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Article ; Online: Evaluation of sequence-based predictors for phase-separating protein.

Liao, Shaofeng / Zhang, Yujun / Qi, Yifei / Zhang, Zhuqing

2023 Volume 24, Issue 4

Abstract: Liquid-liquid phase separation (LLPS) of proteins and nucleic acids underlies the formation of biomolecular condensates in cell. Dysregulation of protein LLPS is closely implicated in a range of intractable diseases. A variety of tools for predicting ... ...

Abstract	Liquid-liquid phase separation (LLPS) of proteins and nucleic acids underlies the formation of biomolecular condensates in cell. Dysregulation of protein LLPS is closely implicated in a range of intractable diseases. A variety of tools for predicting phase-separating proteins (PSPs) have been developed with the increasing experimental data accumulated and several related databases released. Comparing their performance directly can be challenging due to they were built on different algorithms and datasets. In this study, we evaluate eleven available PSPs predictors using negative testing datasets, including folded proteins, the human proteome, and non-PSPs under near physiological conditions, based on our recently updated LLPSDB v2.0 database. Our results show that the new generation predictors FuzDrop, DeePhase and PSPredictor perform better on folded proteins as a negative test set, while LLPhyScore outperforms other tools on the human proteome. However, none of the predictors could accurately identify experimentally verified non-PSPs. Furthermore, the correlation between predicted scores and experimentally measured saturation concentrations of protein A1-LCD and its mutants suggests that, these predictors could not consistently predict the protein LLPS propensity rationally. Further investigation with more diverse sequences for training, as well as considering features such as refined sequence pattern characterization that comprehensively reflects molecular physiochemical interactions, may improve the performance of PSPs prediction.
MeSH term(s)	Humans ; Proteome ; Computational Biology ; Proteins/chemistry
Chemical Substances	Proteome ; Proteins
Language	English
Publishing date	2023-05-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbad213
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Article: Entrapment of Asphaltene-Stabilized Emulsions in Microfluidic Porous Media

Lin, Yu-Jiun / Zhang, Zhuqing / Biswal, Sibani Lisa

Energy & fuels. 2022 July 20, v. 36, no. 16

2022

Abstract: Asphaltene-related flow assurance problems are prevalent in oil and gas production, with issues related to plugging of pipelines, damage to rock formations, and formation of viscous emulsions. In this study, entrapment of asphaltene-stabilized water/ ... ...

Abstract	Asphaltene-related flow assurance problems are prevalent in oil and gas production, with issues related to plugging of pipelines, damage to rock formations, and formation of viscous emulsions. In this study, entrapment of asphaltene-stabilized water/brine-in-oil emulsions in microfluidic porous media is characterized by two mechanisms: adhesion and hydrodynamic bridging. At lower water fractions, the droplets adhere to deposited asphaltenes, whereas erosion and bridging between posts are more prevalent at higher water fractions. Pressure drop measurements are used to calculate permeability reduction. With added salinity, weaker adhesion between droplets and deposited asphaltenes is observed; however, the increased droplet size leads to increased bridging. Interfacial rheology measurements are made to examine the stability of the interface. Higher salinity lowers the elasticity of the interface, resulting in larger emulsions, which exhibit more substantial erosion but increased bridging. The insights from this study can lead to better methods to demulsify and separate entrained water in produced crude oils, which can cause severe corrosion and fouling issues.
Keywords	adhesion ; asphaltenes ; corrosion ; droplet size ; energy ; hydrodynamics ; oils ; permeability ; rheology ; salinity
Language	English
Dates of publication	2022-0720
Size	p. 8760-8768.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1483539-3
ISSN	1520-5029 ; 0887-0624
ISSN (online)	1520-5029
ISSN	0887-0624
DOI	10.1021/acs.energyfuels.2c01340
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Article ; Online: Phosphorylation and specific DNA improved the incorporation ability of p53 into functional condensates.

Chen, Qunyang / Wu, Yiping / Dai, Zhuojun / Zhang, Zhuqing / Yang, Xiaorong

International journal of biological macromolecules

2023 Volume 230, Page(s) 123221

Abstract: The transcription factor p53 acted as a critical tumor suppressor by activating the expression of various target genes to regulate diverse cellular responses. The phosphorylation of p53 influenced the binding of p53 to promotor-specific DNA and the ... ...

