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  • 1
    Online Resource
    Online Resource
    Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
    Wiley ; 2023
    In:  Proteins: Structure, Function, and Bioinformatics Vol. 91, No. 12 ( 2023-12), p. 1658-1683
    Details
    In: Proteins: Structure, Function, and Bioinformatics, Wiley, Vol. 91, No. 12 ( 2023-12), p. 1658-1683
    Abstract: We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High‐quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2‐Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2‐Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
    Type of Medium: Online Resource
    ISSN: 0887-3585 , 1097-0134
    URL: Issue
    URL: Article
    DOI: 10.1002/prot.v91.12
    DOI: 10.1002/prot.26609
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 1475032-6
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Prognostic value of modified model for end-stage liver disease scores in patients with significant tricuspid regurgitation
    Oxford University Press (OUP) ; 2023
    In:  European Heart Journal - Quality of Care and Clinical Outcomes Vol. 9, No. 3 ( 2023-04-26), p. 227-239
    Details
    In: European Heart Journal - Quality of Care and Clinical Outcomes, Oxford University Press (OUP), Vol. 9, No. 3 ( 2023-04-26), p. 227-239
    Abstract: Tricuspid regurgitation (TR) may cause damage to liver and kidney function. The Model for End-Stage Liver Disease excluding international normalized ratio (MELD-XI) and the model with albumin replacing international normalized ratio (MELD-Albumin) scores, which include both liver and kidney function indexes, may predict mortality in patients with TR. The study aimed to analyse the prognostic value of MELD-XI and MELD-Albumin scores in patients with significant TR. Methods and results A total of 1825 patients with at least moderate pure native TR from the China Valvular Heart Disease study between April and June 2018, were included in this analysis. The primary outcome was all-cause death within 2 years. Of 1825 patients, 165 (9.0%) died during follow-up. Restricted cubic splines revealed that hazard ratio for death increased monotonically with greater modified MELD scores. The MELD-XI and MELD-Albumin scores, as continuous variables or categorized using thresholds determined by maximally selected rank statistics, were independently associated with 2-year mortality (all adjusted P  & lt; 0.001). Both scores provided incremental value over prognostic model without hepatorenal indexes {MELD-XI score: net reclassification index [95% confidence interval (95% CI), 0.237 (0.138–0.323)]; MELD-Albumin score: net reclassification index (95% CI), 0.220 (0.122–0.302)}. Results were similar in clinically meaningful subgroups, including but not limited to patients under medical treatment and those with normal left ventricular ejection fraction. Models including modified MELD scores were established for prognostic evaluation of significant TR. Conclusion Both MELD-XI and MELD-Albumin scores provided incremental prognostic information and could play important roles in risk assessment in patients with significant TR.
    Type of Medium: Online Resource
    ISSN: 2058-5225 , 2058-1742
    URL: Article
    DOI: 10.1093/ehjqcco/qcac027
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2823451-0
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  • 3
    Online Resource
    Online Resource
    Sodium houttuyfonate inhibits LPS‑induced mastitis in mice via the NF‑κB signalling pathway
    Spandidos Publications ; 2019
    In:  Molecular Medicine Reports ( 2019-01-10)
    Details
    In: Molecular Medicine Reports, Spandidos Publications, ( 2019-01-10)
    Type of Medium: Online Resource
    ISSN: 1791-2997 , 1791-3004
    URL: Journal
    URL: Article
    DOI: 10.3892/mmr
    DOI: 10.3892/mmr.2019.9846
    Language: Unknown
    Publisher: Spandidos Publications
    Publication Date: 2019
    detail.hit.zdb_id: 2469505-1
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  • 4
    Online Resource
    Online Resource
    Simultaneously optimizing the strength and ductility of high-entropy alloys by magnetic field-assisted additive manufacturing
    Elsevier BV ; 2023
    In:  Journal of Alloys and Compounds Vol. 947 ( 2023-06), p. 169688-
    Details
    In: Journal of Alloys and Compounds, Elsevier BV, Vol. 947 ( 2023-06), p. 169688-
    Type of Medium: Online Resource
    ISSN: 0925-8388
    URL: Article
    DOI: 10.1016/j.jallcom.2023.169688
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2012675-X
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  • 5
    Online Resource
    Online Resource
    Recent advances in hyper-velocity flyer launch experiments on PTS
    Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences ; 2014
    In:  Acta Physica Sinica Vol. 63, No. 19 ( 2014), p. 196201-
    Details
    In: Acta Physica Sinica, Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences, Vol. 63, No. 19 ( 2014), p. 196201-
    Abstract: Magnetically driven loading technology is to load the large pulse current to the test area through the pulsed power, which forms a smooth magnetic pressure rising over time to achieve a quasi-isentropic compression of sample and hyper-velocity flyer launch. Based on the output characteristics and parameters of PTS accelerator, two types of hyper-velocity flyer launch experiments with different load configurations, such as the load, flyer plates size, current waveform and diagnostic systems etc, are designed and tested. LY12 aluminum flyer plates with dimensions of 10 mm0.725 mm was launched by single-sided stripline load configuration to 11.5 km/s while the magnetic drive load pressure is near 0.9 10^5 MPa. Simulation and experimental results agrees well with those of in the flyer launch process and the ultimate velocity. Further simulation shows that the launch velocity of aluminum flyer plates with dimensions of 8.5 mm1 mm is expected to exceed 15 km/s under the program of optimizing the structural parameters and regulation. The design and experiment technology of hyper-velocity flyer launch based on multi-branch pulsed power generator has been mastered during the designs and experiments.
