1
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Giraldo-Castaño MC, Littlejohn KA, Avecilla ARC, Barrera-Villamizar N, Quiroz FG. Programmability and biomedical utility of intrinsically-disordered protein polymers. Adv Drug Deliv Rev 2024; 212:115418. [PMID: 39094909 DOI: 10.1016/j.addr.2024.115418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/03/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Intrinsically disordered proteins (IDPs) exhibit molecular-level conformational dynamics that are functionally harnessed across a wide range of fascinating biological phenomena. The low sequence complexity of IDPs has led to the design and development of intrinsically-disordered protein polymers (IDPPs), a class of engineered repeat IDPs with stimuli-responsive properties. The perfect repetitive architecture of IDPPs allows for repeat-level encoding of tunable protein functionality. Designer IDPPs can be modeled on endogenous IDPs or engineered de novo as protein polymers with dual biophysical and biological functionality. Their properties can be rationally tailored to access enigmatic IDP biology and to create programmable smart biomaterials. With the goal of inspiring the bioengineering of multifunctional IDP-based materials, here we synthesize recent multidisciplinary progress in programming and exploiting the bio-functionality of IDPPs and IDPP-containing proteins. Collectively, expanding beyond the traditional sequence space of extracellular IDPs, emergent sequence-level control of IDPP functionality is fueling the bioengineering of self-assembling biomaterials, advanced drug delivery systems, tissue scaffolds, and biomolecular condensates -genetically encoded organelle-like structures. Looking forward, we emphasize open challenges and emerging opportunities, arguing that the intracellular behaviors of IDPPs represent a rich space for biomedical discovery and innovation. Combined with the intense focus on IDP biology, the growing landscape of IDPPs and their biomedical applications set the stage for the accelerated engineering of high-value biotechnologies and biomaterials.
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Affiliation(s)
- Maria Camila Giraldo-Castaño
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Kai A Littlejohn
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Alexa Regina Chua Avecilla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Natalia Barrera-Villamizar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Felipe Garcia Quiroz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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2
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Puertas-Bartolomé M, Venegas-Bustos D, Acosta S, Rodríguez-Cabello JC. Contribution of the ELRs to the development of advanced in vitro models. Front Bioeng Biotechnol 2024; 12:1363865. [PMID: 38650751 PMCID: PMC11033926 DOI: 10.3389/fbioe.2024.1363865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Developing in vitro models that accurately mimic the microenvironment of biological structures or processes holds substantial promise for gaining insights into specific biological functions. In the field of tissue engineering and regenerative medicine, in vitro models able to capture the precise structural, topographical, and functional complexity of living tissues, prove to be valuable tools for comprehending disease mechanisms, assessing drug responses, and serving as alternatives or complements to animal testing. The choice of the right biomaterial and fabrication technique for the development of these in vitro models plays an important role in their functionality. In this sense, elastin-like recombinamers (ELRs) have emerged as an important tool for the fabrication of in vitro models overcoming the challenges encountered in natural and synthetic materials due to their intrinsic properties, such as phase transition behavior, tunable biological properties, viscoelasticity, and easy processability. In this review article, we will delve into the use of ELRs for molecular models of intrinsically disordered proteins (IDPs), as well as for the development of in vitro 3D models for regenerative medicine. The easy processability of the ELRs and their rational design has allowed their use for the development of spheroids and organoids, or bioinks for 3D bioprinting. Thus, incorporating ELRs into the toolkit of biomaterials used for the fabrication of in vitro models, represents a transformative step forward in improving the accuracy, efficiency, and functionality of these models, and opening up a wide range of possibilities in combination with advanced biofabrication techniques that remains to be explored.
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Affiliation(s)
- María Puertas-Bartolomé
- Technical Proteins Nanobiotechnology, S.L. (TPNBT), Valladolid, Spain
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Desiré Venegas-Bustos
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Sergio Acosta
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
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3
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Morrison C, Chan EP, Lee T, Deming TJ. Switchable Coacervate Formation via Amino Acid Functionalization of Poly(dehydroalanine). Biomacromolecules 2024; 25:2554-2562. [PMID: 38426942 PMCID: PMC11005011 DOI: 10.1021/acs.biomac.4c00048] [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: 01/15/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Our group recently developed a family of side-chain amino acid-functionalized poly(S-alkyl-l-homocysteines), Xaa-CH (Xaa = generic amino acid), which possess the ability to form environmentally responsive coacervates in water. In an effort to further study how the molecular structure affects polypeptide coacervate formation, we prepared side-chain amino acid-functionalized poly(S-alkyl-rac-cysteines), Xaa-rac-C, via post-polymerization modification of poly(dehydroalanine), ADH. The use of the ADH platform allowed straightforward synthesis of a diverse range of side-chain amino acid-functionalized polypeptides via direct reaction of unprotected l-amino acid 2-mercaptoethylamides with ADH. Despite their differences in the main-chain structure, we found that Xaa-rac-C can form coacervates with properties similar to those seen with Xaa-CH. These results suggest that the incorporation of side-chain amino acids onto polypeptides may be a way to generally favor coacervation. The incorporation of l-methionine in Met-rac-C allowed the preparation of coacervates with improved stability against high ionic strength media. Further, the presence of additional thioether groups in Met-rac-C resulted in an increased solubility change upon oxidation allowing facile reversible redox switching of coacervate formation in aqueous media.
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Affiliation(s)
- Casey
A. Morrison
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ethan P. Chan
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Thatcher Lee
- Department
of Chemistry, Smith College, Northampton, Massachusetts 01063, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Timothy J. Deming
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
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4
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Zhou H, Zhu Y, Yang B, Huo Y, Yin Y, Jiang X, Ji W. Stimuli-responsive peptide hydrogels for biomedical applications. J Mater Chem B 2024; 12:1748-1774. [PMID: 38305498 DOI: 10.1039/d3tb02610h] [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: 02/03/2024]
Abstract
Stimuli-responsive hydrogels can respond to external stimuli with a change in the network structure and thus have potential application in drug release, intelligent sensing, and scaffold construction. Peptides possess robust supramolecular self-assembly ability, enabling spontaneous formation of nanostructures through supramolecular interactions and subsequently hydrogels. Therefore, peptide-based stimuli-responsive hydrogels have been widely explored as smart soft materials for biomedical applications in the last decade. Herein, we present a review article on design strategies and research progress of peptide hydrogels as stimuli-responsive materials in the field of biomedicine. The latest design and development of peptide hydrogels with responsive behaviors to stimuli are first presented. The following part provides a systematic overview of the functions and applications of stimuli-responsive peptide hydrogels in tissue engineering, drug delivery, wound healing, antimicrobial treatment, 3D cell culture, biosensors, etc. Finally, the remaining challenges and future prospects of stimuli-responsive peptide hydrogels are proposed. It is believed that this review will contribute to the rational design and development of stimuli-responsive peptide hydrogels toward biomedical applications.
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Affiliation(s)
- Haoran Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
| | - Yanhua Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
| | - Bingbing Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
| | - Yehong Huo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
| | - Yuanyuan Yin
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, P. R. China
| | - Xuemei Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
| | - Wei Ji
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.
