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Yang Y, Jones HB, Dao TP, Castañeda CA. Single Amino Acid Substitutions in Stickers, but Not Spacers, Substantially Alter UBQLN2 Phase Transitions and Dense Phase Material Properties. J Phys Chem B 2019; 123:3618-3629. [PMID: 30925840 DOI: 10.1021/acs.jpcb.9b01024] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
UBQLN2 450-624 oligomerizes and undergoes temperature-responsive liquid-liquid phase transitions following a closed-loop temperature-concentration phase diagram. We recently showed that disease-linked mutations to UBQLN2 450-624 impart highly varying effects to its phase behavior, ranging from little change to significant decrease of saturation concentration and formation of gels and aggregates. However, how single mutations lead to these properties is unknown. Here, we use UBQLN2 450-624 as a model system to study the sequence determinants of phase separation. We hypothesized that UBQLN2 450-624 regions previously identified to promote its oligomerization are the "stickers" that drive interchain interactions and phase separation. We systematically investigated how phase behavior is affected by all 19 possible single amino acid substitutions at three sticker and two "spacer" (sequences separating stickers) positions. Overall, substitutions to stickers, but not spacers, substantially altered the shape of the phase diagram. Within the sticker regions, increasing hydrophobicity decreased saturation concentrations at low temperatures and enhanced oligomerization propensity and viscoelasticity of the dense phase. Conversely, substitutions to acidic residues at all positions greatly increased saturation concentrations. Our data demonstrate that single amino acid substitutions follow a molecular code to tune phase transition behavior of biopolymers.
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Quintanilla-Sierra L, García-Arévalo C, Rodriguez-Cabello J. Self-assembly in elastin-like recombinamers: a mechanism to mimic natural complexity. Mater Today Bio 2019; 2:100007. [PMID: 32159144 PMCID: PMC7061623 DOI: 10.1016/j.mtbio.2019.100007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022] Open
Abstract
The topic of self-assembled structures based on elastin-like recombinamers (ELRs, i.e., elastin-like polymers recombinantly bio-produced) has released a noticeable amount of references in the last few years. Most of them are intended for biomedical applications. In this review, a complete revision of the bibliography is carried out. Initially, the self-assembly (SA) concept is considered from a general point of view, and then ELRs are described and characterized based on their intrinsic disorder. A classification of the different self-assembled ELR-based structures is proposed based on their morphologies, paying special attention to their tentative modeling. The impact of the mechanism of SA on these biomaterials is analyzed. Finally, the implications of ELR SA in biological systems are considered.
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Affiliation(s)
| | | | - J.C. Rodriguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, University of Valladolid, 47011, Valladolid, Spain
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Klass SH, Smith MJ, Fiala TA, Lee JP, Omole AO, Han BG, Downing KH, Kumar S, Francis MB. Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain. J Am Chem Soc 2019; 141:4291-4299. [DOI: 10.1021/jacs.8b10688] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sarah H. Klass
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew J. Smith
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tahoe A. Fiala
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jess P. Lee
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Anthony O. Omole
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | | | | | - Sanjay Kumar
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Garcia Garcia C, Kiick KL. Methods for producing microstructured hydrogels for targeted applications in biology. Acta Biomater 2019; 84:34-48. [PMID: 30465923 PMCID: PMC6326863 DOI: 10.1016/j.actbio.2018.11.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 12/29/2022]
Abstract
Hydrogels have been broadly studied for applications in clinically motivated fields such as tissue regeneration, drug delivery, and wound healing, as well as in a wide variety of consumer and industry uses. While the control of mechanical properties and network structures are important in all of these applications, for regenerative medicine applications in particular, matching the chemical, topographical and mechanical properties for the target use/tissue is critical. There have been multiple alternatives developed for fabricating materials with microstructures with goals of controlling the spatial location, phenotypic evolution, and signaling of cells. The commonly employed polymers such as poly(ethylene glycol) (PEG), polypeptides, and polysaccharides (as well as others) can be processed by various methods in order to control material heterogeneity and microscale structures. We review here the more commonly used polymers, chemistries, and methods for generating microstructures in biomaterials, highlighting the range of possible morphologies that can be produced, and the limitations of each method. With a focus in liquid-liquid phase separation, methods and chemistries well suited for stabilizing the interface and arresting the phase separation are covered. As the microstructures can affect cell behavior, examples of such effects are reviewed as well. STATEMENT OF SIGNIFICANCE: Heterogeneous hydrogels with enhanced matrix complexity have been studied for a variety of biomimetic materials. A range of materials based on poly(ethylene glycol), polypeptides, proteins, and/or polysaccharides, have been employed in the studies of materials that by virtue of their microstructure, can control the behaviors of cells. Methods including microfluidics, photolithography, gelation in the presence of porogens, and liquid-liquid phase separation, are presented as possible strategies for producing materials, and their relative advantages and disadvantages are discussed. We also describe in more detail the various processes involved in LLPS, and how they can be manipulated to alter the kinetics of phase separation and to yield different microstructured materials.
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Affiliation(s)
- Cristobal Garcia Garcia
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA; Biomedical Engineering, University of Delaware, Newark, DE 19176, USA; Delaware Biotechnology Institute, Newark, DE 19716, USA
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Das S, Amin AN, Lin YH, Chan HS. Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters. Phys Chem Chem Phys 2018; 20:28558-28574. [PMID: 30397688 DOI: 10.1039/c8cp05095c] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biomolecular condensates undergirded by phase separations of proteins and nucleic acids serve crucial biological functions. To gain physical insights into their genetic basis, we study how liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) depends on their sequence charge patterns using a continuum Langevin chain model wherein each amino acid residue is represented by a single bead. Charge patterns are characterized by the "blockiness" measure κ and the "sequence charge decoration" (SCD) parameter. Consistent with random phase approximation (RPA) theory and lattice simulations, LLPS propensity as characterized by critical temperature Tcr* increases with increasingly negative SCD for a set of sequences showing a positive correlation between κ and -SCD. Relative to RPA, the simulated sequence-dependent variation in Tcr* is often-though not always-smaller, whereas the simulated critical volume fractions are higher. However, for a set of sequences exhibiting an anti-correlation between κ and -SCD, the simulated Tcr*'s are quite insensitive to either parameter. Additionally, we find that blocky sequences that allow for strong electrostatic repulsion can lead to coexistence curves with upward concavity as stipulated by RPA, but the LLPS propensity of a strictly alternating charge sequence was likely overestimated by RPA and lattice models because interchain stabilization of this sequence requires spatial alignments that are difficult to achieve in real space. These results help delineate the utility and limitations of the charge pattern parameters and of RPA, pointing to further efforts necessary for rationalizing the newly observed subtleties.
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Affiliation(s)
- Suman Das
- Department of Biochemistry, University of Toronto, Medical Sciences Building - 5th Fl., 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo. Cell Mol Life Sci 2018; 75:3907-3929. [PMID: 30066087 PMCID: PMC11105604 DOI: 10.1007/s00018-018-2894-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022]
Abstract
Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers. J Mol Biol 2018; 430:4619-4635. [DOI: 10.1016/j.jmb.2018.06.031] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022]
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