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  1. Article ; Online: Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation.

    Zhu, Tong / Sun, Jinyuan / Pang, Hua / Wu, Bian

    JACS Au

    2024  Volume 4, Issue 2, Page(s) 788–797

    Abstract: The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical ... ...

    Abstract The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Journal Article
    ISSN 2691-3704
    ISSN (online) 2691-3704
    DOI 10.1021/jacsau.3c00792
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  2. Article: Protein design with a machine-learned potential about backbone designability.

    Sun, Jinyuan / Wu, Bian

    Trends in biochemical sciences

    2022  Volume 47, Issue 8, Page(s) 638–640

    Abstract: Proteins are fundamental molecules that mediate diverse biological processes, and protein design can shed light on the molecular mechanisms underlying their biological functions. Huang and colleagues have developed a sequence-independent statistical ... ...

    Abstract Proteins are fundamental molecules that mediate diverse biological processes, and protein design can shed light on the molecular mechanisms underlying their biological functions. Huang and colleagues have developed a sequence-independent statistical model for de novo protein design using neural networks (NNs) to learn the distribution of backbone structures with minimal side-chain information.
    MeSH term(s) Protein Conformation ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2022-04-21
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.04.004
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1207: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article: Protein design with a machine-learned potential about backbone designability

    Sun, Jinyuan / Wu, Bian

    Trends in biochemical sciences. 2022,

    2022  

    Abstract: Proteins are fundamental molecules that mediate diverse biological processes, and protein design can shed light on the molecular mechanisms underlying their biological functions. Huang and colleagues have developed a sequence-independent statistical ... ...

    Abstract Proteins are fundamental molecules that mediate diverse biological processes, and protein design can shed light on the molecular mechanisms underlying their biological functions. Huang and colleagues have developed a sequence-independent statistical model for de novo protein design using neural networks (NNs) to learn the distribution of backbone structures with minimal side-chain information.
    Keywords neural networks ; proteins ; statistical models
    Language English
    Publishing place Elsevier Ltd
    Document type Article
    Note Pre-press version
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.04.004
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    In stock of ZB MED Bonn / Germany

    Z 78/716: Show issues

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  4. Article: Wine, beer and Chinese Baijiu in relation to cardiovascular health: the impact of moderate drinking

    Kang, Qiao / Sun, Jinyuan / Wang, Bowen / Sun, Baoguo

    Food science and human wellness. 2023 Jan., v. 12, no. 1

    2023  

    Abstract: Excessive alcohol consumption (≥15 drinks per week) causes chronic diseases and multiple other health conditions. Nevertheless, alcohol beverages have been used as a vital medicine ingredient in various cultures since ancient times. A wealth of ... ...

    Abstract Excessive alcohol consumption (≥15 drinks per week) causes chronic diseases and multiple other health conditions. Nevertheless, alcohol beverages have been used as a vital medicine ingredient in various cultures since ancient times. A wealth of epidemiological and experimental research has shown that light-moderate alcohol consumption, regardless of beverage type, is associated with reducing cardiovascular incidence and mortality rate. Due to the disparities in raw materials, fermentation techniques, production environment, etc., alcoholic beverages tend to possess different non-ethanol component profiles, thus resulting in varying degrees of health effects. Furthermore, bioactive compounds in alcohol are continuously discovered as well as the mechanisms underlying their cardioprotective contributions at a molecular level. This article elucidates the epidemiology of moderate alcohol consumption and various cardiovascular conditions, along with the limitations and controversies of current studies. In addition, protective effects and putative mechanisms of both ethanol and non-ethanol components of wine, beer, and Chinese Baijiu, the three most representative alcoholic beverages worldwide, are to be evaluated within the context of a rational drinking pattern.
    Keywords alcohol drinking ; beers ; epidemiology ; ethanol ; fermentation ; food science ; humans ; ingredients ; medicine ; mortality ; wines
    Language English
    Dates of publication 2023-01
    Size p. 1-13.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2712869-6
    ISSN 2213-4530
    ISSN 2213-4530
    DOI 10.1016/j.fshw.2022.07.013
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  5. Book ; Online: HRI Challenges Influencing Low Usage of Robotic Systems in Disaster Response and Rescue Operations

    Hoque, Shahinul / Riya, Farhin Farhad / Sun, Jinyuan

    2024  

    Abstract: The breakthrough in AI and Machine Learning has brought a new revolution in robotics, resulting in the construction of more sophisticated robotic systems. Not only can these robotic systems benefit all domains, but also can accomplish tasks that seemed ... ...