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5
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [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: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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6
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [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: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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7
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Pesce F, Bremer A, Tesei G, Hopkins JB, Grace CR, Mittag T, Lindorff-Larsen K. Design of intrinsically disordered protein variants with diverse structural properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563461. [PMID: 37961110 PMCID: PMC10634714 DOI: 10.1101/2023.10.22.563461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) perform a wide range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Designing IDPs with specific structural or functional properties has, however, been difficult, in part because determining accurate conformational ensembles of IDPs generally requires a combination of computational modelling and experiments. Motivated by recent advancements in efficient physics-based models for simulations of IDPs, we have developed a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs with different levels of compaction and that vary more than 100 fold in their propensity to undergo phase separation, even while keeping a fixed amino acid composition. We experimentally tested designs of variants of the low-complexity domain of hnRNPA1 and find high accuracy in our computational predictions, both in terms of single-chain compaction and propensity to undergo phase separation. We analyze the sequence features that determine changes in compaction and propensity to phase separate and find an overall good agreement with previous findings for naturally occurring sequences. Our general, physics-based method enables the design of disordered sequences with specified conformational properties. Our algorithm thus expands the toolbox for protein design to include also the most flexible proteins and will enable the design of proteins whose functions exploit the many properties afforded by protein disorder.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giulio Tesei
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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8
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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9
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Huber MC, Schreiber A, Stühn LG, Schiller SM. Programming protein phase-separation employing a modular library of intrinsically disordered precision block copolymer-like proteins creating dynamic cytoplasmatic compartmentalization. Biomaterials 2023; 299:122165. [PMID: 37290157 DOI: 10.1016/j.biomaterials.2023.122165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023]
Abstract
The control of supramolecular complexes in living systems at the molecular level is an important goal in life-sciences. Spatiotemporal organization of molecular distribution & flow of such complexes are essential physicochemical processes in living cells and important for pharmaceutical processes. Membraneless organelles (MO) found in eukaryotic cells, formed by liquid-liquid phase-separation (LLPS) of intrinsically disordered proteins (IDPs) control and adjust intracellular organization. Artificially designed compartments based on LLPS open up a novel pathway to control chemical flux and partition in vitro and in vivo. We designed a library of chemically precisely defined block copolymer-like proteins based on elastin-like proteins (ELPs) with defined charge distribution and type, as well as polar and hydrophobic block domains. This enables the programmability of physicochemical properties and to control adjustable LLPS in vivo attaining control over intracellular partitioning and flux as role model for in vitro and in vivo applications. Tailor-made ELP-like block copolymer proteins exhibiting IDP-behavior enable LLPS formation in vitro and in vivo allowing the assembly of membrane-based and membraneless superstructures via protein phase-separation in E. coli. Subsequently, we demonstrate the responsiveness of protein phase-separated spaces (PPSSs) to environmental physicochemical triggers and their selective, charge-dependent and switchable interaction with DNA or extrinsic and intrinsic molecules enabling their selective shuttling across semipermeable phase boundaries including (cell)membranes. This paves the road for adjustable artificial PPSS-based storage and reaction spaces and the specific transport across phase boundaries for applications in pharmacy and synthetic biology.
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Affiliation(s)
- Matthias C Huber
- Institut für Pharmazeutische Technologie, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Andreas Schreiber
- Hahn-Schickard Gesellschaft für angewandte Forschung e. V., Georges-Köhler-Allee 103, D-79110, Freiburg, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
| | - Stefan M Schiller
- Institut für Pharmazeutische Technologie, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
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10
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Patkar SS, Tang Y, Bisram AM, Zhang T, Saven JG, Pochan DJ, Kiick KL. Genetic Fusion of Thermoresponsive Polypeptides with UCST-type Behavior Mediates 1D Assembly of Coiled-Coil Bundlemers. Angew Chem Int Ed Engl 2023; 62:e202301331. [PMID: 36988077 DOI: 10.1002/anie.202301331] [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: 01/26/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 03/30/2023]
Abstract
Thermoresponsive resilin-like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil-forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature-triggered phase separation of the RLP units. Their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet-visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic-transmission electron microscopy and coarse-grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.
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Affiliation(s)
- Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Arriana M Bisram
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Tianren Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darrin J Pochan
- 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
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
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11
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García-Arévalo C, Quintanilla-Sierra L, Santos M, Ferrero S, Acosta S, Rodríguez-Cabello J. Impact of aromatic residues on the intrinsic disorder and transitional behaviour of model IDPs. Mater Today Bio 2022; 16:100400. [PMID: 36060106 PMCID: PMC9434135 DOI: 10.1016/j.mtbio.2022.100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/28/2022]
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12
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Gleason JM, Klass SH, Huang P, Ozawa T, Santos RA, Fogarty MM, Raleigh DR, Berger MS, Francis MB. Intrinsically Disordered Protein Micelles as Vehicles for Convection-Enhanced Drug Delivery to Glioblastoma Multiforme. ACS APPLIED BIO MATERIALS 2022; 5:3695-3702. [PMID: 35857070 DOI: 10.1021/acsabm.2c00215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lipid and micelle-based nanocarriers have been explored for anticancer drug delivery to improve accumulation and uptake in tumor tissue. As an experimental opportunity in this area, our lab has developed a protein-based micelle nanocarrier consisting of a hydrophilic intrinsically disordered protein (IDP) domain bound to a hydrophobic tail, termed IDP-2Yx2A. This construct can be used to encapsulate hydrophobic chemotherapeutics that would otherwise be too insoluble in water to be administered. In this study, we evaluate the in vivo efficacy of IDP-2Yx2A by delivering a highly potent but water-insoluble cancer drug, SN38, into glioblastoma multiforme (GBM) tumors via convection-enhanced delivery (CED). The protein carriers alone are shown to elicit minimal toxicity effects in mice; furthermore, they can encapsulate and deliver concentrations of SN38 that would otherwise be lethal without the carriers. CED administration of these drug-loaded micelles into mice bearing U251-MG GBM xenografts resulted in slowed tumor growth and significant increases in median survival times compared to nonencapsulated SN38 and PBS controls.
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Affiliation(s)
- Jamie M Gleason
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Sarah H Klass
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Paul Huang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tomoko Ozawa
- Department of Neurological Surgery, University of California, San Francisco, California 94158, United States
| | - Raquel A Santos
- Department of Neurological Surgery, University of California, San Francisco, California 94158, United States
| | - Miko M Fogarty
- Department of Neurological Surgery, University of California, San Francisco, California 94158, United States
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, California 94158, United States.,Department of Radiation Oncology, University of California, San Francisco, California 94518, United States
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, California 94158, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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13
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Horn JM, Zhu Y, Ahn SY, Obermeyer AC. Self-assembly of globular proteins with intrinsically disordered protein polyelectrolytes and block copolymers. SOFT MATTER 2022; 18:5759-5769. [PMID: 35912826 PMCID: PMC9446422 DOI: 10.1039/d2sm00415a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intrinsically disordered polypeptides are a versatile class of materials, combining the biocompatibility of peptides with the disordered structure and diverse phase behaviors of synthetic polymers. Synthetic polyelectrolytes are capable of complex phase behavior when mixed with oppositely charged polyelectrolytes, facilitating nanoparticle formation and bulk phase separation. However, there has been limited exploration of intrinsically disordered protein polyelectrolytes as potential bio-based replacements for synthetic polyelectrolytes. Here, we produce negatively charged, intrinsically disordered polypeptides, capable of high-yield expression in E. coli and use this intrinsically disordered peptide to produce entirely protein-based polyelectrolyte complexes. The complexes display rich phase behavior, showing sensitivity to charge density, salt concentration, temperature, and charge fraction. We characterize this behavior through a combination of turbidity assays, dynamic light scattering, and transmission electron microscopy. The robust expression profile and stimuli-responsive phase behavior of the intrinsically disordered peptides demonstrates their potential as easily producible, biocompatible substitutes for synthetic polyelectrolytes.
