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LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro

2019 Nucleic Acids Research  
Liquid-liquid phase separation (LLPS) leads to a conversion of homogeneous solution into a dense phase that often resembles liquid droplets, and a dilute phase.  ...  Here, we introduce LLPSDB (http://bio-comp.ucas.ac.cn/llpsdb or http://bio-comp.org.cn/llpsdb), a web-accessible database providing comprehensive, carefully curated collection of proteins involved in LLPS  ...  We also thank the authors of some retrieved publications for their kind replying to our request about LLPS data. This work was supported by University of Chinese Academy of Sciences.  ... 
doi:10.1093/nar/gkz778 pmid:31906602 pmcid:PMC6943074 fatcat:6ofo2yyzjbgv3alqnuoffydpaq

Protein Databases Related to Liquid-Liquid Phase Separation

Qian Li, Xi Wang, Zhihui Dou, Weishan Yang, Beifang Huang, Jizhong Lou, Zhuqing Zhang
2020 International Journal of Molecular Sciences  
These resources are invaluable for a deeper understanding of the cellular function of biomolecular phase separation, as well as the development of phase-separating protein prediction and design.  ...  Liquid-liquid phase separation (LLPS) of biomolecules, which underlies the formation of membraneless organelles (MLOs) or biomolecular condensates, has been investigated intensively in recent years.  ...  PhaSePro PhaSePro (https://phasepro.elte.hu) is a novel database in which proteins verified to drive phase separation in vivo and/or in vitro are manually curated [45] .  ... 
doi:10.3390/ijms21186796 pmid:32947964 pmcid:PMC7555049 fatcat:q7kewqa5eba7vg3u5m5scpolxq

Integration of Data from Liquid–Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers

Nazanin Farahi, Tamas Lazar, Shoshana J. Wodak, Peter Tompa, Rita Pancsa
2021 International Journal of Molecular Sciences  
Liquidliquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized liquid-like cellular condensates formed by proteins  ...  Analysis of the supporting evidence for our dataset uncovered a systematic and potentially concerning difference between protein concentrations used in a good fraction of the in vitro LLPS experiments,  ...  act as drivers/scaffolds in liquid-liquid phase separation processes.  ... 
doi:10.3390/ijms22063017 pmid:33809541 pmcid:PMC8002189 fatcat:si4i5k5fe5fhzpngdgmwbau6be

Concentration and dosage sensitivity of proteins driving liquid-liquid phase separation [article]

Nazanin Farahi, Tamas Lazar, Shoshana J. Wodak, Peter Tompa, Rita Pancsa
2021 bioRxiv   pre-print
AbstractLiquid-liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles (MLOs), i.e. functionally specialized liquid-like cellular condensates formed  ...  The validity of in vitro LLPS experiments is further supported by in vivo phase-separation experiments and by the observation that the corresponding genes show a strong propensity for dosage sensitivity  ...  act as drivers/scaffolds in liquid-liquid phase separation processes.  ... 
doi:10.1101/2021.02.19.430946 fatcat:k3s7vwmrrjfjfmycvtjh2wi3la

Prediction of liquid–liquid phase separating proteins using machine learning

Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei
2022 BMC Bioinformatics  
Background The liquidliquid 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  ...  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.  ...  QL and ZQZ participated the construction of positive datasets. YJX built the online webserver. JFP, ZQZ and LHL conceived the project. TLS, XQC, JFP, ZQZ and LHL wrote the draft.  ... 
doi:10.1186/s12859-022-04599-w pmid:35168563 pmcid:PMC8845408 fatcat:4xlffvddrvbpvcu5i7wjs5m6ra

Widespread occurrence of the droplet state of proteins in the human proteome

Maarten Hardenberg, Attila Horvath, Viktor Ambrus, Monika Fuxreiter, Michele Vendruscolo
2020 Proceedings of the National Academy of Sciences of the United States of America  
These observations prompt the question of how many proteins can undergo liquid-liquid phase separation.  ...  A wide range of proteins have been reported to condensate into a dense liquid phase, forming a reversible droplet state.  ...  The third dataset is LLPSDB (http://bio-comp.org.cn/llpsdb) (31) , which assembles proteins observed to undergo in vitro liquid-liquid phase separation with well-defined experimental conditions and phase  ... 
doi:10.1073/pnas.2007670117 pmid:33318217 fatcat:hnml6yueurfwjmz4dbylxnnpqy

Prediction of liquid-liquid phase separation proteins using machine learning [article]

Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei
2019 bioRxiv   pre-print
The liquid-liquid phase separation (LLPS) of bio-molecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles  ...  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.  ...  Each entry in the database contained the information of whether the protein (alone or with DNA/RNA or with other proteins) phase separated under a specific experimental condition in vitro.  ... 
doi:10.1101/842336 fatcat:nkhbcec7b5gltfh3e6gm47pbpy

RNAPhaSep: a resource of RNAs undergoing phase separation

Haibo Zhu, Hao Fu, Tianyu Cui, Lin Ning, Huaguo Shao, Yehan Guo, Yanting Ke, Jiayi Zheng, Hongyan Lin, Xin Wu, Guanghao Liu, Jun He (+7 others)
2021 Nucleic Acids Research  
To better utilize the knowledge dispersed in published literature, we here introduce RNAPhaSep (http://www.rnaphasep.cn), a manually curated database of RNAs undergoing LLPS.  ...  Liquid-liquid phase separation (LLPS) partitions cellular contents, underlies the formation of membraneless organelles and plays essential biological roles.  ...  Five databases focused on proteins undergoing LLPS have been created, including LLPSDB, PhaSePro, PhaSepDB, DrLLPS and RNAGranuleDB (29) (30) (31) (32) (33) .  ... 
doi:10.1093/nar/gkab985 pmid:34718740 pmcid:PMC8728120 fatcat:oyrk5g6xujd2nopskkwpvmkhg4

