1
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Phillips M, Muthukumar M, Ghosh K. Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins. PNAS NEXUS 2024; 3:pgae367. [PMID: 39253398 PMCID: PMC11382291 DOI: 10.1093/pnasnexus/pgae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024]
Abstract
Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.
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Affiliation(s)
- Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
- Molecular and Cellular Biophysics, University of Denver, Denver, CO 80208, USA
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2
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Pal T, Wessén J, Das S, Chan HS. Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins. J Phys Chem Lett 2024; 15:8248-8256. [PMID: 39105804 DOI: 10.1021/acs.jpclett.4c01973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact of sequence-local versus sequence-nonlocal features of an IDP's charge pattern on its conformational dimensions and its phase-separation propensity, the charge "blockiness" κ and the nonlocality-weighted sequence charge decoration (SCD) parameters are compared for their correlations with isolated-chain radii of gyration (Rgs) and upper critical solution temperatures (UCSTs) of polyampholytes modeled by random phase approximation, field-theoretic simulation, and coarse-grained molecular dynamics. SCD is superior to κ in predicting Rg because SCD accounts for effects of contact order, i.e., nonlocality, on dimensions of isolated chains. In contrast, κ and SCD are comparably good, though nonideal, predictors of UCST because frequencies of interchain contacts in the multiple-chain condensed phase are less sensitive to sequence positions than frequencies of intrachain contacts of an isolated chain, as reflected by κ correlating better with condensed-phase interaction energy than SCD.
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Affiliation(s)
- Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, Gandhi Institute of Technology and Management, Visakhapatnam, Andhra Pradesh 530045, India
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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3
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An Y, Gao T, Wang T, Zhang D, Bharti B. Effects of charge asymmetry on the liquid-liquid phase separation of polyampholytes and their condensate properties. SOFT MATTER 2024; 20:6150-6159. [PMID: 39044475 DOI: 10.1039/d4sm00532e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Liquid-liquid phase separation (LLPS) is the mechanism underlying the formation of bio-molecular condensates which are important compartments regulating intra- and extra-cellular functions. Electrostatic interactions are some of the important driving forces of the LLPS behaviors of biomolecules. However, the understanding of the electrostatic interactions is still limited, especially in the mixtures of biomolecules with different charge patterns. Here, we focus on the electrostatic interactions in mixtures of charge-asymmetric and charge-symmetric polyampholytes and their roles in the phase separation behaviors. We build charge-asymmetric and charge-symmetric model proteins consisting of both glutamic acid (E, negatively charged) and lysine (K, positively charged), i.e. polyampholytes of E35K15 (charge asymmetric) and E25K25 (charge symmetric). Pure E25K25 can undergo LLPS. To investigate the effects of charge-asymmetric polyampholytes on the mixtures of E25K25/E35K15, we perform coarse-grained simulations to determine their phase separation. The charge-asymmetric polyampholyte E35K15 is resistant to the LLPS of the mixtures of E25K25/E35K15. The condensate density decreases with the molar fraction of E35K15 increasing to 0.4, and no LLPS occurs at the molar fraction of 0.5 and above. This can be attributed to the electrostatic repulsion between the negatively charged E35K15 polymers. We further investigate the effects of charge asymmetry on the conformations and properties of the condensates. The E35K15 polymers in the condensates exhibit a more collapsed state as the molar fraction of E35K15 increases. However, the conformation of E25K25 polymers changes slightly across different condensates. The surface tensions of condensates decline with the increase of the molar fraction of E35K15 polymers, while the diffusivity of polymers in the condensed phases is enhanced. This work elucidates the role of charge-asymmetric polyampholytes in determining the LLPS behaviours of binary mixtures of charge-symmetric and charge-asymmetric proteins as well as the properties of condensed phases.
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Affiliation(s)
- Yaxin An
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tong Gao
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tianyi Wang
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Donghui Zhang
- Department of Chemistry, Louisiana State University, USA
| | - Bhuvnesh Bharti
- Department of Chemical Engineering, Louisiana State University, USA.
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4
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Welles RM, Sojitra KA, Garabedian MV, Xia B, Wang W, Guan M, Regy RM, Gallagher ER, Hammer DA, Mittal J, Good MC. Determinants that enable disordered protein assembly into discrete condensed phases. Nat Chem 2024; 16:1062-1072. [PMID: 38316988 DOI: 10.1038/s41557-023-01423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024]
Abstract
Cells harbour numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein- and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids, resulting in demixing via liquid-liquid phase separation. Proteins harbouring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modelling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.
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Affiliation(s)
- Rachel M Welles
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mikael V Garabedian
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boao Xia
- Bioengineering Graduate Program, Rice University, Houston, TX, USA
| | - Wentao Wang
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Muyang Guan
- Chemical and Biomolecular Engineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Roshan M Regy
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Elizabeth R Gallagher
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel A Hammer
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
- Chemical and Biomolecular Engineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
- Chemical and Biomolecular Engineering Department, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA.
| | - Matthew C Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee PR. RNAs undergo phase transitions with lower critical solution temperatures. Nat Chem 2023; 15:1693-1704. [PMID: 37932412 PMCID: PMC10872781 DOI: 10.1038/s41557-023-01353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.