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Affiliation(s)
- Justin M Horn
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - Yuncan Zhu
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - So Yeon Ahn
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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14
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Thermoresponsive Polymer Assemblies: From Molecular Design to Theranostics Application. Prog Polym Sci 2022. [DOI: 10.1016/j.progpolymsci.2022.101578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Ban E, Kim A. Coacervates: recent developments as nanostructure delivery platforms for therapeutic biomolecules. Int J Pharm 2022; 624:122058. [PMID: 35905931 DOI: 10.1016/j.ijpharm.2022.122058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 10/16/2022]
Abstract
Coacervation is a liquid-liquid phase separation that can occur in solutions of macromolecules through self-assembly or electrostatic interactions. Recently, coacervates composed of biocompatible macromolecules have been actively investigated as nanostructure platforms to encapsulate and deliver biomolecules such as proteins, RNAs, and DNAs. One particular advantage of coacervates is that they are derived from aqueous solutions, unlike other nanoparticle delivery systems that often require organic solvents. In addition, coacervates achieve high loading while maintaining the viability of the cargo material. Here, we review recent developments in the applications of coacervates and their limitations in the delivery of therapeutic biomolecules. Important factors for coacervation include molecular structures of the polyelectrolytes, mixing ratio, the concentration of polyelectrolytes, and reaction conditions such as ionic strength, pH, and temperature. Various compositions of coacervates have been shown to deliver biomolecules in vitro and in vivo with encouraging activities. However, major hurdles remain for the systemic route of administration other than topical or local delivery. The scale-up of manufacturing methods suitable for preclinical and clinical evaluations remains to be addressed. We conclude with a few research directions to overcome current challenges, which may lead to successful translation into the clinic.
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Affiliation(s)
- Eunmi Ban
- College of Pharmacy, CHA University, Seongnam 13488, Korea
| | - Aeri Kim
- College of Pharmacy, CHA University, Seongnam 13488, Korea.
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16
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Lee JS, Kang MJ, Lee JH, Lim DW. Injectable Hydrogels of Stimuli-Responsive Elastin and Calmodulin-Based Triblock Copolypeptides for Controlled Drug Release. Biomacromolecules 2022; 23:2051-2063. [PMID: 35411765 DOI: 10.1021/acs.biomac.2c00053] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of block copolypeptides with stimuli responsiveness have been of growing interest for dynamic self-assembly. Here, multistimuli-responsive triblock copolypeptides composed of thermosensitive elastin-based polypeptides (EBP) and ligand-responsive calmodulin (CalM) were genetically engineered, over-expressed, and nonchromatographically purified by inverse transition cycling. Diluted EBP-CalM-EBP (ECE) triblock copolypeptides under physiological conditions self-assembled into vesicles at the nanoscale by temperature-triggered aggregation of the EBP block with lower critical solution temperature behaviors. Furthermore, concentrated ECE triblock copolypeptides under identical conditions exhibited thermally induced gelation, resulting in physically crosslinked hydrogels. They showed controlled rheological and mechanical properties depending on the conformational change of the CalM middle block induced by binding either Ca2+ or Ca2+ and trifluoperazines (TFPs) as ligands. In addition, both Ca2+-free and Ca2+-bound ECE triblock copolypeptide hydrogels exhibited biocompatibility, while those bound to both Ca2+ and TFPs showed severe cytotoxicity because of controlled TFP release of the CalM blocks. The ECE triblock hydrogels with stimuli responsiveness would be useful as injectable drug delivery depots for biomedical applications.
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Affiliation(s)
- Jae Sang Lee
- Department of Bionano Engineering and Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Min Jeong Kang
- Department of Bionano Engineering and Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Jae Hee Lee
- Department of Bionano Engineering and Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Dong Woo Lim
- Department of Bionano Engineering and Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
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17
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Klass SH, Gleason JM, Omole AO, Onoa B, Bustamante CJ, Francis MB. Preparation of Bioderived and Biodegradable Surfactants Based on an Intrinsically Disordered Protein Sequence. Biomacromolecules 2022; 23:1462-1470. [PMID: 35238203 DOI: 10.1021/acs.biomac.2c00051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Surfactants, block copolymers, and other types of micellar systems are used in a wide variety of biomedical and industrial processes. However, most commonly used surfactants are synthetically derived and pose environmental and toxicological concerns throughout their product life cycle. Because of this, bioderived and biodegradable surfactants are promising alternatives. For biosurfactants to be implemented industrially, they need to be produced on a large scale and also have tailorable properties that match those afforded by the polymerization of synthetic surfactants. In this paper, a scalable and versatile production method for biosurfactants based on a hydrophilic intrinsically disordered protein (IDP) sequence with a genetically engineered hydrophobic domain is used to study variables that impact their physicochemical and self-assembling properties. These amphiphilic sequences were found to self-assemble into micelles over a broad range of temperatures, pH values, and ionic strengths. To investigate the role of the IDP hydrophilic domain on self-assembly, variants with increased overall charges and systematically decreased IDP domain lengths were produced and examined for their sizes, morphologies, and critical micelle concentrations (CMCs). The results of these studies indicate that decreasing the length of the IDP domain and consequently the molecular weight and hydrophilic fraction leads to smaller micelles. In addition, significantly increasing the amount of charged residues in the hydrophilic IDP domain results in micelles of similar sizes but with higher CMC values. This represents an initial step in developing a quantitative model for the future engineering of biosurfactants based on this IDP sequence.
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Affiliation(s)
- Sarah H Klass
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Jamie M Gleason
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Anthony O Omole
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Bibiana Onoa
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Carlos J Bustamante
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States.,Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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18
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Cohan MC, Shinn MK, Lalmansingh JM, Pappu RV. Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins. J Mol Biol 2022; 434:167373. [PMID: 34863777 PMCID: PMC10178624 DOI: 10.1016/j.jmb.2021.167373] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/24/2021] [Accepted: 11/16/2021] [Indexed: 01/21/2023]
Abstract
Sequence-ensemble relationships of intrinsically disordered proteins (IDPs) are governed by binary patterns such as the linear clustering or mixing of specific residues or residue types with respect to one another. To enable the discovery of potentially important, shared patterns across sequence families, we describe a computational method referred to as NARDINI for Non-random Arrangement of Residues in Disordered Regions Inferred using Numerical Intermixing. This work was partially motivated by the observation that parameters that are currently in use for describing different binary patterns are not interoperable across IDPs of different amino acid compositions and lengths. In NARDINI, we generate an ensemble of scrambled sequences to set up a composition-specific null model for the patterning parameters of interest. We then compute a series of pattern-specific z-scores to quantify how each pattern deviates from a null model for the IDP of interest. The z-scores help in identifying putative non-random linear sequence patterns within an IDP. We demonstrate the use of NARDINI derived z-scores by identifying sequence patterns in three well-studied IDP systems. We also demonstrate how NARDINI can be deployed to study archetypal IDPs across homologs and orthologs. Overall, NARDINI is likely to aid in designing novel IDPs with a view toward engineering new sequence-function relationships or uncovering cryptic ones. We further propose that the z-scores introduced here are likely to be useful for theoretical and computational descriptions of sequence-ensemble relationships across IDPs of different compositions and lengths.