Computational resources for identifying and describing proteins driving liquid–liquid phase separation

Rita Pancsa, Wim Vranken, Bálint Mészáros
2021 Briefings in Bioinformatics  
One of the most intriguing fields emerging in current molecular biology is the study of membraneless organelles formed via liquidliquid phase separation (LLPS).  ...  Through hands-on application of these resources on example proteins and representative datasets, we give a practical guide to show how they can be used in conjunction to provide in silico information on  ...  Data Availability The data underlying this article are available in the article and in its online supplementary material. Funding  ... 
doi:10.1093/bib/bbaa408 pmid:33517364 pmcid:PMC8425267 fatcat:ne6fikf7anfirdd637ktb7oyxu

Sequence determinants of the aggregation of proteins within condensates generated by liquid-liquid phase separation

Michele Vendruscolo, Monika Fuxreiter
2021 Journal of Molecular Biology  
through liquid-liquid phase separation.  ...  The transition between the native and amyloid states of proteins can proceed via a deposition pathway via oligomeric intermediates or via a condensation pathway involving liquid droplet intermediates generated  ...  in vitro liquid-liquid phase separation.  ... 
doi:10.1016/j.jmb.2021.167201 pmid:34391803 fatcat:t25zj6u32zffnb2gmm32h3zmje

Widespread occurrence of the droplet state of proteins in the human proteome [article]

Marteen Hardenberg, Attila Horvath, Viktor Ambrus, MONIKA FUXREITER, Michele Vendruscolo
2020 bioRxiv   pre-print
These observations prompt the question of how many proteins can undergo liquid-liquid phase separation.  ...  A wide range of proteins have been reported to condensate into a dense liquid phase, forming a reversible droplet state.  ...  Acknowledgement M.F. acknowledges the financial support of HAS-11015.  ... 
doi:10.1101/2020.10.21.348532 fatcat:tai2rl3tfnbmvkcga5cklcew2u

Sequence determinants for the aggregation and cytotoxicity of proteins within condensates generated by liquid-liquid phase separation [article]

Michele Vendruscolo, MONIKA FUXREITER
2020 bioRxiv   pre-print
generated through liquid-liquid phase separation.  ...  The transition between the native and amyloid states of proteins can proceed via a deposition pathway through oligomeric intermediates or via a condensation pathway through liquid droplet intermediates  ...  vitro liquid-liquid phase separation.  ... 
doi:10.1101/2020.12.07.414409 fatcat:gxwow4zrhndl5dgs6oycoqodri

BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid–Liquid Phase Separation

Aleksandra E. Badaczewska-Dawid, Vladimir N. Uversky, Davit A. Potoyan
2022 International Journal of Molecular Sciences  
The liquidliquid phase separation (LLPS) of biomolecules is a phenomenon which is nowadays recognized as the driving force for the biogenesis of numerous functional membraneless organelles and cellular  ...  To uncover the sequence-encoded signals of protein capable of undergoing LLPS, we developed a novel web platform named BIAPSS (Bioinformatics Analysis of LLPS Sequences).  ...  Conclusions In conclusion, many proteins undergo liquid-liquid phase separation (LLPS), which drives the biogenesis of various membraneless organelles.  ... 
doi:10.3390/ijms23116204 pmid:35682883 pmcid:PMC9181037 fatcat:fvyvh4givzflznmizolbbkmeni

Machine learning models for predicting protein condensate formation from sequence determinants and embeddings [article]

Kadi L Saar, Alexey S Morgunov, Runzhang Qi, William E Arter, Georg Krainer, Alpha Albert Lee, Tuomas Knowles
2020 bioRxiv   pre-print
information to construct machine learning classifiers for predicting liquid-liquid phase separation (LLPS) from protein sequence.  ...  Moreover, in combination with a classifier that had developed a nuanced insight into the features governing protein phase behaviour by learning to distinguish between sequences of varying LLPS propensity  ...  been observed to undergo phase separation experimentally either in vitro or in vivo.  ... 
doi:10.1101/2020.10.26.354753 fatcat:rxytcohddrbypdwarenrnfhek4

Learning the molecular grammar of protein condensates from sequence determinants and embeddings

Kadi L. Saar, Alexey S. Morgunov, Runzhang Qi, William E. Arter, Georg Krainer, Alpha A. Lee, Tuomas P. J. Knowles
2021 Proceedings of the National Academy of Sciences of the United States of America  
machine-learning models for predicting protein liquidliquid phase separation (LLPS).  ...  Intracellular phase separation of proteins into biomolecular condensates is increasingly recognized as a process with a key role in cellular compartmentalization and regulation.  ...  been observed to undergo phase separation experimentally either in vitro or in vivo.  ... 
doi:10.1073/pnas.2019053118 pmid:33827920 pmcid:PMC8053968 fatcat:kwkc5kl7erfppfxc6tb2yfulj4
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