Abstract	The transcription factor p53 acted as a critical tumor suppressor by activating the expression of various target genes to regulate diverse cellular responses. The phosphorylation of p53 influenced the binding of p53 to promotor-specific DNA and the choice of cell fate. In this study, we found that full-length wild-type p53 and pol II CTD could form heterotypic phase separation condensates in vitro. The heterotypic condensates of p53 and pol II CTD were mediated by electrostatic and hydrophobic interactions between pol II CTD and multiple domains of p53. The mobility of heterotypic p53 and pol II CTD droplets was significantly higher than that of p53 droplet. The phosphorylation promoted p53 to be recruited into pol II CTD droplets and transcription condensates. The specific DNA could further enhance the incorporation ability of p53 into functional condensates. Therefore, we proposed that the p53 droplet might be in a mediate state, the mutations resulting in p53 mutants with gain-of-function impelled the aggregate of p53, while the phosphorylation promoted p53 to be recruited into functional condensates as a client molecule to exert its function. This study might provide insights into the regulation mechanism that the phosphorylation and nuclei acid affected the phase behavior of p53.
MeSH term(s)	Humans ; Phosphorylation ; Tumor Suppressor Protein p53/metabolism ; DNA/genetics ; DNA/metabolism ; RNA Polymerase II/chemistry ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription Factors/genetics ; Transcription, Genetic
Chemical Substances	Tumor Suppressor Protein p53 ; DNA (9007-49-2) ; RNA Polymerase II (EC 2.7.7.-) ; Transcription Factors
Language	English
Publishing date	2023-01-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.123221
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Article ; Online: Phosphorylation and specific DNA improved the incorporation ability of p53 into functional condensates

Chen, Qunyang / Wu, Yiping / Dai, Zhuojun / Zhang, Zhuqing / Yang, Xiaorong

International Journal of Biological Macromolecules. 2023 Mar., v. 230 p.123221-

2023

Abstract	The transcription factor p53 acted as a critical tumor suppressor by activating the expression of various target genes to regulate diverse cellular responses. The phosphorylation of p53 influenced the binding of p53 to promotor-specific DNA and the choice of cell fate. In this study, we found that full-length wild-type p53 and pol II CTD could form heterotypic phase separation condensates in vitro. The heterotypic condensates of p53 and pol II CTD were mediated by electrostatic and hydrophobic interactions between pol II CTD and multiple domains of p53. The mobility of heterotypic p53 and pol II CTD droplets was significantly higher than that of p53 droplet. The phosphorylation promoted p53 to be recruited into pol II CTD droplets and transcription condensates. The specific DNA could further enhance the incorporation ability of p53 into functional condensates. Therefore, we proposed that the p53 droplet might be in a mediate state, the mutations resulting in p53 mutants with gain-of-function impelled the aggregate of p53, while the phosphorylation promoted p53 to be recruited into functional condensates as a client molecule to exert its function. This study might provide insights into the regulation mechanism that the phosphorylation and nuclei acid affected the phase behavior of p53.
Keywords	DNA ; droplets ; gain-of-function mutation ; hydrophobicity ; neoplasms ; phosphorylation ; separation ; transcription factors ; Phase separation ; p53 ; Pol II CTD
Language	English
Dates of publication	2023-03
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.123221
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Article ; Online: Fine-mapping and transcriptome analysis of the photosensitive leaf -yellowing gene CaLY1 in pepper (Capsicum annuum L.)

Yang, Sha / Zhang, Zhuqing / Chen, Wenchao / Liang, Chengliang / Li, Xuefeng / Liu, Zhoubin / Cui, Qingzhi / Ma, Yanqing / Zou, Xuexiao

Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS). Horticultural Plant Journal. 2023 Feb., v. 9, no. 1 p.122-132

2023

Abstract: Leaf color is directly related to altered photosynthesis. Hence, leaf yellowing mutants can be widely used for the researching plant physiology and functional genomes, for cultivating new varieties of popular horticultural plants, and for identifying ... ...