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Affiliation(s)
- Megan C Cohan
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA
| | - Min Kyung Shinn
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA.
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19
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Lüdeke S, Lohner P, Stühn LG, Betschart MU, Huber MC, Schreiber A, Schiller SM. Dynamische Strukturänderung und Thermodynamik von Phasentrennprozessen eines Proteinmodells mit intrinsisch ungeordneter/geordneter Struktur. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Steffen Lüdeke
- Institut für Pharmazeutische und Biomedizinische Wissenschaften (IPBW) Johannes Gutenberg-Universität Mainz Staudinger Weg 5 55128 Mainz Deutschland
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg Deutschland
| | - Philipp Lohner
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg Deutschland
| | - Lara G. Stühn
- Zentrum für Biosystemanalyse (ZBSA) Albert-Ludwigs-Universität Freiburg Habsburgerstraße 49 79104 Freiburg Deutschland
| | - Martin U. Betschart
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg Deutschland
| | - Matthias C. Huber
- Cluster of Excellence livMatS @ FIT – Freiburg Center for Interactive Materials and Bioinspired Technologies Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee 105 79104 Freiburg Deutschland
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA) Albert-Ludwigs-Universität Freiburg Habsburgerstraße 49 79104 Freiburg Deutschland
| | - Stefan M. Schiller
- Zentrum für Biosystemanalyse (ZBSA) Albert-Ludwigs-Universität Freiburg Habsburgerstraße 49 79104 Freiburg Deutschland
- Cluster of Excellence livMatS @ FIT – Freiburg Center for Interactive Materials and Bioinspired Technologies Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee 105 79104 Freiburg Deutschland
- IMTEK – Institut für Mikrosystemtechnik Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee 103 79104 Freiburg Deutschland
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20
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Chu S, Wang AL, Bhattacharya A, Montclare JK. Protein Based Biomaterials for Therapeutic and Diagnostic Applications. PROGRESS IN BIOMEDICAL ENGINEERING (BRISTOL, ENGLAND) 2022; 4:012003. [PMID: 34950852 PMCID: PMC8691744 DOI: 10.1088/2516-1091/ac2841] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proteins are some of the most versatile and studied macromolecules with extensive biomedical applications. The natural and biological origin of proteins offer such materials several advantages over their synthetic counterparts, such as innate bioactivity, recognition by cells and reduced immunogenic potential. Furthermore, proteins can be easily functionalized by altering their primary amino acid sequence and can often be further self-assembled into higher order structures either spontaneously or under specific environmental conditions. This review will feature the recent advances in protein-based biomaterials in the delivery of therapeutic cargo such as small molecules, genetic material, proteins, and cells. First, we will discuss the ways in which secondary structural motifs, the building blocks of more complex proteins, have unique properties that enable them to be useful for therapeutic delivery. Next, supramolecular assemblies, such as fibers, nanoparticles, and hydrogels, made from these building blocks that are engineered to behave in a cohesive manner, are discussed. Finally, we will cover additional modifications to protein materials that impart environmental responsiveness to materials. This includes the emerging field of protein molecular robots, and relatedly, protein-based theranostic materials that combine therapeutic potential with modern imaging modalities, including near-infrared fluorescence spectroscopy (NIRF), single-photo emission computed tomography/computed tomography (SPECT/CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and ultrasound/photoacoustic imaging (US/PAI).
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Affiliation(s)
- Stanley Chu
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrew L Wang
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, NY, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Aparajita Bhattacharya
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Molecular and Cellular Biology, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Chemistry, NYU, New York, NY, USA
- Department of Biomaterials, NYU College of Dentistry, New York, NY, USA
- Department of Radiology, NYU Langone Health, New York, NY, USA
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21
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Cracking the Skin Barrier: Liquid-Liquid Phase Separation Shines under the Skin. JID INNOVATIONS 2021; 1:100036. [PMID: 34909733 PMCID: PMC8659386 DOI: 10.1016/j.xjidi.2021.100036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/07/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
Central to forming and sustaining the skin’s barrier, epidermal keratinocytes (KCs) fluxing to the skin surface undergo a rapid and enigmatic transformation into flat, enucleated squames. At the crux of this transformation are intracellular keratohyalin granules (KGs) that suddenly disappear as terminally differentiating KCs transition to the cornified skin surface. Defects in KGs have long been linked to skin barrier disorders. Through the biophysical lens of liquid-liquid phase separation (LLPS), these enigmatic KGs recently emerged as liquid-like membraneless organelles whose assembly and subsequent pH-triggered disassembly drive squame formation. To stimulate future efforts toward cracking the complex process of skin barrier formation, in this review, we integrate the key concepts and foundational work spanning the fields of LLPS and epidermal biology. We review the current progress in the skin and discuss implications in the broader context of membraneless organelles across stratifying epithelia. The discovery of environmentally sensitive LLPS dynamics in the skin points to new avenues for dissecting the skin barrier and for addressing skin barrier disorders. We argue that skin and its appendages offer outstanding models to uncover LLPS-driven mechanisms in tissue biology.
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Key Words
- 3D, three-dimensional
- AD, atopic dermatitis
- CE, cornified envelope
- EDC, epidermal differentiation complex
- ER, endoplasmic reticulum
- IDP, intrinsically-disordered protein
- KC, keratinocyte
- KG, keratohyalin granule
- LCST, lower critical solution temperature
- LLPS, liquid-liquid phase separation
- PTM, post-translational modification
- TG, trichohyalin granule
- UCST, upper critical solution temperature
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22
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Lüdeke S, Lohner P, Stühn LG, Betschart MU, Huber MC, Schreiber A, Schiller SM. Dynamic Structural Changes and Thermodynamics in Phase Separation Processes of an Intrinsically Disordered-Ordered Protein Model. Angew Chem Int Ed Engl 2021; 61:e202112738. [PMID: 34806270 PMCID: PMC9299898 DOI: 10.1002/anie.202112738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/21/2021] [Indexed: 01/03/2023]
Abstract
Elastin-like proteins (ELPs) are biologically important proteins and models for intrinsically disordered proteins (IDPs) and dynamic structural transitions associated with coacervates and liquid-liquid phase transitions. However, the conformational status below and above coacervation temperature and its role in the phase separation process is still elusive. Employing matrix least-squares global Boltzmann fitting of the circular dichroism spectra of the ELPs (VPGVG)20 , (VPGVG)40 , and (VPGVG)60 , we found that coacervation occurs sharply when a certain number of repeat units has acquired β-turn conformation (in our sequence setting a threshold of approx. 20 repeat units). The character of the differential scattering of the coacervate suspensions indicated that this fraction of β-turn structure is still retained after polypeptide assembly. Such conformational thresholds may also have a role in other protein assembly processes with implications for the design of protein-based smart materials.