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Affiliation(s)
- Gable M Wadsworth
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong, China
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Paul Pullara
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Lien B Lai
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Priya R Banerjee
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA.
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6
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Welles RM, Sojitra KA, Garabedian MV, Xia B, Wang W, Guan M, Regy RM, Gallagher ER, Hammer DA, Mittal J, Good MC. Determinants of Disordered Protein Co-Assembly Into Discrete Condensed Phases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532134. [PMID: 36945618 PMCID: PMC10028963 DOI: 10.1101/2023.03.10.532134] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Cells harbor numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids resulting in demixing via liquid-liquid phase separation (LLPS). Proteins harboring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modeling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.
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7
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Jedlinska ZM, Riggleman RA. The effect of monomer polarizability on the stability and salt partitioning in model coacervates. SOFT MATTER 2023; 19:7000-7010. [PMID: 37668019 DOI: 10.1039/d3sm00706e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Coacervation of charged polymer chains has been a topic of major interest in both polymer and biological sciences, as it is a subset of a phenomenon called liquid-liquid phase separation (LLPS). In this process the polymer-rich phase separates from the polymer-lean supernatant while still maintaining its liquid-like properties. LLPS has been shown to play a crucial role in cellular homeostasis by driving the formation of membraneless organelles. It also has the potential to be harnessed to aid in novel therapeutical applications. Recent studies have demonstrated that there is no one simple mechanism which drives LLPS, which is instead a result of the combined effect of electrostatic, dipolar, hydrophobic, and other weak interactions. Using coarse-grained polymer simulations we investigate the relatively unexplored effects of monomer polarizability and spatially varying dielectric constant on LLPS propensity, and these factors affect the properties of the resulting condensates. In order to produce spatial variations in the dielectric constant, all our simulations include explicit solvent and counterions. We demonstrate that polarizability has only a minor effect on the bulk behaviour of the condensates but plays a major role when ion partitioning and microstructure are considered. We observe that the major contribution comes from the nature of the neutral blocks as endowing them with an induced dipole changes their character from hydrophobic to hydrophilic. We hypothesize that the results of this work can aid in guiding future studies concerned with LLPS by providing a general framework and by highlighting important factors which influence LLPS.
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Affiliation(s)
- Zuzanna M Jedlinska
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, USA
| | - Robert A Riggleman
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, USA.
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8
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Saar KL, Qian D, Good LL, Morgunov AS, Collepardo-Guevara R, Best RB, Knowles TPJ. Theoretical and Data-Driven Approaches for Biomolecular Condensates. Chem Rev 2023; 123:8988-9009. [PMID: 37171907 PMCID: PMC10375482 DOI: 10.1021/acs.chemrev.2c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 05/14/2023]
Abstract
Biomolecular condensation processes are increasingly recognized as a fundamental mechanism that living cells use to organize biomolecules in time and space. These processes can lead to the formation of membraneless organelles that enable cells to perform distinct biochemical processes in controlled local environments, thereby supplying them with an additional degree of spatial control relative to that achieved by membrane-bound organelles. This fundamental importance of biomolecular condensation has motivated a quest to discover and understand the molecular mechanisms and determinants that drive and control this process. Within this molecular viewpoint, computational methods can provide a unique angle to studying biomolecular condensation processes by contributing the resolution and scale that are challenging to reach with experimental techniques alone. In this Review, we focus on three types of dry-lab approaches: theoretical methods, physics-driven simulations and data-driven machine learning methods. We review recent progress in using these tools for probing biomolecular condensation across all three fields and outline the key advantages and limitations of each of the approaches. We further discuss some of the key outstanding challenges that we foresee the community addressing next in order to develop a more complete picture of the molecular driving forces behind biomolecular condensation processes and their biological roles in health and disease.
