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Zhang Y, Prasad R, Su S, Lee D, Zhou HX. Amino Acid-Dependent Material Properties of Tetrapeptide Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594233. [PMID: 38798623 PMCID: PMC11118382 DOI: 10.1101/2024.05.14.594233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Condensates formed by intrinsically disordered proteins mediate a myriad of cellular processes and are linked to pathological conditions including neurodegeneration. Rules of how different types of amino acids (e.g., π-π pairs) dictate the physical properties of biomolecular condensates are emerging, but our understanding of the roles of different amino acids is far from complete. Here we studied condensates formed by tetrapeptides of the form XXssXX, where X is an amino acid and ss represents a disulfide bond along the backbone. Eight peptides form four types of condensates at different concentrations and pH values: droplets (X = F, L, M, P, V, A); amorphous dense liquids (X = L, M, P, V, A); amorphous aggregates (X = W), and gels (X = I, V, A). The peptides exhibit enormous differences in phase equilibrium and material properties, including a 368-fold range in the threshold concentration for phase separation and a 3856-fold range in viscosity. All-atom molecular dynamics simulations provide physical explanations of these results. The present work also reveals widespread critical behaviors, including critical slowing down manifested by the formation of amorphous dense liquids and critical scaling obeyed by fusion speed, with broad implications for condensate function.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Siyuan Su
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Daesung Lee
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago IL 60607, USA
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Sundaravadivelu Devarajan D, Wang J, Szała-Mendyk B, Rekhi S, Nikoubashman A, Kim YC, Mittal J. Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations. Nat Commun 2024; 15:1912. [PMID: 38429263 PMCID: PMC10907393 DOI: 10.1038/s41467-024-46223-w] [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] [Received: 05/17/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Material properties of phase-separated biomolecular condensates, enriched with disordered proteins, dictate many cellular functions. Contrary to the progress made in understanding the sequence-dependent phase separation of proteins, little is known about the sequence determinants of condensate material properties. Using the hydropathy scale and Martini models, we computationally decipher these relationships for charge-rich disordered protein condensates. Our computations yield dynamical, rheological, and interfacial properties of condensates that are quantitatively comparable with experimentally characterized condensates. Interestingly, we find that the material properties of model and natural proteins respond similarly to charge segregation, despite different sequence compositions. Molecular interactions within the condensates closely resemble those within the single-chain ensembles. Consequently, the material properties strongly correlate with molecular contact dynamics and single-chain structural properties. We demonstrate the potential to harness the sequence characteristics of disordered proteins for predicting and engineering the material properties of functional condensates, with insights from the dilute phase properties.
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Affiliation(s)
| | - Jiahui Wang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Beata Szała-Mendyk
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Shiv Rekhi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069, Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC, 20375, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, 77843, USA.
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Alshareedah I, Singh A, Yang S, Ramachandran V, Quinn A, Potoyan DA, Banerjee PR. Determinants of viscoelasticity and flow activation energy in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadi6539. [PMID: 38363841 PMCID: PMC10871536 DOI: 10.1126/sciadv.adi6539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
The form and function of biomolecular condensates are intimately linked to their material properties. Here, we integrate microrheology with molecular simulations to dissect the physical determinants of condensate fluid phase dynamics. By quantifying the timescales and energetics of network relaxation in a series of heterotypic viscoelastic condensates, we uncover distinctive roles of sticker motifs, binding energy, and chain length in dictating condensate dynamical properties. We find that the mechanical relaxation times of condensate-spanning networks are determined by both intermolecular interactions and chain length. We demonstrate, however, that the energy barrier for network reconfiguration, termed flow activation energy, is independent of chain length and only varies with the strengths of intermolecular interactions. Biomolecular diffusion in the dense phase depends on a complex interplay between viscoelasticity and flow activation energy. Our results illuminate distinctive roles of chain length and sequence-specific multivalent interactions underlying the complex material and transport properties of biomolecular condensates.
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Affiliation(s)
| | - Anurag Singh
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
| | - Sean Yang
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Alexander Quinn
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
| | - Davit A. Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Priya R. Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
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Kota D, Prasad R, Zhou HX. Adenosine Triphosphate Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks. J Am Chem Soc 2024; 146:1326-1336. [PMID: 38174879 PMCID: PMC10843746 DOI: 10.1021/jacs.3c09134] [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] [Indexed: 01/05/2024]
Abstract
Adenosine triphosphate (ATP) is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients up to 7700) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (∼25 pN/μm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (∼1 μm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.
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Affiliation(s)
- Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago IL 60607, USA
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Kota D, Prasad R, Zhou HX. ATP Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554035. [PMID: 37645809 PMCID: PMC10462115 DOI: 10.1101/2023.08.20.554035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
ATP is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients at 200-5000) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (~25 pN/μm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (~1 μm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.
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Affiliation(s)
- Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago IL 60607, USA
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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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Mazarakos K, Qin S, Zhou HX. Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections. Methods Mol Biol 2023; 2563:1-35. [PMID: 36227466 PMCID: PMC9577455 DOI: 10.1007/978-1-0716-2663-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We illustrate three methods for calculating the binodals of phase-separated condensates from molecular simulations. Because molecular simulations can only be carried out for small system sizes, correction for finite sizes may be required for making direct comparison between calculated results and experimental data. We first summarize the three methods and then present detailed implementation of each method on a Lennard-Jones fluid. In the first method, chemical potentials are calculated over a range of particle densities in canonical-ensemble simulations; the densities of the dilute and dense phases at the given temperature are then found by a Maxwell equal-area construction. In Gibbs-ensemble Monte Carlo, the exchange between separated dilute and dense phases is simulated to obtain their densities. Lastly, slab-geometry molecular dynamics simulations model the dilute and dense phases in coexistence and yield not only their densities but also their interfacial tension. The three types of simulations are carried out for a range of system sizes, and the results are scaled to generate the binodals corrected for finite system sizes. Size-corrected interfacial tension is also produced from slab-geometry molecular dynamics simulations.
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Affiliation(s)
| | - Sanbo Qin
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Huan-Xiang Zhou
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
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