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Affiliation(s)
- Steffen Lüdeke
- Institut für Pharmazeutische und Biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128, Mainz, Germany.,Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Philipp Lohner
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lara G Stühn
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Martin U Betschart
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Matthias C Huber
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, 79104, Freiburg, Germany
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, 79104, Freiburg, Germany.,IMTEK-Institut für Mikrosystemtechnik, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 103, 79104, Freiburg, Germany
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23
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Scott WA, Gharakhanian EG, Bell AG, Evans D, Barun E, Houk KN, Deming TJ. Active Controlled and Tunable Coacervation Using Side-Chain Functional α-Helical Homopolypeptides. J Am Chem Soc 2021; 143:18196-18203. [PMID: 34669392 DOI: 10.1021/jacs.1c07925] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the development of new side-chain amino acid-functionalized α-helical homopolypeptides that reversibly form coacervate phases in aqueous media. The designed multifunctional nature of the side-chains was found to provide a means to actively control coacervation via mild, biomimetic redox chemistry as well as allow response to physiologically relevant environmental changes in pH, temperature, and counterions. These homopolypeptides were found to possess properties that mimic many of those observed in natural coacervate forming intrinsically disordered proteins. Despite ordered α-helical conformations that are thought to disfavor coacervation, molecular dynamics simulations of a polypeptide model revealed a high degree of side-chain conformational disorder and hydration around the ordered backbone, which may explain the ability of these polypeptides to form coacervates. Overall, the modular design, uniform nature, and ordered chain conformations of these polypeptides were found to provide a well-defined platform for deconvolution of molecular elements that influence biopolymer coacervation and tuning of coacervate properties for downstream applications.
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Affiliation(s)
- Wendell A Scott
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Eric G Gharakhanian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexandra G Bell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ehab Barun
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Timothy J Deming
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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24
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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: 41] [Impact Index Per Article: 13.7] [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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25
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Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform 2021; 21:458-472. [PMID: 30698641 PMCID: PMC7299295 DOI: 10.1093/bib/bbz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Lisanna Paladin
- Department of Biomedical Science, University of Padova, Padova, Italy
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia Petrosian
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Annika Urbanek
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Gliwice, Poland
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Christos A Ouzounis
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS-UMR, Institut de Biologie Computationnelle, Universite de Montpellier, Montpellier, France.,Institute of Bioengineering, University ITMO, St. Petersburg, Russia
| | - John M Hancock
- Earlham Institute, Norwich, UK.,ELIXIR Hub, Welcome Genome Campus, Hinxton, UK
| | - Silvio C E Tosatto
- Department of Biomedical Science, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
| | - Zsuzsanna Dosztanyi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
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26
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Dai M, Georgilis E, Goudounet G, Garbay B, Pille J, van Hest JCM, Schultze X, Garanger E, Lecommandoux S. Refining the Design of Diblock Elastin-Like Polypeptides for Self-Assembly into Nanoparticles. Polymers (Basel) 2021; 13:1470. [PMID: 34062852 PMCID: PMC8125372 DOI: 10.3390/polym13091470] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Diblock copolymers based-on elastin-like polypeptide (ELP) have the potential to undergo specific phase transitions when thermally stimulated. This ability is especially suitable to form carriers, micellar structures for instance, for delivering active cargo molecules. Here, we report the design and study of an ELP diblock library based on ELP-[M1V3-i]-[I-j]. First, ELP-[M1V3-i]-[I-j] (i = 20, 40, 60; j = 20, 90) that showed a similar self-assembly propensity (unimer-to-aggregate transition) as their related monoblocks ELP-[M1V3-i] and ELP-[I-j]. By selectively oxidizing methionines of ELP-[M1V3-i] within the different diblocks structures, we have been able to access a thermal phase transition with three distinct regimes (unimers, micelles, aggregates) characteristic of well-defined ELP diblocks.
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Affiliation(s)
- Michèle Dai
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
- L’Oréal Recherche Avancée, 1 Avenue Eugène Schueller, 93600 Aulnay-sous-Bois, France;
| | - Evangelos Georgilis
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
- Current affiliation E.G. (Evangelos Georgilis): CIC nanoGUNE (BRTA), Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain
| | - Guillaume Goudounet
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Bertrand Garbay
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Jan Pille
- Bio-organic Chemistry Lab, Eindhoven University of Technology, P.O. Box 513 (STO 3.31), 5600 MB Eindhoven, The Netherlands; (J.P.); (J.C.M.v.H.)
| | - Jan C. M. van Hest
- Bio-organic Chemistry Lab, Eindhoven University of Technology, P.O. Box 513 (STO 3.31), 5600 MB Eindhoven, The Netherlands; (J.P.); (J.C.M.v.H.)
| | - Xavier Schultze
- L’Oréal Recherche Avancée, 1 Avenue Eugène Schueller, 93600 Aulnay-sous-Bois, France;
| | - Elisabeth Garanger
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Sébastien Lecommandoux
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
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27
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Yoshikawa M, Yoshii T, Ikuta M, Tsukiji S. Synthetic Protein Condensates That Inducibly Recruit and Release Protein Activity in Living Cells. J Am Chem Soc 2021; 143:6434-6446. [PMID: 33890764 DOI: 10.1021/jacs.0c12375] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Compartmentation of proteins into biomolecular condensates or membraneless organelles formed by phase separation is an emerging principle for the regulation of cellular processes. Creating synthetic condensates that accommodate specific intracellular proteins on demand would have various applications in chemical biology, cell engineering, and synthetic biology. Here, we report the construction of synthetic protein condensates capable of recruiting and/or releasing proteins of interest in living mammalian cells in response to a small molecule or light. By a modular combination of a tandem fusion of two oligomeric proteins, which forms phase-separated synthetic protein condensates in cells, with a chemically induced dimerization tool, we first created a chemogenetic protein condensate system that can rapidly recruit target proteins from the cytoplasm to the condensates by addition of a small-molecule dimerizer. We next coupled the protein-recruiting condensate system with an engineered proximity-dependent protease, which gave a second protein condensate system wherein target proteins previously expressed inside the condensates are released into the cytoplasm by small-molecule-triggered protease recruitment. Furthermore, an optogenetic condensate system that allows reversible release and sequestration of protein activity in a repeatable manner using light was constructed successfully. These condensate systems were applicable to control protein activity and cellular processes such as membrane ruffling and ERK signaling in a time scale of minutes. This proof-of-principle work provides a new platform for chemogenetic and optogenetic control of protein activity in mammalian cells and represents a step toward tailor-made engineering of synthetic protein condensate-based soft materials with various functionalities for biological and biomedical applications.