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Affiliation(s)
- Kadi L. Saar
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Transition
Bio Ltd., Cambridge, United Kingdom
| | - Daoyuan Qian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Lydia L. Good
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Alexey S. Morgunov
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
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9
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Jonas F, Carmi M, Krupkin B, Steinberger J, Brodsky S, Jana T, Barkai N. The molecular grammar of protein disorder guiding genome-binding locations. Nucleic Acids Res 2023; 51:4831-4844. [PMID: 36938874 PMCID: PMC10250222 DOI: 10.1093/nar/gkad184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023] Open
Abstract
Intrinsically disordered regions (IDRs) direct transcription factors (TFs) towards selected genomic occurrences of their binding motif, as exemplified by budding yeast's Msn2. However, the sequence basis of IDR-directed TF binding selectivity remains unknown. To reveal this sequence grammar, we analyze the genomic localizations of >100 designed IDR mutants, each carrying up to 122 mutations within this 567-AA region. Our data points at multivalent interactions, carried by hydrophobic-mostly aliphatic-residues dispersed within a disordered environment and independent of linear sequence motifs, as the key determinants of Msn2 genomic localization. The implications of our results for the mechanistic basis of IDR-based TF binding preferences are discussed.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beniamin Krupkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Steinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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10
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Hagan MF, Mohajerani F. Self-assembly coupled to liquid-liquid phase separation. PLoS Comput Biol 2023; 19:e1010652. [PMID: 37186597 PMCID: PMC10212142 DOI: 10.1371/journal.pcbi.1010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/25/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Affiliation(s)
- Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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11
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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12
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Zhang M, Xue B, Li Q, Shi R, Cao Y, Wang W, Li J. Sequence Tendency for the Interaction between Low-Complexity Intrinsically Disordered Proteins. JACS AU 2023; 3:93-104. [PMID: 36711093 PMCID: PMC9875249 DOI: 10.1021/jacsau.2c00414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Reversible interaction between intrinsically disordered proteins (IDPs) is considered as the driving force for liquid-liquid phase separation (LLPS), while the detailed description of such a transient interaction process still remains a challenge. And the mechanisms underlying the behavior of IDP interaction, for example, the possible relationship with its inherent conformational fluctuations and sequence features, remain elusive. Here, we use atomistic molecular dynamics (MD) simulation to investigate the reversible association of the LAF-1 RGG domain, the IDP with ultra-low LLPS concentration (0.06 mM). We find that the duration of the association between two RGG domains is highly heterogeneous, and the sustained associations essentially dominate the IDP interaction. More interestingly, such sustained associations are mediated by a finite region, that is, the C-terminal region 138-168 (denoted as a contact-prone region). We noticed that such sequence tendency is attributed to the extended conformation of the RGG domain during its inherent conformational fluctuations. Hence, our results suggest that there is a certain region in this low-complexity IDP which can essentially dominate their interaction and should be also important to the LLPS. And the inherent conformational fluctuations are actually essential for the emergence of such a hot region of IDP interaction. The importance of this hot region to LLPS is verified by experiment.
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Affiliation(s)
- Moxin Zhang
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
| | - Bin Xue
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Qingtai Li
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Rui Shi
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
| | - Yi Cao
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Wei Wang
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Jingyuan Li
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
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13
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Lin YH, Wessén J, Pal T, Das S, Chan HS. Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins. Methods Mol Biol 2023; 2563:51-94. [PMID: 36227468 DOI: 10.1007/978-1-0716-2663-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical importance. In the face of experimental discoveries, analytical formulations emerged as a powerful yet tractable tool in recent theoretical investigations of the role of LLPS in the assembly and dissociation of these condensates. The pertinent LLPS often involves, though not exclusively, intrinsically disordered proteins engaging in multivalent interactions that are governed by their amino acid sequences. For researchers interested in applying these theoretical methods, here we provide a practical guide to a set of computational techniques devised for extracting sequence-dependent LLPS properties from analytical formulations. The numerical procedures covered include those for the determination of spinodal and binodal phase boundaries from a general free energy function with examples based on the random phase approximation in polymer theory, construction of tie lines for multiple-component LLPS, and field-theoretic simulation of multiple-chain heteropolymeric systems using complex Langevin dynamics. Since a more accurate physical picture often requires comparing analytical theory against explicit-chain model predictions, a commonly utilized methodology for coarse-grained molecular dynamics simulations of sequence-specific LLPS is also briefly outlined.
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Affiliation(s)
- Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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14
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Laghmach R, Malhotra I, Potoyan DA. Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium. Methods Mol Biol 2023; 2563:117-133. [PMID: 36227470 PMCID: PMC11186142 DOI: 10.1007/978-1-0716-2663-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A vast number of intracellular membraneless bodies also known as biomolecular condensates form through a liquid-liquid phase separation (LLPS) of biomolecules. To date, phase separation has been identified as the main driving force for a membraneless organelles such as nucleoli, Cajal bodies, stress granules, and chromatin compartments. Recently, the protein-RNA condensation is receiving increased attention, because it is closely related to the biological function of cells such as transcription, translation, and RNA metabolism. Despite the multidisciplinary efforts put forth to study the biophysical properties of protein-RNA condensates, there are many fundamental unanswered questions regarding the mechanism of formation and regulation of protein-RNA condensates in eukaryotic cells. Major challenges in studying protein-RNA condensation stem from (i) the molecular heterogeneity and conformational flexibility of RNA and protein chains and (ii) the nonequilibrium nature of transcription and cellular environment. Computer simulations, bioinformatics, and mathematical models are uniquely positioned for shedding light on the microscopic nature of protein-RNA phase separation. To this end, there is an urgent need for innovative models with the right spatiotemporal resolution for confronting the experimental observables in a comprehensive and physics-based manner. In this chapter, we will summarize the currently emerging research efforts, which employ atomistic and coarse-grained molecular models and field theoretical models to understand equilibrium and nonequilibrium aspects of protein-RNA condensation.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, IA, USA
| | - Isha Malhotra
- Department of Chemistry, Iowa State University, Ames, IA, USA
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, USA.
