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Serebryany E, Martin RW, Takahashi GR. The Functional Significance of High Cysteine Content in Eye Lens γ-Crystallins. Biomolecules 2024; 14:594. [PMID: 38786000 PMCID: PMC11118217 DOI: 10.3390/biom14050594] [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: 03/28/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Cataract disease is strongly associated with progressively accumulating oxidative damage to the extremely long-lived crystallin proteins of the lens. Cysteine oxidation affects crystallin folding, interactions, and light-scattering aggregation especially strongly due to the formation of disulfide bridges. Minimizing crystallin aggregation is crucial for lifelong lens transparency, so one might expect the ubiquitous lens crystallin superfamilies (α and βγ) to contain little cysteine. Yet, the Cys content of γ-crystallins is well above the average for human proteins. We review literature relevant to this longstanding puzzle and take advantage of expanding genomic databases and improved machine learning tools for protein structure prediction to investigate it further. We observe remarkably low Cys conservation in the βγ-crystallin superfamily; however, in γ-crystallin, the spatial positioning of Cys residues is clearly fine-tuned by evolution. We propose that the requirements of long-term lens transparency and high lens optical power impose competing evolutionary pressures on lens βγ-crystallins, leading to distinct adaptations: high Cys content in γ-crystallins but low in βB-crystallins. Aquatic species need more powerful lenses than terrestrial ones, which explains the high methionine content of many fish γ- (and even β-) crystallins. Finally, we discuss synergies between sulfur-containing and aromatic residues in crystallins and suggest future experimental directions.
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Affiliation(s)
- Eugene Serebryany
- Department of Physiology & Biophysics, Stony Brook University, SUNY, Stony Brook, NY 11794, USA
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, SUNY, Stony Brook, NY 11794, USA
| | - Rachel W. Martin
- Department of Chemistry, UCI Irvine, Irvine, CA 92697-2025, USA
- Department of Molecular Biology & Biochemistry, UCI Irvine, Irvine, CA 92697-3900, USA
| | - Gemma R. Takahashi
- Department of Molecular Biology & Biochemistry, UCI Irvine, Irvine, CA 92697-3900, USA
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2
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Kim J, Qin S, Zhou HX, Rosen MK. Surface Charge Can Modulate Phase Separation of Multidomain Proteins. J Am Chem Soc 2024; 146:3383-3395. [PMID: 38262618 PMCID: PMC10859935 DOI: 10.1021/jacs.3c12789] [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: 11/14/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.
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Affiliation(s)
- Jonggul Kim
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| | - Sanbo Qin
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Huan-Xiang Zhou
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Department
of Physics, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Michael K. Rosen
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
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3
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Qin S, Zhou HX. Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence. Commun Biol 2023; 6:886. [PMID: 37644195 PMCID: PMC10465548 DOI: 10.1038/s42003-023-05270-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature (Tc). We obtain a higher Tc for a known high-Tc γ-crystallin, γF, than for a low-Tc paralog, γB. The difference in Tc is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in Tc. This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
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Affiliation(s)
- Sanbo Qin
- 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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4
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Qin S, Zhou HX. Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538329. [PMID: 37162827 PMCID: PMC10168431 DOI: 10.1101/2023.04.25.538329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature ( T c ). We obtain a higher T c for a known high- T c γ-crystallin, γF, than for a low- T c paralog, γB. The difference in T c is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in T c . This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
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Affiliation(s)
- Sanbo Qin
- 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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5
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Lebold KM, Best RB. Tuning Formation of Protein-DNA Coacervates by Sequence and Environment. J Phys Chem B 2022; 126:2407-2419. [PMID: 35317553 DOI: 10.1021/acs.jpcb.2c00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high concentration of nucleic acids and positively charged proteins in the cell nucleus provides many possibilities for complex coacervation. We consider a prototypical mixture of nucleic acids together with the polycationic C-terminus of histone H1 (CH1). Using a minimal coarse-grained model that captures the shape, flexibility, and charge distributions of the molecules, we find that coacervates are readily formed at physiological ionic strengths, in agreement with experiment, with a progressive increase in local ordering at low ionic strength. Variation of the positions of charged residues in the protein tunes phase separation: for well-mixed or only moderately blocky distributions of charge, there is a modest increase of local ordering with increasing blockiness that is also associated with an increased propensity to phase separate. This ordering is also associated with a slowdown of rotational and translational diffusion in the dense phase. However, for more extreme blockiness (and consequently higher local charge density), we see a qualitative change in the condensed phase to become a segregated structure with a dramatically increased ordering of the DNA. Naturally occurring proteins with these sequence properties, such as protamines in sperm cells, are found to be associated with very dense packing of nucleic acids.