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Affiliation(s)
- Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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28
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Zeng X, Liu C, Fossat MJ, Ren P, Chilkoti A, Pappu RV. Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures. APL MATERIALS 2021; 9:021119. [PMID: 38362050 PMCID: PMC10868716 DOI: 10.1063/5.0037438] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Many naturally occurring elastomers are intrinsically disordered proteins (IDPs) built up of repeating units and they can demonstrate two types of thermoresponsive phase behavior. Systems characterized by lower critical solution temperatures (LCST) undergo phase separation above the LCST whereas systems characterized by upper critical solution temperatures (UCST) undergo phase separation below the UCST. There is congruence between thermoresponsive coil-globule transitions and phase behavior whereby the theta temperatures above or below which the IDPs transition from coils to globules serve as useful proxies for the LCST / UCST values. This implies that one can design sequences with desired values for the theta temperature with either increasing or decreasing radii of gyration above the theta temperature. Here, we show that the Monte Carlo simulations performed in the so-called intrinsic solvation (IS) limit version of the temperature-dependent the ABSINTH (self-Assembly of Biomolecules Studied by an Implicit, Novel, Tunable Hamiltonian) implicit solvation model, yields a useful heuristic for discriminating between sequences with known LCST versus UCST phase behavior. Accordingly, we use this heuristic in a supervised approach, integrate it with a genetic algorithm, combine this with IS limit simulations, and demonstrate that novel sequences can be designed with LCST phase behavior. These calculations are aided by direct estimates of temperature dependent free energies of solvation for model compounds that are derived using the polarizable AMOEBA (atomic multipole optimized energetics for biomolecular applications) forcefield. To demonstrate the validity of our designs, we calculate coil-globule transition profiles using the full ABSINTH model and combine these with Gaussian Cluster Theory calculations to establish the LCST phase behavior of designed IDPs.
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Affiliation(s)
- Xiangze Zeng
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Martin J. Fossat
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
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29
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Ramanathan A, Ma H, Parvatikar A, Chennubhotla SC. Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. Curr Opin Struct Biol 2021; 66:216-224. [PMID: 33421906 DOI: 10.1016/j.sbi.2020.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022]
Abstract
We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships-however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.
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Affiliation(s)
- Arvind Ramanathan
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States; Consortium for Advanced Science and Engineering (CASE), University of Chicago, Hyde Park, IL, United States.
| | - Heng Ma
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Akash Parvatikar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
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30
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Huihui J, Ghosh K. An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins. J Chem Phys 2020; 152:161102. [PMID: 32357776 DOI: 10.1063/5.0004619] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically Disordered Proteins (IDPs), unlike folded proteins, lack a unique folded structure and rapidly interconvert among ensembles of disordered states. However, they have specific conformational properties when averaged over their ensembles of disordered states. It is critical to develop a theoretical formalism to predict these ensemble average conformational properties that are encoded in the IDP sequence (the specific order in which amino acids/residues are linked). We present a general heteropolymer theory that analytically computes the ensemble average distance profiles (⟨Rij 2⟩) between any two (i, j) monomers (amino acids for IDPs) as a function of the sequence. Information rich distance profiles provide a detailed description of the IDP in contrast to typical metrics such as scaling exponents, radius of gyration, or end-to-end distance. This generalized formalism supersedes homopolymer-like models or models that are built only on the composition of amino acids but ignore sequence details. The prediction of these distance profiles for highly charged polyampholytes and naturally occurring IDPs unmasks salient features that are hidden in the sequence. Moreover, the model reveals strategies to modulate the entire distance map to achieve local or global swelling/compaction by subtle changes/modifications-such as phosphorylation, a biologically relevant process-in specific hotspots in the sequence. Sequence-specific distance profiles and their modulation have been benchmarked against all-atom simulations. Our new formalism also predicts residue-pair specific coil-globule transitions. The analytical nature of the theory will facilitate design of new sequences to achieve specific target distance profiles with broad applications in synthetic biology and polymer science.
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Affiliation(s)
- Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, USA and Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, USA and Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, USA
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31
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Wunder T, Mueller-Cajar O. Biomolecular condensates in photosynthesis and metabolism. CURRENT OPINION IN PLANT BIOLOGY 2020; 58:1-7. [PMID: 32966943 DOI: 10.1016/j.pbi.2020.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/29/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
The transient assembly or sequestration of enzymes into clusters permits the channeling of metabolites, but requires spatiotemporal control. Liquid liquid phase separation (LLPS) has recently emerged as a fundamental concept enabling formation of such assemblies into non-membrane bound organelles. The role of LLPS in the formation of condensates containing the CO2-fixing enzyme Rubisco has recently become appreciated. Both prokaryotic carboxysomes and eukaryotic pyrenoids enhance the carboxylation reaction by enabling the saturation of the enzyme with CO2 gas. Biochemical reconstitution and structural biology are revealing the mechanistic basis of these photosynthetic condensates. At the same time other enzyme clusters, such as purinosomes for de-novo purine biosynthesis and G-bodies containing glycolytic enzymes, are emerging to behave like phase-separated systems. In the near future we anticipate details of many more such metabolic condensates to be revealed, deeply informing our ability to influence metabolic fluxes.
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Affiliation(s)
- Tobias Wunder
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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32
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Acosta S, Ye Z, Aparicio C, Alonso M, Rodríguez-Cabello JC. Dual Self-Assembled Nanostructures from Intrinsically Disordered Protein Polymers with LCST Behavior and Antimicrobial Peptides. Biomacromolecules 2020; 21:4043-4052. [PMID: 32786727 PMCID: PMC7558458 DOI: 10.1021/acs.biomac.0c00865] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial peptides (AMPs) have attracted great interest as they constitute one of the most promising alternatives against drug-resistant infections. Their amphipathic nature not only provides them antimicrobial and immunomodulatory properties but also the ability to self-assemble into supramolecular nanostructures. Here, we propose their use as self-assembling domains to drive hierarchical organization of intrinsically disordered protein polymers (IDPPs). Using a modular approach, hybrid protein-engineered polymers were recombinantly produced, thus combining designer AMPs and a thermoresponsive IDPP, an elastin-like recombinamer (ELR). We exploited the ability of these AMPs and ELRs to self-assemble to develop supramolecular nanomaterials by way of a dual-assembly process. First, the AMPs trigger the formation of nanofibers; then, the thermoresponsiveness of the ELRs enables assembly into fibrillar aggregates. The interplay between the assembly of AMPs and ELRs provides an innovative molecular tool in the development of self-assembling nanosystems with potential use for biotechnological and biomedical applications.
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Affiliation(s)
- Sergio Acosta
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, University of Valladolid, 47011 Valladolid, Spain
| | - Zhou Ye
- MDRCBB, Minnesota Dental Research Center for Biomaterials and Biomechanics, University of Minnesota, Minneapolis, 55455 Minnesota, United States
| | - Conrado Aparicio
- MDRCBB, Minnesota Dental Research Center for Biomaterials and Biomechanics, University of Minnesota, Minneapolis, 55455 Minnesota, United States
| | - Matilde Alonso
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, University of Valladolid, 47011 Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, University of Valladolid, 47011 Valladolid, Spain
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33
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Dzuricky M, Rogers BA, Shahid A, Cremer PS, Chilkoti A. De novo engineering of intracellular condensates using artificial disordered proteins. Nat Chem 2020; 12:814-825. [PMID: 32747754 DOI: 10.1038/s41557-020-0511-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/18/2020] [Indexed: 11/09/2022]
Abstract
Phase separation of intrinsically disordered proteins (IDPs) is a remarkable feature of living cells to dynamically control intracellular partitioning. Despite the numerous new IDPs that have been identified, progress towards rational engineering in cells has been limited. To address this limitation, we systematically scanned the sequence space of native IDPs and designed artificial IDPs (A-IDPs) with different molecular weights and aromatic content, which exhibit variable condensate saturation concentrations and temperature cloud points in vitro and in cells. We created A-IDP puncta using these simple principles, which are capable of sequestering an enzyme and whose catalytic efficiency can be manipulated by the molecular weight of the A-IDP. These results provide a robust engineered platform for creating puncta with new, phase-separation-mediated control of biological function in living cells.