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15
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Chen X, Chen EQ, Yang S. Multiphase Coacervation of Polyelectrolytes Driven by Asymmetry of Charged Sequence. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Er-Qiang Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
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16
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Latham AP, Zhang B. Molecular Determinants for the Layering and Coarsening of Biological Condensates. AGGREGATE (HOBOKEN, N.J.) 2022; 3:e306. [PMID: 37065433 PMCID: PMC10101022 DOI: 10.1002/agt2.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many membraneless organelles, or biological condensates, form through phase separation, and play key roles in signal sensing and transcriptional regulation. While the functional importance of these condensates has inspired many studies to characterize their stability and spatial organization, the underlying principles that dictate these emergent properties are still being uncovered. In this review, we examine recent work on biological condensates, especially multicomponent systems. We focus on connecting molecular factors such as binding energy, valency, and stoichiometry with the interfacial tension, explaining the nontrivial interior organization in many condensates. We further discuss mechanisms that arrest condensate coalescence by lowering the surface tension or introducing kinetic barriers to stabilize the multidroplet state.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
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17
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Wessén J, Das S, Pal T, Chan HS. Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Protein-Like Heteropolymers with Short- and Long-Spatial-Range Interactions. J Phys Chem B 2022; 126:9222-9245. [PMID: 36343363 DOI: 10.1021/acs.jpcb.2c06181] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A theory for sequence-dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic simulation (FTS) of heteropolymers with spatially long-range Coulomb interactions to include the fundamental effects of short-range, hydrophobic-like interactions between amino acid residues. To this end, short-range effects are modeled by Yukawa interactions between multiple nonelectrostatic charges derived from an eigenvalue decomposition of pairwise residue-residue contact energies. Chain excluded volume is afforded by incompressibility constraints. A mean-field approximation leads to an effective Flory-Huggins χ parameter, which, in conjunction with RPA, accounts for the contact-interaction effects of amino acid composition and the sequence-pattern effects of long-range electrostatics in IDP LLPS, whereas FTS based on the formulation provides full sequence dependence for both short- and long-range interactions. This general approach is illustrated here by applications to variants of a natural IDP in the context of several different amino-acid interaction schemes as well as a set of different model hydrophobic-polar sequences sharing the same composition. Effectiveness of the methodology is verified by coarse-grained explicit-chain molecular dynamics simulations.
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Affiliation(s)
- Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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18
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Qian D, Michaels TCT, Knowles TPJ. Analytical Solution to the Flory-Huggins Model. J Phys Chem Lett 2022; 13:7853-7860. [PMID: 35977086 PMCID: PMC9421911 DOI: 10.1021/acs.jpclett.2c01986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
Abstract
A self-consistent analytical solution for binodal concentrations of the two-component Flory-Huggins phase separation model is derived. We show that this form extends the validity of the Ginzburg-Landau expansion away from the critical point to cover the whole phase space. Furthermore, this analytical solution reveals an exponential scaling law of the dilute phase binodal concentration as a function of the interaction strength and chain length. We demonstrate explicitly the power of this approach by fitting experimental protein liquid-liquid phase separation boundaries to determine the effective chain length and solute-solvent interaction energies. Moreover, we demonstrate that this strategy allows us to resolve differences in interaction energy contributions of individual amino acids. This analytical framework can serve as a new way to decode the protein sequence grammar for liquid-liquid phase separation.
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Affiliation(s)
- Daoyuan Qian
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
| | - Thomas C. T. Michaels
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
- Department
of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, U.K.
- Laboratory
for Molecular Cell Biology, University College
London, London, WC1E 6BT, U.K.
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J J Thomson
Avenue, Cambridge, CB3
0HE, U.K.
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19
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Arora L, Mukhopadhyay S. Conformational Characteristics and Phase Behavior of Intrinsically Disordered Proteins─Where Physical Chemistry Meets Biology. J Phys Chem B 2022; 126:5137-5139. [PMID: 35860904 DOI: 10.1021/acs.jpcb.2c04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
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20
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Ghosh K, Huihui J, Phillips M, Haider A. Rules of Physical Mathematics Govern Intrinsically Disordered Proteins. Annu Rev Biophys 2022; 51:355-376. [PMID: 35119946 PMCID: PMC9190209 DOI: 10.1146/annurev-biophys-120221-095357] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In stark contrast to foldable proteins with a unique folded state, intrinsically disordered proteins and regions (IDPs) persist in perpetually disordered ensembles. Yet an IDP ensemble has conformational features-even when averaged-that are specific to its sequence. In fact, subtle changes in an IDP sequence can modulate its conformational features and its function. Recent advances in theoretical physics reveal a set of elegant mathematical expressions that describe the intricate relationships among IDP sequences, their ensemble conformations, and the regulation of their biological functions. These equations also describe the molecular properties of IDP sequences that predict similarities and dissimilarities in their functions and facilitate classification of sequences by function, an unmet challenge to traditional bioinformatics. These physical sequence-patterning metrics offer a promising new avenue for advancing synthetic biology at a time when multiple novel functional modes mediated by IDPs are emerging.