    Abstract The breakthrough in AI and Machine Learning has brought a new revolution in robotics, resulting in the construction of more sophisticated robotic systems. Not only can these robotic systems benefit all domains, but also can accomplish tasks that seemed to be unimaginable a few years ago. From swarms of autonomous small robots working together to more very heavy and large objects, to seemingly indestructible robots capable of going to the harshest environments, we can see robotic systems designed for every task imaginable. Among them, a key scenario where robotic systems can benefit is in disaster response scenarios and rescue operations. Robotic systems are capable of successfully conducting tasks such as removing heavy materials, utilizing multiple advanced sensors for finding objects of interest, moving through debris and various inhospitable environments, and not the least have flying capabilities. Even with so much potential, we rarely see the utilization of robotic systems in disaster response scenarios and rescue missions. Many factors could be responsible for the low utilization of robotic systems in such scenarios. One of the key factors involve challenges related to Human-Robot Interaction (HRI) issues. Therefore, in this paper, we try to understand the HRI challenges involving the utilization of robotic systems in disaster response and rescue operations. Furthermore, we go through some of the proposed robotic systems designed for disaster response scenarios and identify the HRI challenges of those systems. Finally, we try to address the challenges by introducing ideas from various proposed research works.
    Keywords Computer Science - Robotics ; Computer Science - Human-Computer Interaction
    Subject code 629
    Publishing date 2024-01-28
    Publishing country us
    Document type Book ; Online
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  6. Article ; Online: [Structure motif guided mining of MHET hydrolase and development of a two-enzyme cascade for plastics depolymerization at mild temperature].

    Liu, Xinyue / Geng, Wenchao / Sun, Jinyuan / Chen, Zehua / Cui, Yinglu / Wu, Bian

    Sheng wu gong cheng xue bao = Chinese journal of biotechnology

    2024  Volume 40, Issue 3, Page(s) 773–785

    Abstract: The utilization of polyethylene terephthalate (PET) has caused significant and prolonged ecological repercussions. Enzymatic degradation is an environmentally friendly approach to addressing PET contamination. Hydrolysis of mono(2-hydroxyethyl) ... ...

    Abstract The utilization of polyethylene terephthalate (PET) has caused significant and prolonged ecological repercussions. Enzymatic degradation is an environmentally friendly approach to addressing PET contamination. Hydrolysis of mono(2-hydroxyethyl) terephthalate (MHET), a competitively inhibited intermediate in PET degradation, is catalyzed by MHET degrading enzymes. Herein, we employed bioinformatic methods that combined with sequence and structural information to discover an MHET hydrolase,
    MeSH term(s) Hydrolases/metabolism ; Plastics ; Temperature ; Hydrolysis ; Polyethylene Terephthalates/metabolism
    Chemical Substances Hydrolases (EC 3.-) ; Plastics ; Polyethylene Terephthalates
    Language Chinese
    Publishing date 2024-03-28
    Publishing country China
    Document type English Abstract ; Journal Article
    ZDB-ID 1042206-7
    ISSN 1872-2075 ; 1042-749X
    ISSN (online) 1872-2075
    ISSN 1042-749X
    DOI 10.13345/j.cjb.230358
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    Zs.A 3505: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Extraction, Identification, and In Vitro Anti-Inflammatory Activity of Feruloylated Oligosaccharides from Baijiu Distillers' Grains.

    Yin, Zhongtian / Liu, Mengyao / Wang, Bowen / Zhao, Dongrui / Li, Hehe / Sun, Jinyuan

    Foods (Basel, Switzerland)

    2024  Volume 13, Issue 8

    Abstract: The structure and function of phenoyl oligosaccharides in baijiu distillers' grains (BDGs) have not been identified and investigated yet. This study aimed to elucidate the major phenolic oligosaccharides present in BDGs, optimize their extraction process ...

    Abstract The structure and function of phenoyl oligosaccharides in baijiu distillers' grains (BDGs) have not been identified and investigated yet. This study aimed to elucidate the major phenolic oligosaccharides present in BDGs, optimize their extraction process via a central composite design, and assess their anti-inflammatory properties utilizing the LPS-induced RAW264.7 inflammation model. The main results are as follows: feruloylated oligosaccharides (FOs) were identified as the main phenoyl oligosaccharides in BDGs with a structure of ferulic acid esterified on arabinooligosaccharide xylose. Then, the preparation process of FOs was optimized using the following conditions: pH 5, temperature 55 °C, time 12 h, xylanase addition amount 7 g/L, BDG concentration 120 g/L. Furthermore, the acquired FOs demonstrated notable scavenging activity against DPPH and ABTS free radicals, with Trolox equivalent values of 366.8 ± 10.38 and 0.35 ± 0.01 mM Trolox/mg sample, respectively. However, their efficacy was comparatively lower than that of ferulic acid. Finally, the obtained FOs could effectively inhibit the LPS-induced secretion of TNF-α, IL-6, and IL-1β and promote the secretion of IL-10 in RAW264.7 cells. Based on the above results, FOs from BDGs were determined to have certain antioxidant and anti-inflammatory activities.
    Language English
    Publishing date 2024-04-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods13081283
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  8. Article: Dynamic changes of volatile and phenolic components during the whole manufacturing process of Wuyi Rock tea (Rougui)

    Liu, Zhibin / Chen, Fuchen / Sun, Jinyuan / Ni, Li

    Food chemistry. 2022 Jan. 15, v. 367

    2022  

    Abstract: Wuyi Rock tea (WRT), a top-ranking oolong tea, possesses characteristic woody, floral, nutty flavor. WRT flavor is mainly formed during the manufacturing process. However, details regarding its formation process are not fully understood yet. In this ... ...