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Affiliation(s)
- Kathryn M Lebold
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Robert B Best
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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Vorontsova I, Vallmitjana A, Torrado B, Schilling TF, Hall JE, Gratton E, Malacrida L. In vivo macromolecular crowding is differentially modulated by aquaporin 0 in zebrafish lens: Insights from a nanoenvironment sensor and spectral imaging. SCIENCE ADVANCES 2022; 8:eabj4833. [PMID: 35171678 PMCID: PMC8849302 DOI: 10.1126/sciadv.abj4833] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 05/14/2023]
Abstract
Macromolecular crowding is crucial for cellular homeostasis. In vivo studies of macromolecular crowding and water dynamics are needed to understand their roles in cellular physiology and fate determination. Macromolecular crowding in the lens is essential for normal optics, and an understanding of its regulation will help prevent cataract and presbyopia. Here, we combine the use of the nanoenvironmental sensor [6-acetyl-2-dimethylaminonaphthalene (ACDAN)] to visualize lens macromolecular crowding with in vivo studies of aquaporin 0 zebrafish mutants that disrupt its regulation. Spectral phasor analysis of ACDAN fluorescence reveals water dipolar relaxation and demonstrates that mutations in two zebrafish aquaporin 0s, Aqp0a and Aqp0b, alter water state and macromolecular crowding in living lenses. Our results provide in vivo evidence that Aqp0a promotes fluid influx in the deeper lens cortex, whereas Aqp0b facilitates fluid efflux. This evidence reveals previously unidentified spatial regulation of macromolecular crowding and spatially distinct roles for Aqp0 in the lens.
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Affiliation(s)
- Irene Vorontsova
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | | | - Belén Torrado
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Thomas F. Schilling
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - James E. Hall
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay
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7
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Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem 2021; 22:1329-1346. [PMID: 33569867 PMCID: PMC8052307 DOI: 10.1002/cbic.202000739] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/17/2020] [Indexed: 11/10/2022]
Abstract
βγ-Crystallins are the primary structural and refractive proteins found in the vertebrate eye lens. Because crystallins are not replaced after early eye development, their solubility and stability must be maintained for a lifetime, which is even more remarkable given the high protein concentration in the lens. Aggregation of crystallins caused by mutations or post-translational modifications can reduce crystallin protein stability and alter intermolecular interactions. Common post-translational modifications that can cause age-related cataracts include deamidation, oxidation, and tryptophan derivatization. Metal ion binding can also trigger reduced crystallin solubility through a variety of mechanisms. Interprotein interactions are critical to maintaining lens transparency: crystallins can undergo domain swapping, disulfide bonding, and liquid-liquid phase separation, all of which can cause opacity depending on the context. Important experimental techniques for assessing crystallin conformation in the absence of a high-resolution structure include dye-binding assays, circular dichroism, fluorescence, light scattering, and transition metal FRET.
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Affiliation(s)
- Megan A. Rocha
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
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Garcia Garcia C, Patkar SS, Jovic N, Mittal J, Kiick KL. Alteration of Microstructure in Biopolymeric Hydrogels via Compositional Modification of Resilin-Like Polypeptides. ACS Biomater Sci Eng 2021; 7:4244-4257. [DOI: 10.1021/acsbiomaterials.0c01543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Cristobal Garcia Garcia
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Sai S. Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Delaware Biotechnology Institute, Newark, Delaware 19716, United States
- Biomedical Engineering, University of Delaware, Newark, Delaware 19176, United States
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9
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Rizvi A, Patel U, Ianiro A, Hurst PJ, Merham JG, Patterson JP. Nonionic Block Copolymer Coacervates. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00979] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Urja Patel
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Alessandro Ianiro
- Adolphe Merkle Institute, University of Fribourg, Fribourg 1700, Switzerland
| | - Paul J. Hurst
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Jovany G. Merham
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P. Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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10
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Driving Forces of Liquid-Liquid Phase Separation in Biological Systems. Biomolecules 2019; 9:biom9090473. [PMID: 31510097 PMCID: PMC6770153 DOI: 10.3390/biom9090473] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/02/2019] [Indexed: 12/03/2022] Open
Abstract
Analysis of liquid–liquid phase separation in biological systems shows that this process is similar to the phase separation observed in aqueous two-phase systems formed by nonionic polymers, proteins, and polysaccharides. The emergence of interfacial tension is a necessary condition of phase separation. The situation in this regard is similar to that of phase separation in mixtures of partially miscible solvents. It is suggested that the evaluation of the effects of biological macromolecules on the solvent properties of aqueous media and the measurement of the interfacial tension as a function of these solvent properties may be more productive for gaining insights into the mechanism of liquid–liquid phase separation than the study of structural details of proteins and RNAs engaged in the process.
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11
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Cinar S, Cinar H, Chan HS, Winter R. Pressure-Sensitive and Osmolyte-Modulated Liquid–Liquid Phase Separation of Eye-Lens γ-Crystallins. J Am Chem Soc 2019; 141:7347-7354. [DOI: 10.1021/jacs.8b13636] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Süleyman Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hasan Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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