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Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA,Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, USA
| | - Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA
| | - Austin Haider
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, USA
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21
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Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS. Sci Rep 2022; 12:7101. [PMID: 35501371 PMCID: PMC9061845 DOI: 10.1038/s41598-022-11177-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Liquid droplets of a host protein, formed by liquid–liquid phase separation, recruit guest proteins and provide functional fields. Recruitment into p53 droplets is similar between disordered and folded guest proteins, whereas the diffusion of guest proteins inside droplets depends on their structural types. In this study, to elucidate how the recruitment and diffusion properties of guest proteins are affected by a host protein, we characterized the properties of guest proteins in fused in sarcoma (FUS) droplets using single-molecule fluorescence microscopy in comparison with p53 droplets. Unlike p53 droplets, disordered guest proteins were recruited into FUS droplets more efficiently than folded guest proteins, suggesting physical exclusion of the folded proteins from the small voids of the droplet. The recruitment did not appear to depend on the physical parameters (electrostatic or cation–π) of guests, implying that molecular size exclusion limits intermolecular interaction-assisted uptake. The diffusion of disordered guest proteins was comparable to that of the host FUS, whereas that of folded proteins varied widely, similar to the results for host p53. The scaling exponent of diffusion highlights the molecular sieving of large folded proteins in droplets. Finally, we proposed a molecular recruitment and diffusion model for guest proteins in FUS droplets.
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22
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Lin YH, Wu H, Jia B, Zhang M, Chan HS. Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding. Biophys J 2022; 121:157-171. [PMID: 34637756 PMCID: PMC8758407 DOI: 10.1016/j.bpj.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023] Open
Abstract
The assembly of functional biomolecular condensates often involves liquid-liquid phase separation (LLPS) of proteins with multiple modular domains, which can be folded or conformationally disordered to various degrees. To understand the LLPS-driving domain-domain interactions, a fundamental question is how readily the interactions in the condensed phase can be inferred from interdomain interactions in dilute solutions. In particular, are the interactions leading to LLPS exclusively those underlying the formation of discrete interdomain complexes in homogeneous solutions? We address this question by developing a mean-field LLPS theory of two stoichiometrically constrained solute species. The theory is applied to the neuronal proteins SynGAP and PSD-95, whose complex coacervate serves as a rudimentary model for neuronal postsynaptic densities (PSDs). The predicted phase behaviors are compared with experiments. Previously, a three SynGAP/two PSD-95 ratio was determined for SynGAP/PSD-95 complexes in dilute solutions. However, when this 3:2 stoichiometry is uniformly imposed in our theory encompassing both dilute and condensed phases, the tie-line pattern of the predicted SynGAP/PSD-95 phase diagram differs drastically from that obtained experimentally. In contrast, theories embodying alternate scenarios postulating auxiliary SynGAP-PSD-95 as well as SynGAP-SynGAP and PSD-95-PSD-95 interactions, in addition to those responsible for stoichiometric SynGAP/PSD-95 complexes, produce tie-line patterns consistent with experiment. Hence, our combined theoretical-experimental analysis indicates that weaker interactions or higher-order complexes beyond the 3:2 stoichiometry, but not yet documented, are involved in the formation of SynGAP/PSD-95 condensates, imploring future efforts to ascertain the nature of these auxiliary interactions in PSD-like LLPS and underscoring a likely general synergy between stoichiometric, structurally specific binding and stochastic, multivalent "fuzzy" interactions in the assembly of functional biomolecular condensates.
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Affiliation(s)
- Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada,Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Haowei Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Bowen Jia
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China,School of Life Sciences, Southern University of Science and Technology, Shenzhen, China,Corresponding author
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada,Corresponding author
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23
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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24
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Abstract
Flexibility in complexes between intrinsically disordered proteins and folded ligands is widespread in nature. However, timescales and spatial amplitudes of such dynamics remained unexplored for most systems. Our results show that the disordered cytoplasmic tail of the cell adhesion protein E-cadherin diffuses across the entire surface of its folded binding partner β-catenin at fast submillisecond timescales. The nanometer amplitude of these motions could allow kinases to access their recognition motifs without requiring a dissociation of the complex. We expect that the rugged energy landscape found in the E-cadherin/β-catenin complex is a defining feature of dynamic and partially disordered protein complexes. Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 kBT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.