    Type of Medium: Online Resource
    ISSN: 1000-3290 , 1000-3290
    URL: Journal
    URL: Article
    DOI: 10.7498/aps
    DOI: 10.7498/aps.63.196201
    Language: Unknown
    Publisher: Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences
    Publication Date: 2014
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  • 6
    Online Resource
    Online Resource
    A Case Study of Optimization and Application of Soft-Rock Roadway Support in Xiaokang Coal Mine, China
    Hindawi Limited ; 2021
    In:  Advances in Civil Engineering Vol. 2021 ( 2021-7-15), p. 1-14
    Details
    In: Advances in Civil Engineering, Hindawi Limited, Vol. 2021 ( 2021-7-15), p. 1-14
    Abstract: The roadway of S2S2 fully mechanized caving face (FMCF) in Xiaokang Coal Mine is one of the most typical deep-buried soft-rock roadways in China and had been repaired several times. In order to figure out the failure reasons of the original roadway support, the geological conditions were investigated, the surrounding rock stress was monitored, the rib displacement, roof separation, and floor heave were in situ measured, and the performance of the U-shaped steel support was simulated. The above analysis results indicated that the support failure was mainly caused by (1) the unreasonable arch roadway section, (2) the high and complex surrounding rock stress, (3) the failure control of the floor heave, and (4) the inadequate self-supporting capacity of the surrounding rock. For optimizing, the roadway section was changed to circle and a new full-section combined support system of “belt-cable-mesh-shotcrete and U-shaped steel-filling behind the support” was adopted, which could specifically control the floor heave, allow the roadway deformation in control, and improve the self-supporting ability and stress field of the surrounding rock. To determine the support parameters, the selected U-shaped steel support was verified by simulation, and various bolt-cable support schemes were simulated and compared. Finally, such an optimized support scheme was applied in the roadway of the next replacement FMCF. The in situ monitoring showed that the rib-to-rib convergence and roof-to-floor convergence were both controlled within 600 mm, which indicated that the roadway was effectively controlled. This case study has important reference value and guiding function for the optimal design of the soft-rock roadway support with similar geological conditions.
    Type of Medium: Online Resource
    ISSN: 1687-8094 , 1687-8086
    URL: Article
    DOI: 10.1155/2021/3731124
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2021
    detail.hit.zdb_id: 2449760-5
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  • 7
    Online Resource
    Online Resource
    A Hydrophobic‐Interaction‐Based Mechanism Triggers Docking between the SARS‐CoV‐2 Spike and Angiotensin‐Converting Enzyme 2
    Wiley ; 2020
    In:  Global Challenges Vol. 4, No. 12 ( 2020-12)
    Details
    In: Global Challenges, Wiley, Vol. 4, No. 12 ( 2020-12)
    Abstract: A recent experimental study found that the binding affinity between the cellular receptor human angiotensin‐converting enzyme 2 (ACE2) and receptor‐binding domain (RBD) in the spike (S) protein of novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is more than tenfold higher than that of the original severe acute respiratory syndrome coronavirus (SARS‐CoV). However, main chain structures of the SARS‐CoV‐2 RBD are almost the same with that of the SARS‐CoV RBD. Understanding the physical mechanism responsible for the outstanding affinity between the SARS‐CoV‐2 S and ACE2 is an “urgent challenge” for developing blockers, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID‐19) pandemic. Taking into account the mechanisms of hydrophobic interaction, hydration shell, surface tension, and the shielding effect of water molecules, this study reveals a hydrophobic‐interaction‐based mechanism by means of which SARS‐CoV‐2 S and ACE2 bind together in an aqueous environment. The hydrophobic interaction between the SARS‐CoV‐2 S and ACE2 protein is found to be significantly greater than that between SARS‐CoV S and ACE2. At the docking site, the hydrophobic portions of the hydrophilic side chains of SARS‐CoV‐2 S are found to be involved in the hydrophobic interaction between SARS‐CoV‐2 S and ACE2.
    Type of Medium: Online Resource
    ISSN: 2056-6646 , 2056-6646
    URL: Issue
    URL: Article
    DOI: 10.1002/gch2.v4.12
    DOI: 10.1002/gch2.202000067
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2844367-6
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  • 8
    Online Resource
    Online Resource
    Entropy-Enthalpy Compensations Fold Proteins in Precise Ways
    MDPI AG ; 2021
    In:  International Journal of Molecular Sciences Vol. 22, No. 17 ( 2021-09-06), p. 9653-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 22, No. 17 ( 2021-09-06), p. 9653-
    Abstract: Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms22179653
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape
    MDPI AG ; 2021
    In:  International Journal of Molecular Sciences Vol. 22, No. 22 ( 2021-11-09), p. 12114-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 22, No. 22 ( 2021-11-09), p. 12114-
    Abstract: Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of “variants of concern”, probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD’s binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the “urgent challenge” in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy–enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein–protein complexes is proposed based on the entropy–enthalpy compensation rule. All known structures of RBD–antibody complexes and the RBD–ACE2 complex comply with the entropy–enthalpy compensation rule in providing the driving force behind the spontaneous protein–protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation’s reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy–enthalpy compensations between antibodies and the virus at the binding sites.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms222212114
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    A Hydrophobic‐Interaction‐Based Mechanism Triggers Docking between the SARS‐CoV‐2 Spike and Angiotensin‐Converting Enzyme 2 (Global Challenges 12/2020)
    Wiley ; 2020
    In:  Global Challenges Vol. 4, No. 12 ( 2020-12)
    Details
    In: Global Challenges, Wiley, Vol. 4, No. 12 ( 2020-12)
    Type of Medium: Online Resource
    ISSN: 2056-6646 , 2056-6646
    URL: Issue
    URL: Article
    DOI: 10.1002/gch2.v4.12
    DOI: 10.1002/gch2.202070121
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2844367-6
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