Abstract	Leaf color is directly related to altered photosynthesis. Hence, leaf yellowing mutants can be widely used for the researching plant physiology and functional genomes, for cultivating new varieties of popular horticultural plants, and for identifying hybrid purity (as markers). Here, we constructed a ⁶⁰Co-γ F₂ population from the leaf -yellowing mutant R24 via radiation mutation with the inbred line WT21 of pepper. Genetic analysis showed that the leaf-yellowing of the mutant was controlled by a single recessive gene. By applying the Bulk Segregation Analysis and Kompetitive Allele Specific PCR markers, the leaf-yellowing gene CaLY1 (Capsicum annuum Leaf yellow 1) was mapped on chromosome 9, SNP5791587-SNP6011215, with a size of 214.5 kb. One non-synonymous mutated gene Capana09g000166 was found in the interval. The gene encoded a PsbX, which is the core complex of PSII. Transcriptome analysis further showed that 2301 differentially expressed genes were identified under shading treatment for 24 h in R24. The Gene Ontology enrichment pathways were related to photosynthesis light harvesting, cell wall, activity of quercetin 3-O-glucosyltransferase and flavonoid metabolic process, which likely regulate the response of pepper leaves to different light levels. Functional enrichment analysis indicated that the most abundant pathways were photosynthesis antenna proteins and metabolic.
Keywords	Capsicum annuum ; alleles ; cell walls ; chromosomes ; color ; gene expression regulation ; gene ontology ; genetic analysis ; horticultural crops ; horticulture ; hybrids ; inbred lines ; leaves ; mutants ; mutation ; pepper ; photosensitivity ; photosystem II ; plant physiology ; quercetin ; recessive genes ; transcriptomics ; Leaf-color yellow ; Fine-mapping ; Gene ; Photosensitive
Language	English
Dates of publication	2023-02
Size	p. 122-132.
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ISSN	2468-0141
DOI	10.1016/j.hpj.2022.06.007
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Article: Facile synthesis of multifunctional carbon dots with 54.4% orange emission for label-free detection of morin and endogenous/exogenous hypochlorite

Meng, Yating / Zhang, Zhuqing / Zhao, Hongxia / Jiao, Yuan / Li, Jun / Shuang, Shaomin / Dong, Chuan

Journal of hazardous materials. 2022 Feb. 15, v. 424

2022

Abstract: Carbon dots with long-wavelength emission (orange to red), high quantum yield (QY) and good biocompatibility are of great significance for biomedical applications, but achieving this is still a highly challenging task. In this work, multifunctional ... ...

Abstract	Carbon dots with long-wavelength emission (orange to red), high quantum yield (QY) and good biocompatibility are of great significance for biomedical applications, but achieving this is still a highly challenging task. In this work, multifunctional carbon dots with 54.4% orange emission (O-CDs) were prepared through one-pot solvothermal treatment of nileblueasulphate and citric acid as precursor for label-free recognition of morin and endogenous/exogenous hypochlorite (ClO⁻) and bioimaging in cellular and zebrafish. Morin can quench the luminescence of O-CDs by static quenching (SQ). The linear range is 5–125 μM and LOD is 0.84 μM. ClO⁻ reduce the photoluminescence intensity of O-CDs via SQ. The linear range is 2.5–90 μM and LOD was 0.46 μM. In addition, The obtained O-CDs have successfully realized the monitoring of morin and endogenous/ exogenous ClO⁻ in living cells and zebrafish owing to its superior biocompatibility, exceptional photostability and lower toxicity. This work opens up a novel opportunity for the development of long-wavelength emission multifunctional nanomaterial with high quantum yield based on CDs for biosensing, biolabeling and biomedical optical imaging.
Keywords	Danio rerio ; biocompatibility ; bioimaging ; citric acid ; hypochlorites ; photoluminescence ; photostability ; toxicity
Language	English
Dates of publication	2022-0215
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2021.127289
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Article ; Online: Prediction of liquid-liquid phase separating proteins using machine learning.

Chu, Xiaoquan / Sun, Tanlin / Li, Qian / Xu, Youjun / Zhang, Zhuqing / Lai, Luhua / Pei, Jianfeng

BMC bioinformatics

2022 Volume 23, Issue 1, Page(s) 72

Abstract: Background: The liquid-liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular function. Dysregulation of ...