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25
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Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. J Mol Biol 2021; 433:167196. [PMID: 34390736 DOI: 10.1016/j.jmb.2021.167196] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as having no persistent tertiary structure; instead they interconvert between a large number of different and often expanded structures. IDPs and IDRs are involved in an enormously wide range of biological functions and reveal novel mechanisms of interactions, and while they defy the common structure-function paradigm of folded proteins, their structural preferences and dynamics are important for their function. We here discuss open questions in the field of IDPs and IDRs, focusing on areas where machine learning and other computational methods play a role. We discuss computational methods aimed to predict transiently formed local and long-range structure, including methods for integrative structural biology. We discuss the many different ways in which IDPs and IDRs can bind to other molecules, both via short linear motifs, as well as in the formation of larger dynamic complexes such as biomolecular condensates. We discuss how experiments are providing insight into such complexes and may enable more accurate predictions. Finally, we discuss the role of IDPs in disease and how new methods are needed to interpret the mechanistic effects of genomic variants in IDPs.
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Affiliation(s)
- Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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26
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Song J, Li J, Chan HS. Small-Angle X-ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles. J Phys Chem B 2021; 125:6451-6478. [PMID: 34115515 DOI: 10.1021/acs.jpcb.1c02453] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An accurate account of disordered protein conformations is of central importance to deciphering the physicochemical basis of biological functions of intrinsically disordered proteins and the folding-unfolding energetics of globular proteins. Physically, disordered ensembles of nonhomopolymeric polypeptides are expected to be heterogeneous, i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average values of end-to-end distance REE and radius of gyration Rg. It was posited recently, however, that small-angle X-ray scattering (SAXS) data on conformational dimensions of disordered proteins can be rationalized almost exclusively by homopolymer ensembles. Assessing this perspective, chain-model simulations are used to evaluate the discriminatory power of SAXS-determined molecular form factors (MFFs) with regard to homogeneous versus heterogeneous ensembles. The general approach adopted here is not bound by any assumption about ensemble encodability, in that the postulated heterogeneous ensembles we evaluated are not restricted to those entailed by simple interaction schemes. Our analysis of MFFs for certain heterogeneous ensembles with more narrowly distributed REE and Rg indicates that while they deviate from MFFs of homogeneous ensembles, the differences can be rather small. Remarkably, some heterogeneous ensembles with asphericity and REE drastically different from those of homogeneous ensembles can nonetheless exhibit practically identical MFFs, demonstrating that SAXS MFFs do not afford unique characterizations of basic properties of conformational ensembles in general. In other words, the ensemble to MFF mapping is practically many-to-one and likely nonsmooth. Heteropolymeric variations of the REE-Rg relationship were further showcased using an analytical perturbation theory developed here for flexible heteropolymers. Ramifications of our findings for interpretation of experimental data are discussed.
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Affiliation(s)
- Jianhui Song
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Jichen Li
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto Faculty of Medicine, Toronto, Ontario M5S 1A8, Canada
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27
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Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. Biophys J 2021; 120:1565-1577. [PMID: 33617830 PMCID: PMC8204217 DOI: 10.1016/j.bpj.2021.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/10/2023] Open
Abstract
In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.
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Affiliation(s)
- Luke K Davis
- Department of Physics and Astronomy; Institute for the Physics of Living Systems; London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy; Institute for the Physics of Living Systems
| | - Bart W Hoogenboom
- Department of Physics and Astronomy; Institute for the Physics of Living Systems; London Centre for Nanotechnology, University College London, London, United Kingdom.
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute for Biomedical Engineering, Toronto, Ontario, Canada.
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28
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Wessén J, Pal T, Das S, Lin YH, Chan HS. A Simple Explicit-Solvent Model of Polyampholyte Phase Behaviors and Its Ramifications for Dielectric Effects in Biomolecular Condensates. J Phys Chem B 2021; 125:4337-4358. [PMID: 33890467 DOI: 10.1021/acs.jpcb.1c00954] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates such as membraneless organelles, underpinned by liquid-liquid phase separation (LLPS), are important for physiological function, with electrostatics, among other interaction types, being a prominent force in their assembly. Charge interactions of intrinsically disordered proteins (IDPs) and other biomolecules are sensitive to the aqueous dielectric environment. Because the relative permittivity of protein is significantly lower than that of water, the interior of an IDP condensate is expected to be a relatively low-dielectric regime, which aside from its possible functional effects on client molecules should facilitate stronger electrostatic interactions among the scaffold IDPs. To gain insight into this LLPS-induced dielectric heterogeneity, addressing in particular whether a low-dielectric condensed phase entails more favorable LLPS than that posited by assuming IDP electrostatic interactions are uniformly modulated by the higher dielectric constant of the pure solvent, we consider a simplified multiple-chain model of polyampholytes immersed in explicit solvents that are either polarizable or possess a permanent dipole. Notably, simulated phase behaviors of these systems exhibit only minor to moderate differences from those obtained using implicit-solvent models with a uniform relative permittivity equals to that of pure solvent. Buttressed by theoretical treatments developed here using random phase approximation and polymer field-theoretic simulations, these observations indicate a partial compensation of effects between favorable solvent-mediated interactions among the polyampholytes in the condensed phase and favorable polyampholyte-solvent interactions in the dilute phase, often netting only a minor enhancement of overall LLPS propensity from the very dielectric heterogeneity that arises from the LLPS itself. Further ramifications of this principle are discussed.
