Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC00100

Naturally Occurring Mutations in the Nonstructural Region 5B of Hepatitis C Virus (HCV) from Treatment-Naïve Korean Patients Chronically Infected with HCV Genotype 1b

<div><p>The nonstructural 5B (NS5B) protein of the hepatitis C virus (HCV) with RNA-dependent RNA polymerase (RdRp) activity plays a pivotal role in viral replication. Therefore, monitoring of its naturally occurring mutations is very important for the development of antiviral therapies and vaccines. In the present study, mutations in the partial NS5B gene (492 bp) from 166 quasispecies of 15 genotype-1b (GT) treatment-naïve Korean chronic patients were determined and mutation patterns and frequencies mainly focusing on the T cell epitope regions were evaluated. The mutation frequency within the CD8+ T cell epitopes was significantly higher than those outside the CD8+ T cell epitopes. Of note, the mutation frequency within predicted CD4+ T cell epitopes, a particular mutational hotspot in Korean patients was significantly higher than it was in patients from other areas, suggesting distinctive CD4+ T cell-mediated immune pressure against HCV infection in the Korean population. The mutation frequency in the NS5B region was positively correlated with patients with carrier-stage rather than progressive liver disease (chronic hepatitis, liver cirrhosis and hepatocellular carcinoma). Furthermore, the mutation frequency in four codons (Q309, A333, V338 and Q355) known to be related to the sustained virological response (SVR) and end-of treatment response (ETR) was also significantly higher in Korean patients than in patients from other areas. In conclusion, a high degree of mutation frequency in the HCV GT-1b NS5B region, particularly in the predicted CD4+ T cell epitopes, was found in Korean patients, suggesting the presence of distinctive CD4+ T cell pressure in the Korean population. This provides a likely explanation of why relatively high levels of SVR after a combined therapy of pegylated interferon (PEG-IFN) and ribavirin (RBV) in Korean chronic patients with GT-1b infections are observed.</p></div

Active Accumulation of Spherical Analytes on Plasmonic Hot Spots of Double-Bent Au Strip Arrays by Multiple Dip-Coating

To achieve sensitive plasmonic biosensors, it is essential to develop an efficient method for concentrating analytes in hot spots, as well as to develop plasmonic nanostructures for concentrating light. In this study, target analytes were delivered to the surface of double-bent Au strip arrays by a multiple dip-coating method; they were self-aligned in the valleys between neighboring Au strips by capillary forces. As the valleys not only accommodate target analytes but also host strong electromagnetic fields due to the interaction between adjacent strips, sensitive measurement of target analytes was possible by monitoring changes in the wavelength of a localized surface plasmon resonance. Using the proposed plasmonic sensor and target delivery method, the adsorption and saturation of polystyrene beads 100 nm in size on the sensor surface were monitored by the shift of the resonance wavelength. In addition, the pH-dependent stability of exosomes accumulated on the sensor surface was successfully monitored by changing the pH from 7.4 to 4.0

Role of W addition in reducing heat checking and enhancing the mechanical properties of hot work tool steel

The influence of carbide precipitation on the mechanical properties of hot work tool steels was investigated in this study. Compared to the commercial H13 hot work tool steel, the KMoW and RW steels containing W exhibited a reduced high-temperature softening and an enhanced thermal fatigue resistance during long-term aging. These improvements can be attributed to the increased structural and chemical stability of V-rich MC carbides. The increased (W + Mo)/(V + Fe) atomic ratios at MC metallic sites increased their coherency as well as reduced the driving force required for the precipitation of Cr-rich carbides. These findings suggest that the addition of W effectively improves the heat-checking resistance and mechanical properties of hot work tool steels

Reliable and robust method for abdominal muscle mass quantification using CT/MRI: An explorative study in healthy subjects.

BackgroundQuantification of abdominal muscle mass by cross-sectional imaging has been increasingly used to diagnose sarcopenia; however, the technical method for quantification has not been standardized yet. We aimed to determine an optimal method to measure the abdominal muscle area.MethodsAmong 50 consecutive subjects who underwent abdominal CT and MRI for possible liver donation, total abdominal muscle area (TAMA) and total psoas muscle area (TPA) at the L3 inferior endplate level were measured by two blinded readers. Inter-scan agreement between CT and MRI and inter-reader agreement between the two readers were evaluated using intraclass correlation coefficient (ICC) and within-subject coefficient of variation (WSCV). To evaluate the effect of measurement level, one reader measured TAMA and TPA at six levels from the L2 to L4 vertebral bodies.ResultsTAMA was a more reliable biomarker than TPA in terms of inter-scan agreement (ICC: 0.928 vs. 0.788 for reader 1 and 0.853 vs. 0.821 for reader 2, respectively; WSCV: 8.3% vs. 23.4% for reader 1 and 10.4% vs. 22.3% for reader 2, respectively) and inter-reader agreement (ICC: 0.986 vs. 0.886 for CT and 0.865 vs. 0.669 for MRI, respectively; WSCV: 8.2% vs. 16.0% for CT and 11.6% vs. 29.7% for MRI, respectively). In terms of the measurement level, TAMA did not differ from the L2inf to L4inf levels, whereas TPA increased with a decrease in measurement level.ConclusionsTAMA is a better biomarker than TPA in terms of inter-scan and inter-reader agreement and robustness to the measurement level. CT was a more reliable imaging modality than MRI. Our results support the use of TAMA measured by CT as a standard biomarker for abdominal muscle area measurement

Distribution and frequencies of the amino acid mutations in the NS5B AA 308–471 regions.

<p>The blue-shaded regions are the known MHC class I restricted regions and the red-lined regions are regions expected to be Korean-specific CD4+ epitope-binding regions. The region between the dotted lines is a mutational hotspot. The arrow indicates amino acid substitution related to IFN/RBV and other agents in HCV and the asterisks denote the novel mutations found in this study. The letters C and D indicate ‘conserved’ and ‘diverse’ in the subclones, respectively.</p

Comparison of mutation rates in four SVR-related codons (309, 333, 338 and 355) in the NS5B region between 15 Korean consensus sequence and patients from other countries.

<p>a. P-values were determined by a comparison with the mutation rate from 15 Korean consensus sequences.</p><p>b. Statistically significant after a Bonferroni post hoc analysis (p<0.05).</p

Comparison of mutation rates between the CD4+ and CD8+ T cell epitope regions.

<p>a. P-values were determined by a comparison of mutation rates of inside and outside of the CD8+ T cell epitopes.</p><p>b. P-values (<0.001) were obtained by a comparison of the mutation rates of outside of the CD4+ T cell epitopes as well as inside the CD8+ T cell epitopes.</p

Mutation frequency at the major codons including antiviral resistance and SVR-related codons in the sequenced NS5B region.

<p>a. ‘Diverse’ indicates the mutation type of the coexistence with the wild type in a quasispecies distribution of a subject. Otherwise, ‘Conserved’ indicates the presence of only mutation types alone without the wild type in a quasispecies distribution of a subject.</p><p>b. C316/Q464 and N316/E464 were found in an exclusive manner. All the 33 subclones with the C316/Q464 type were found in patients with advanced liver disease, but not in Cs.</p

Comparison of the frequencies of d_N and d_S of the NS5B regions between 15 Korean patients consensus sequence and patients from other countries.

<p>a. China: 15, Japan: 15, Switzerland: 15 and the United States: 15.</p><p>b. p = 0.002;</p><p>c: p = 0.078;</p><p>d: p<0.001.</p