    Abstract Wuyi Rock tea (WRT), a top-ranking oolong tea, possesses characteristic woody, floral, nutty flavor. WRT flavor is mainly formed during the manufacturing process. However, details regarding its formation process are not fully understood yet. In this study, the dynamics of volatile and phenolic components over the whole manufacturing process of WRT were investigated. During withering, despite minor changes in volatile and phenolic components, the central vacuole shrunk remarkably, which reduced the cell mechanical performance and facilitated the subsequent enzymatic fermentation. During fermentation, approximately 78% of flavan-3-ols in fresh tea leaves were oxidized and converted to a diverse mixture of highly heterogeneous oxidation products, such as theaflavins, whereas flavonols, phenolic acids, and xanthine alkaloids remained stable throughout the manufacturing process. Aldehydes, ketones, and heterocyclic compounds, imparting woody, floral, and nutty scent, were mainly formed during the roasting steps. This detailed information can expand our understanding on the formation of WRT flavor.
    Keywords fermentation ; flavanols ; flavonols ; flavor ; food chemistry ; odors ; oolong tea ; oxidation ; theaflavins ; vacuoles ; xanthine
    Language English
    Dates of publication 2022-0115
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 243123-3
    ISSN 1873-7072 ; 0308-8146
    ISSN (online) 1873-7072
    ISSN 0308-8146
    DOI 10.1016/j.foodchem.2021.130624
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    In stock of ZB MED Bonn / Germany

    Z 3634: Show issues

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  9. Book ; Online: Smart Driver Monitoring Robotic System to Enhance Road Safety

    Riya, Farhin Farhad / Hoque, Shahinul / Zhao, Xiaopeng / Sun, Jinyuan Stella

    A Comprehensive Review

    2024  

    Abstract: The future of transportation is being shaped by technology, and one revolutionary step in improving road safety is the incorporation of robotic systems into driver monitoring infrastructure. This literature review explores the current landscape of driver ...

    Abstract The future of transportation is being shaped by technology, and one revolutionary step in improving road safety is the incorporation of robotic systems into driver monitoring infrastructure. This literature review explores the current landscape of driver monitoring systems, ranging from traditional physiological parameter monitoring to advanced technologies such as facial recognition to steering analysis. Exploring the challenges faced by existing systems, the review then investigates the integration of robots as intelligent entities within this framework. These robotic systems, equipped with artificial intelligence and sophisticated sensors, not only monitor but actively engage with the driver, addressing cognitive and emotional states in real-time. The synthesis of existing research reveals a dynamic interplay between human and machine, offering promising avenues for innovation in adaptive, personalized, and ethically responsible human-robot interactions for driver monitoring. This review establishes a groundwork for comprehending the intricacies and potential avenues within this dynamic field. It encourages further investigation and advancement at the intersection of human-robot interaction and automotive safety, introducing a novel direction. This involves various sections detailing technological enhancements that can be integrated to propose an innovative and improved driver monitoring system.
    Keywords Computer Science - Robotics
    Subject code 629
    Publishing date 2024-01-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Deep Learning model integrity checking mechanism using watermarking technique

    Hoque, Shahinul / Riya, Farhin Farhad / Sun, Jinyuan

    2023  

    Abstract: In response to the growing popularity of Machine Learning (ML) techniques to solve problems in various industries, various malicious groups have started to target such techniques in their attack plan. However, as ML models are constantly updated with ... ...

    Abstract In response to the growing popularity of Machine Learning (ML) techniques to solve problems in various industries, various malicious groups have started to target such techniques in their attack plan. However, as ML models are constantly updated with continuous data, it is very hard to monitor the integrity of ML models. One probable solution would be to use hashing techniques. Regardless of how that would mean re-hashing the model each time the model is trained on newer data which is computationally expensive and not a feasible solution for ML models that are trained on continuous data. Therefore, in this paper, we propose a model integrity-checking mechanism that uses model watermarking techniques to monitor the integrity of ML models. We then demonstrate that our proposed technique can monitor the integrity of ML models even when the model is further trained on newer data with a low computational cost. Furthermore, the integrity checking mechanism can be used on Deep Learning models that work on complex data distributions such as Cyber-Physical System applications.
    Keywords Computer Science - Cryptography and Security
    Subject code 006
    Publishing date 2023-01-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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