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Affiliation(s)
- Jonas Wessén
- Department of Biochemistry, University of Toronto, Medical Sciences Building-5th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Tanmoy Pal
- Department of Biochemistry, University of Toronto, Medical Sciences Building-5th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Medical Sciences Building-5th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Medical Sciences Building-5th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Medical Sciences Building-5th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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29
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Huihui J, Ghosh K. Intrachain interaction topology can identify functionally similar intrinsically disordered proteins. Biophys J 2021; 120:1860-1868. [PMID: 33865811 DOI: 10.1016/j.bpj.2020.11.2282] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 01/06/2023] Open
Abstract
Functionally similar IDPs (intrinsically disordered proteins) often have little sequence similarity. This is in stark contrast to folded proteins and poses a challenge for the inverse problem, functional classification of IDPs using sequence alignment. The problem is further compounded because of the lack of structure in IDPs, preventing structural alignment as an alternate tool for classification. Recent advances in heteropolymer theory unveiled a powerful set of sequence-patterning metrics bridging molecular interaction with chain conformation. Focusing only on charge patterning, these set of metrics yield a sequence charge decoration matrix (SCDM). SCDMs can potentially identify functionally similar IDPs not apparent from sequence alignment alone. Here, we illustrate how these information-rich "molecular blueprints" encoded in SCDMs can be used for functional classification of IDPs with specific application in three protein families-Ste50, PSC, and RAM-in which electrostatics is known to be important. For both the Ste50 and PSC protein family, the set of metrics appropriately classifies proteins in functional and nonfunctional groups in agreement with experiment. Furthermore, our algorithm groups synthetic variants of the disordered RAM region of the Notch receptor protein-important in gene expression-in reasonable accordance with classification based on experimentally measured binding constants of RAM and transcription factor. Taken together, the novel classification scheme reveals the critical role of a high-dimensional set of metrics-manifest in self-interaction maps and topology-in functional annotation of IDPs even when there is low sequence homology, providing the much-needed alternate to a traditional sequence alignment tool.
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Affiliation(s)
- Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado.
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Shea JE, Best RB, Mittal J. Physics-based computational and theoretical approaches to intrinsically disordered proteins. Curr Opin Struct Biol 2021; 67:219-225. [PMID: 33545530 PMCID: PMC8150118 DOI: 10.1016/j.sbi.2020.12.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of proteins that do not fold to a well-defined three-dimensional shape but rather adopt an ensemble of inter-converting conformations. This feature makes their experimental characterization challenging and invites a theoretical and computational approach to complement experimental studies. In this review, we highlight the recent progress in developing new computational and theoretical approaches to study the structure and dynamics of monomeric and order higher assemblies of IDPs, with a particular emphasis on their phase separation into protein-rich condensates.
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Affiliation(s)
- Joan-Emma Shea
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Physics, University of California, Santa Barbara, CA 93106, United States.
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, United States.
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31
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Pal T, Wessén J, Das S, Chan HS. Subcompartmentalization of polyampholyte species in organelle-like condensates is promoted by charge-pattern mismatch and strong excluded-volume interaction. Phys Rev E 2021; 103:042406. [PMID: 34005864 DOI: 10.1103/physreve.103.042406] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Polyampholyte field theory and explicit-chain molecular dynamics models of sequence-specific phase separation of a system with two intrinsically disordered protein (IDP) species indicate consistently that a substantial polymer excluded volume and a significant mismatch of the IDP sequence charge patterns can act in concert, but not in isolation, to demix the two IDP species upon condensation. This finding reveals an energetic-geometric interplay in a stochastic, "fuzzy" molecular recognition mechanism that may facilitate subcompartmentalization of membraneless organelles.
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Affiliation(s)
- Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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32
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Rumyantsev AM, Jackson NE, Johner A, de Pablo JJ. Scaling Theory of Neutral Sequence-Specific Polyampholytes. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02515] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Artem M. Rumyantsev
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas E. Jackson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Albert Johner
- Institut Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 Rue du Loess, Strasbourg, 67034 Cedex 2, France
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
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33
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Hazra MK, Levy Y. Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions. J Phys Chem B 2021; 125:2202-2211. [PMID: 33629837 PMCID: PMC8028311 DOI: 10.1021/acs.jpcb.0c09975] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Intrinsically disordered proteins
play a crucial role in cellular
phase separation, yet the diverse molecular forces driving phase separation
are not fully understood. It is of utmost importance to understand
how peptide sequence, and particularly the balance between the peptides’
short- and long-range interactions with other peptides, may affect
the stability, structure, and dynamics of liquid–liquid phase
separation in protein condensates. Here, using coarse-grained molecular
dynamics simulations, we studied the liquid properties of the condensate
in a series of polymers in which the ratio of short-range dispersion
interactions to long-range electrostatic interactions varied. As the
fraction of mutations that participate in short-range interactions
increases at the expense of long-range electrostatic interactions,
a significant decrease in the critical temperature of phase separation
is observed. Nevertheless, sequences with a high fraction of short-range
interactions exhibit stabilization, which suggests compensation for
the loss of long-range electrostatic interactions. Decreased condensate
stability is coupled with decreased translational diffusion of the
polymers in the condensate, which may result in the loss of liquid
characteristics in the presence of a high fraction of uncharged residues.