Abstract	Background: The liquid-liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular function. Dysregulation of LLPS is implicated in a number of diseases. Although the LLPS of biomolecules has been investigated intensively in recent years, the knowledge of the prevalence and distribution of phase separation proteins (PSPs) is still lag behind. Development of computational methods to predict PSPs is therefore of great importance for comprehensive understanding of the biological function of LLPS. Results: Based on the PSPs collected in LLPSDB, we developed a sequence-based prediction tool for LLPS proteins (PSPredictor), which is an attempt at general purpose of PSP prediction that does not depend on specific protein types. Our method combines the componential and sequential information during the protein embedding stage, and, adopts the machine learning algorithm for final predicting. The proposed method achieves a tenfold cross-validation accuracy of 94.71%, and outperforms previously reported PSPs prediction tools. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which is accessible for prediction of potential PSPs. Conclusions: PSPredictor could identifie novel scaffold proteins for stress granules and predict PSPs candidates in the human genome for further study. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which provides valuable information for potential PSPs recognition.
MeSH term(s)	Humans ; Machine Learning ; Organelles ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-022-04599-w
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Article ; Online: Physicochemical Characterization of Asphaltenes Using Microfluidic Analysis.

Pagán Pagán, Nataira M / Zhang, Zhuqing / Nguyen, Thao Vy / Marciel, Amanda B / Biswal, Sibani Lisa

Chemical reviews

2022 Volume 122, Issue 7, Page(s) 7205–7235

Abstract: Crude oils are complex mixtures of organic molecules, of which asphaltenes are the heaviest component. Asphaltene precipitation and deposition have been recognized to be a significant problem in oil production, transmission, and processing facilities. ... ...

Abstract	Crude oils are complex mixtures of organic molecules, of which asphaltenes are the heaviest component. Asphaltene precipitation and deposition have been recognized to be a significant problem in oil production, transmission, and processing facilities. These macromolecular aromatics are challenging to characterize due to their heterogeneity and complex molecular structure. Microfluidic devices are able to capture key characteristics of reservoir rocks and provide new insights into the transport, reactions, and chemical interactions governing fluids used in the oil and gas industry. Understanding the microscale phenomena has led to better design of macroscale processes used by the industry. One area that has seen significant growth is in the area of chemical analysis under flowing conditions. Microfluidics and microscale analysis have advanced the understanding of complex mixtures by providing
MeSH term(s)	Complex Mixtures ; Microfluidic Analytical Techniques ; Polycyclic Aromatic Hydrocarbons/chemistry ; Water/chemistry
Chemical Substances	Complex Mixtures ; Polycyclic Aromatic Hydrocarbons ; asphaltene ; Water (059QF0KO0R)
Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c00897
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Article: Integrative analysis of non-targeted metabolome and transcriptome reveals the mechanism of volatile formation in pepper fruit.

Liu, Yuhua / Zhou, Jiahao / Yi, Cheng / Chen, Fengqingyang / Liu, Yan / Liao, Yi / Zhang, Zhuqing / Liu, Wei / Lv, Junheng

Frontiers in genetics

2023 Volume 14, Page(s) 1290492

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2023-11-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1290492
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Article ; Online: A sequence-based model for identifying proteins undergoing liquid-liquid phase separation/forming fibril aggregates via machine learning.

Liao, Shaofeng / Zhang, Yujun / Han, Xinchen / Wang, Tinglan / Wang, Xi / Yan, Qinglin / Li, Qian / Qi, Yifei / Zhang, Zhuqing

Protein science : a publication of the Protein Society

2023 Volume 33, Issue 3, Page(s) e4927

Abstract: Liquid-liquid phase separation (LLPS) and the solid aggregate (also referred to as amyloid aggregates) formation of proteins, have gained significant attention in recent years due to their associations with various physiological and pathological ... ...

Abstract	Liquid-liquid phase separation (LLPS) and the solid aggregate (also referred to as amyloid aggregates) formation of proteins, have gained significant attention in recent years due to their associations with various physiological and pathological processes in living organisms. The systematic investigation of the differences and connections between proteins undergoing LLPS and those forming amyloid fibrils at the sequence level has not yet been explored. In this research, we aim to address this gap by comparing the two types of proteins across 36 features using collected data available currently. The statistical comparison results indicate that, 24 of the selected 36 features exhibit significant difference between the two protein groups. A LLPS-Fibrils binary classification model built on these 24 features using random forest reveals that the fraction of intrinsically disordered residues (F
MeSH term(s)	Phase Separation ; Amyloid/chemistry ; Machine Learning ; Intrinsically Disordered Proteins/chemistry
Chemical Substances	Amyloid ; Intrinsically Disordered Proteins
Language	English
Publishing date	2023-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4927
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