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Affiliation(s)
- Michael Dzuricky
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Bradley A Rogers
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Abdulla Shahid
- Department of Computer Science, Duke University, Durham, NC, USA.,Department of Biology, Duke University, Durham, NC, USA
| | - Paul S Cremer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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34
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Zeng X, Holehouse AS, Chilkoti A, Mittag T, Pappu RV. Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins. Biophys J 2020; 119:402-418. [PMID: 32619404 PMCID: PMC7376131 DOI: 10.1016/j.bpj.2020.06.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023] Open
Abstract
Phase separation is thought to underlie spatial and temporal organization that is required for controlling biochemical reactions in cells. Multivalence of interaction motifs, also known as stickers, is a defining feature of proteins that drive phase separation. Intrinsically disordered proteins with stickers uniformly distributed along the linear sequence can serve as scaffold molecules that drive phase separation. The sequence-intrinsic contributions of disordered proteins to phase separation can be discerned by computing or measuring sequence-specific phase diagrams. These help to delineate the combinations of protein concentration and a suitable control parameter, such as temperature, that support phase separation. Here, we present an approach that combines detailed simulations with a numerical adaptation of an analytical Gaussian cluster theory to enable the calculation of sequence-specific phase diagrams. Our approach leverages the known equivalence between the driving forces for single-chain collapse in dilute solutions and the driving forces for phase separation in concentrated solutions. We demonstrate the application of the theory-aided computations through calculation of phase diagrams for a set of archetypal intrinsically disordered low-complexity domains. We also leverage theories to compute sequence-specific percolation lines and thereby provide a thermodynamic framework for hardening transitions that have been observed for many biomolecular condensates.
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Affiliation(s)
- Xiangze Zeng
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Alex S Holehouse
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri.
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35
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Lim ZW, Varma VB, Ramanujan RV, Miserez A. Magnetically responsive peptide coacervates for dual hyperthermia and chemotherapy treatments of liver cancer. Acta Biomater 2020; 110:221-230. [PMID: 32422317 DOI: 10.1016/j.actbio.2020.04.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Liver cancer is an aggressive malignancy associated with high levels of mortality and morbidity. Doxorubicin (Dox) is often used to slow down liver cancer progression; however its efficacy is limited, and its severe side effects prevent its routine use at therapeutic concentrations. We present a biomimetic peptide that coacervates into micro-droplets, within which both Dox and magnetic nanoparticles (MNPs) can be sequestered. These Dox-loaded Magnetic Coacervates (DMCs) can be used for thermo-chemotherapy, with the controlled release of Dox triggered by an external Alternating Magnetic Field (AMF). The DMCs are internalized by the cells via an energy-independent mechanism which is not based on endocytosis. Application of AMF generates a temperature of 45 °C within the DMCs, triggering their disassembly and the simultaneous release of Dox, thereby resulting in dual hyperthermia and chemotherapy for more efficient cancer therapy. In vitro studies conducted under AMF reveal that DMCs are cytocompatible and effective in inducing HepG2 liver cancer cell death. Thermo-chemotherapy treatment against HepG2 cells is also shown to be more effective compared to either hyperthermia or chemotherapy treatments alone. Thus, our novel peptide DMCs can open avenues in theranostic strategies against liver cancer through programmable, wireless, and remote control of Dox release. STATEMENT OF SIGNIFICANCE: Simultaneous administration of chemical and thermal therapy (thermo-chemotherapy) is more effective in inducing liver cancer cell death and improving survival rate. Thus, there is a keen interest in developing suitable carriers for thermo-chemotherapy. Coacervate micro-droplets display significant advantages, including high loading capacity, fast self-assembly in aqueous environments, and liquid-like behavior. However, they have not yet been explored as carriers for thermo-chemotherapy. Here, we demonstrate that peptide coacervate micro-droplets can co-encapsulate Dox and magnetic nanoparticles and cross the cell membrane. Applying an alternating magnetic field to cells containing drug-loaded coacervates triggers the release of Dox as well as the localized heating by magnetic hyperthermia, resulting in efficient liver cancer cell death by dual thermo-chemotherapy.
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Affiliation(s)
- Zhi Wei Lim
- Biological and Biomimetic Materials Laboratory, Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 637553
| | - Vijaykumar B Varma
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Raju V Ramanujan
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Ali Miserez
- Biological and Biomimetic Materials Laboratory, Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 637553; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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36
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Schuster BS, Dignon GL, Tang WS, Kelley FM, Ranganath AK, Jahnke CN, Simpkins AG, Regy RM, Hammer DA, Good MC, Mittal J. Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior. Proc Natl Acad Sci U S A 2020; 117:11421-11431. [PMID: 32393642 PMCID: PMC7261017 DOI: 10.1073/pnas.2000223117] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.
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Affiliation(s)
- Benjamin S Schuster
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Wai Shing Tang
- Department of Physics, Brown University, Providence, RI 02912
| | - Fleurie M Kelley
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | | | - Craig N Jahnke
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison G Simpkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
| | - Daniel A Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Matthew C Good
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015;
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37
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Abstract
Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated biomolecular condensates. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. We discuss how the valence of stickers impacts the driving forces for condensate formation and elaborate on how stickers can be distinguished from spacers in different contexts. We touch on the impact of sticker- and spacer-mediated interactions on the rheological properties of condensates and show how the model can be mapped to known drivers of different types of biomolecular condensates.
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Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
- Natural Science Research Institute, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
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38
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Zhao H, Ibrahimova V, Garanger E, Lecommandoux S. Dynamic Spatial Formation and Distribution of Intrinsically Disordered Protein Droplets in Macromolecularly Crowded Protocells. Angew Chem Int Ed Engl 2020; 59:11028-11036. [PMID: 32207864 DOI: 10.1002/anie.202001868] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/23/2020] [Indexed: 11/09/2022]
Abstract
Elastin-like polypeptides (ELPs) have been proposed as a simple model of intrinsically disordered proteins (IDPs) which can form membraneless organelles by liquid-liquid phase separation (LLPS) in cells. Herein, the behavior of fluorescently labeled ELP is studied in cytomimetic aqueous two-phase system (ATPS) encapsulated protocells that are formed using microfluidics, which enabled confinement, changes in temperature, and statistical analysis. The spatial organization of ELP could be observed in the ATPS. Furthermore, changes in temperature triggered the dynamic formation and distribution of ELP-rich droplets within the ATPS, resulting from changes in conformation. Proteins were encapsulated along with ELP in the synthetic protocells and distinct partitioning properties of these proteins and ELP in the ATPS were observed. Therefore, the ability of ELP to coacervate with temperature can be maintained inside a cell-mimicking system.