The effect of exchanging long-range electrostatic interactions for
short-range interactions can be explained by the kinetics of breaking
intermolecular contacts with neighboring polymers and the kinetics
of intramolecular fluctuations. While both time scales are coupled
and increase as electrostatic interactions are lost, for sequences
that are dominated by short-range interactions, the kinetics of intermolecular
contact breakage significantly slows down. Our study supports the
contention that different types of interactions can maintain protein
condensates, however, long-range electrostatic interactions enhance
its liquid-like behavior.
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Affiliation(s)
- Milan Kumar Hazra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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34
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Perdikari TM, Jovic N, Dignon GL, Kim YC, Fawzi NL, Mittal J. A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophys J 2021; 120:1187-1197. [PMID: 33582133 DOI: 10.1016/j.bpj.2021.01.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Biomolecules undergo liquid-liquid phase separation (LLPS), resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post-translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed-charge atomistic force fields, we parameterize the size and atomistic hydropathy of the coarse-grained-modified amino acid beads and, hence, the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein's single-chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of Fused in Sarcoma (FUS) and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.
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Affiliation(s)
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Young C Kim
- Center for Materials Physics and Technology, U.S. Naval Research Laboratory, Washington D.C
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology; Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island.
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania.
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35
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Das S, Lin YH, Vernon RM, Forman-Kay JD, Chan HS. Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins. Proc Natl Acad Sci U S A 2020; 117:28795-28805. [PMID: 33139563 PMCID: PMC7682375 DOI: 10.1073/pnas.2008122117] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS) of proteins, we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4, as a test case, to assess roles of electrostatic, hydrophobic, cation-π, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated three different residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-aromatic cation-π interactions consistently accounted for available experimental LLPS data on the wild-type, a charge-scrambled, a phenylalanine-to-alanine (FtoA), and an arginine-to-lysine (RtoK) mutant of Ddx4 IDR. In contrast, interactions based on contact statistics among folded globular protein structures reproduce the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. Consistency between simulation and experiment was also found for RtoK mutants of P-granule protein LAF-1, underscoring that, to a degree, important LLPS-driving π-related interactions are embodied in classical statistical potentials. Further elucidation is necessary, however, especially of phenylalanine's role in condensate assembly because experiments on FtoA and tyrosine-to-phenylalanine mutants suggest that LLPS-driving phenylalanine interactions are significantly weaker than posited by common statistical potentials. Protein-protein electrostatic interactions are modulated by relative permittivity, which in general depends on aqueous protein concentration. Analytical theory suggests that this dependence entails enhanced interprotein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to only a modest overall impact on LLPS.
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Affiliation(s)
- Suman Das
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Robert M Vernon
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julie D Forman-Kay
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada;
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36
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Hazra MK, Levy Y. Charge pattern affects the structure and dynamics of polyampholyte condensates. Phys Chem Chem Phys 2020; 22:19368-19375. [PMID: 32822449 DOI: 10.1039/d0cp02764b] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins with intrinsically disordered regions have a tendency to condensate via liquid-liquid phase separation both in vitro and in vivo. Such biomolecular coacervates play various significant roles in biologically important regulatory processes. The present work explores the structural and dynamic features of coacervates formed by model polyampholytes, being intrinsically disordered proteins, that differ in terms of their charged amino acid patterns. Differences in the distribution of charged amino acids along the polyampholyte sequence lead to distinctly different structural features in the dense phase and hence to different liquid properties. Increased charge clustering raises the critical temperature for phase separation and results in each polyampholyte experiencing a larger number of inter-chain contacts with neighboring proteins in the condensate. Consequently, polyampholytes with greater charge clustering adopt a much more extended conformation, having a radius of gyration up to twice that observed in the dilute bulk phase. Translational diffusion within the droplet is pronounced, being just 4-20 times slower than in the bulk, consistently with the high conformational entropy in the dense phase and high exchange rate of the network of intermolecular interactions in the condensate. Coupled to the faster diffusion, the condensate also adopts a more elongated shape and exhibits imperfect packing, which results in cavities. This study quantifies the fundamental microscopic properties of condensates including the effect of long-range electrostatic forces and particularly how they can be modulated by the charge pattern.
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Affiliation(s)
- Milan Kumar Hazra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
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