Theory and Simulation of Multiphase Coexistence in Biomolecular Mixtures

被引:18
作者
Jacobs, William M. [1 ]
机构
[1] Princeton Univ, Dept Chem, Princeton, NJ 08544 USA
基金
美国国家科学基金会;
关键词
INTRINSICALLY DISORDERED PROTEINS; LIQUID-PHASE-SEPARATION; THERMOREVERSIBLE GELATION; SYSTEMS; MODEL; ASSOCIATION; TRANSITIONS; STABILITY; ALGORITHM; NETWORKS;
D O I
10.1021/acs.jctc.3c00198
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Biomolecular condensates constitute a newly recognizedform ofspatial organization in living cells. Although many condensates arebelieved to form as a result of phase separation, the physicochemicalproperties that determine the phase behavior of heterogeneous biomolecularmixtures are only beginning to be explored. Theory and simulationprovide invaluable tools for probing the relationship between moleculardeterminants, such as protein and RNA sequences, and the emergenceof phase-separated condensates in such complex environments. Thisreview covers recent advances in the prediction and computationaldesign of biomolecular mixtures that phase-separate into many coexistingphases. First, we review efforts to understand the phase behaviorof mixtures with hundreds or thousands of species using theoreticalmodels and statistical approaches. We then describe progress in developinganalytical theories and coarse-grained simulation models to predictmultiphase condensates with the molecular detail required to makecontact with biophysical experiments. We conclude by summarizing thechallenges ahead for modeling the inhomogeneous spatial organizationof biomolecular mixtures in living cells.
引用
收藏
页码:3429 / 3445
页数:17
相关论文
共 150 条
[1]   Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry [J].
Abyzov, Anton ;
Blackledge, Martin ;
Zweckstetter, Markus .
CHEMICAL REVIEWS, 2022, 122 (06) :6719-6748
[2]   Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing [J].
Alberti, Simon ;
Hyman, Anthony A. .
NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2021, 22 (03) :196-213
[3]  
Alshareedah I., 2022, bioRxiv, DOI 10.1101/2022.12.30.522262
[4]  
Alshareedah I., 2023, BIORXIV
[5]  
[Anonymous], 2004, Convex Optimization
[6]  
[Anonymous], 2009, Phase Transformations in Metals and Alloys, VThird, DOI 10.12019781439883570
[7]   Biomolecular condensates: organizers of cellular biochemistry [J].
Banani, Salman F. ;
Lee, Hyun O. ;
Hyman, Anthony A. ;
Rosen, Michael K. .
NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2017, 18 (05) :285-298
[8]   The Quickhull algorithm for convex hulls [J].
Barber, CB ;
Dobkin, DP ;
Huhdanpaa, H .
ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE, 1996, 22 (04) :469-483
[9]   Biomolecular condensates formed by designer minimalistic peptides [J].
Baruch Leshem, Avigail ;
Sloan-Dennison, Sian ;
Massarano, Tlalit ;
Ben-David, Shavit ;
Graham, Duncan ;
Faulds, Karen ;
Gottlieb, Hugo E. ;
Chill, Jordan H. ;
Lampel, Ayala .
NATURE COMMUNICATIONS, 2023, 14 (01)
[10]   Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model [J].
Benayad, Zakarya ;
von Buelow, Soren ;
Stelzl, Lukas S. ;
Hummer, Gerhard .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2021, 17 (01) :525-537