adulthood. Chlamydia trachomatis contains a highly conserved surface glycoprotein, the polymorphic membrane protein which are surface antigens and are target for neutralizing antibodies as they are strongly immunogenic hence elicit proinflammatory response. It is suggested that they may be virulence by modulating inflammation and adherence to host cell, therefore one can argue that PMPs may be important in host-cell invasion as a virulence factor; this fact makes it a good entrant for Chlamydia trachomatis vaccine design.In this study a combination of bioinformatics and immunoinformatics methods and tools were applied to design multi-epitope subunit vaccines using Chlamydia trachomatis polymorphic membrane protein G (PMPG). The vaccine candidate was constructed using suitable linkers to link the CTL epitopes, HTC epitopes and adjuvant together, this constructed vaccine candidate was appraised for its antigenic and allergenic properties, the physicochemical parameters which include the molecular formula, theoretical isoelectric point (pI), molecular weight, half-life, instability index, solubility score, GRAVY and aliphatic index were also predicted. The vaccine secondary structure was predicted to evaluate the properties of the secondary structure of the vaccine such as the helices, sheets and coils. The tertiary structure was also predicted, refined and validated using data like Ramachandran plot and Z-score. Disulfide engineering was executed in regions having high mobility in order to improve the protein stability of the candidate vaccine, from this, three pairs of amino acid residues GLY112-THR135, TYR137-ARG139 and THR144-ASN147 were finalized based on their chi3 and B-factor value. Codon adaptation carried out revealed that the vaccine candidate sequence has a GC-content of 53.75% and codon adaptation index of 1.0. In silico cloning was also carried out to determine the vector and cloning site suitable for overproduction of the vaccine protein for large scale production process. To determine the complex stability and binding free energy of the vaccine candidate, molecular docking was performed using the vaccine protein as ligand while TLR-2 and TLR-4 were the receptors. The lowest binding energy for the vaccine-TLR4 complex was −1626.7 and −1305.1 for the vaccine-TLR2 complex. Dynamic simulation provided predictions such as eigenvalue of 5.277774 × 10−06 for TLR-4 receptor and 7.403984 × 10−06 for TLR-2 receptor. From results obtained from the various predictions and validations, it can be concluded that the candidate vaccine will be capable of inducing anti-inflammatory immunity which may be able to prevent Chlamydia trachomatis invasion among human hosts.

Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1

Tripartite motif (TRIM)7 is an E3 ubiquitin ligase that was first identified through its interaction with glycogenin-1 (GN1), the autoglucosyltransferase that initiates glycogen biosynthesis. A growing body of evidence indicates that TRIM7 plays an important role in cancer development, viral pathogenesis, and atherosclerosis and, thus, represents a potential therapeutic target. TRIM family proteins share a multidomain architecture with a conserved N-terminal TRIM and a variable C-terminal domain. Human TRIM7 contains the canonical TRIM motif and a B30.2 domain at the C terminus. To contribute to the understanding of the mechanism of action of TRIM7, we solved the X-ray crystal structure of its B30.2 domain (TRIM7B30.2) in two crystal forms at resolutions of 1.6 Å and 1.8 Å. TRIM7B30.2 exhibits the typical B30.2 domain fold, consisting of two antiparallel β-sheets of seven and six strands, arranged as a distorted β-sandwich. Furthermore, two long loops partially cover the concave face of the β-sandwich defined by the β-sheet of six strands, thus forming a positively charged cavity. We used sequence conservation and mutational analyses to provide evidence of a putative binding interface for GN1. These studies showed that Leu423, Ser499, and Cys501 of TRIM7B30.2 and the C-terminal 33 amino acids of GN1 are critical for this binding interaction. Molecular dynamics simulations also revealed that hydrogen bond and hydrophobic interactions play a major role in the stability of a modeled TRIM7B30.2-GN1 C-terminal peptide complex. These data provide useful information that could be used to target this interaction for the development of potential therapeutic agents.