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Affiliation(s)
- Hang Zhao
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
| | - Vusala Ibrahimova
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
| | - Elisabeth Garanger
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
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39
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Zhao H, Ibrahimova V, Garanger E, Lecommandoux S. Dynamic Spatial Formation and Distribution of Intrinsically Disordered Protein Droplets in Macromolecularly Crowded Protocells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hang Zhao
- Univ. BordeauxCNRSBordeaux INP, LCPO, UMR 5629 33600 Pessac France
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40
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Quiroz FG, Fiore VF, Levorse J, Polak L, Wong E, Pasolli HA, Fuchs E. Liquid-liquid phase separation drives skin barrier formation. Science 2020; 367:367/6483/eaax9554. [PMID: 32165560 DOI: 10.1126/science.aax9554] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 11/20/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
At the body surface, skin's stratified squamous epithelium is challenged by environmental extremes. The surface of the skin is composed of enucleated, flattened surface squames. They derive from underlying, transcriptionally active keratinocytes that display filaggrin-containing keratohyalin granules (KGs) whose function is unclear. Here, we found that filaggrin assembles KGs through liquid-liquid phase separation. The dynamics of phase separation governed terminal differentiation and were disrupted by human skin barrier disease-associated mutations. We used fluorescent sensors to investigate endogenous phase behavior in mice. Phase transitions during epidermal stratification crowded cellular spaces with liquid-like KGs whose coalescence was restricted by keratin filament bundles. We imaged cells as they neared the skin surface and found that environmentally regulated KG phase dynamics drive squame formation. Thus, epidermal structure and function are driven by phase-separation dynamics.
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Affiliation(s)
- Felipe Garcia Quiroz
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA
| | - Vincent F Fiore
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA
| | - John Levorse
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA
| | - Lisa Polak
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA
| | - Ellen Wong
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA.
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41
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Camp CP, Peterson IL, Knoff DS, Melcher LG, Maxwell CJ, Cohen AT, Wertheimer AM, Kim M. Non-cytotoxic Dityrosine Photocrosslinked Polymeric Materials With Targeted Elastic Moduli. Front Chem 2020; 8:173. [PMID: 32232027 PMCID: PMC7082925 DOI: 10.3389/fchem.2020.00173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022] Open
Abstract
Controlling mechanical properties of polymeric biomaterials, including the elastic modulus, is critical to direct cell behavior, such as proliferation and differentiation. Dityrosine photocrosslinking is an attractive and simple method to prepare materials that exhibit a wide range of elastic moduli by rapidly crosslinking tyrosyl-containing polymers. However, high concentrations of commonly used oxidative crosslinking reagents, such as ruthenium-based photoinitiators and persulfates, present cytotoxicity concerns. We found the elastic moduli of materials prepared by crosslinking an artificial protein with tightly controlled tyrosine molarity can be modulated up to 40 kPa by adjusting photoinitiator and persulfate concentrations. Formulations with various concentrations of the crosslinking reagents were able to target a similar material elastic modulus, but excess unreacted persulfate resulted in cytotoxic materials. Therefore, we identified a systematic method to prepare non-cytotoxic photocrosslinked polymeric materials with targeted elastic moduli for potential biomaterials applications in diverse fields, including tissue engineering and 3D bioprinting.
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Affiliation(s)
- Christopher P. Camp
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | - Ingrid L. Peterson
- Applied Biosciences GIDP, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - David S. Knoff
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | | | - Connor J. Maxwell
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | - Audrey T. Cohen
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | - Anne M. Wertheimer
- Applied Biosciences GIDP, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - Minkyu Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
- Department of Materials Science & Engineering, University of Arizona, Tucson, AZ, United States
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42
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Roberts S, Miao V, Costa S, Simon J, Kelly G, Shah T, Zauscher S, Chilkoti A. Complex microparticle architectures from stimuli-responsive intrinsically disordered proteins. Nat Commun 2020; 11:1342. [PMID: 32165622 PMCID: PMC7067844 DOI: 10.1038/s41467-020-15128-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/14/2020] [Indexed: 11/27/2022] Open
Abstract
The controllable production of microparticles with complex geometries is useful for a variety of applications in materials science and bioengineering. The formation of intricate microarchitectures typically requires sophisticated fabrication techniques such as flow lithography or multiple-emulsion microfluidics. By harnessing the molecular interactions of a set of artificial intrinsically disordered proteins (IDPs), we have created complex microparticle geometries, including porous particles, core-shell and hollow shell structures, and a unique ‘fruits-on-a-vine’ arrangement, by exploiting the metastable region of the phase diagram of thermally responsive IDPs within microdroplets. Through multi-site unnatural amino acid (UAA) incorporation, these protein microparticles can also be photo-crosslinked and stably extracted to an all-aqueous environment. This work expands the functional utility of artificial IDPs as well as the available microarchitectures of this class of biocompatible IDPs, with potential applications in drug delivery and tissue engineering. The production of microparticles with complex geometries for biotechnological use historically requires sophisticated fabrication techniques. Here, the authors create complex particle geometries by exploiting the metastable region of the phase diagram of thermally responsive intrinsically disordered proteins within microdroplets.
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Affiliation(s)
- Stefan Roberts
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Vincent Miao
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Simone Costa
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Joseph Simon
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Tejank Shah
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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43
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Lin YH, Brady JP, Chan HS, Ghosh K. A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes. J Chem Phys 2020; 152:045102. [PMID: 32007034 PMCID: PMC7043852 DOI: 10.1063/1.5139661] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022] Open
Abstract
The physical chemistry of liquid-liquid phase separation (LLPS) of polymer solutions bears directly on the assembly of biologically functional dropletlike bodies from proteins and nucleic acids. These biomolecular condensates include certain extracellular materials and intracellular compartments that are characterized as "membraneless organelles." Analytical theories are a valuable, computationally efficient tool for addressing general principles. LLPS of neutral homopolymers is quite well described by theory, but it has been a challenge to develop general theories for the LLPS of heteropolymers involving charge-charge interactions. Here, we present a theory that combines a random-phase-approximation treatment of polymer density fluctuations and an account of intrachain conformational heterogeneity based on renormalized Kuhn lengths to provide predictions of LLPS properties as a function of pH, salt, and charge patterning along the chain sequence. Advancing beyond more limited analytical approaches, our LLPS theory is applicable to a wide variety of charged sequences ranging from highly charged polyelectrolytes to neutral or nearly neutral polyampholytes. This theory should be useful in high-throughput screening of protein and other sequences for their LLPS propensities and can serve as a basis for more comprehensive theories that incorporate nonelectrostatic interactions. Experimental ramifications of our theory are discussed.
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Affiliation(s)
- Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jacob P Brady
- 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
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Colorado, Colorado 80208, USA
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44
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Gabryelczyk B, Cai H, Shi X, Sun Y, Swinkels PJM, Salentinig S, Pervushin K, Miserez A. Hydrogen bond guidance and aromatic stacking drive liquid-liquid phase separation of intrinsically disordered histidine-rich peptides. Nat Commun 2019; 10:5465. [PMID: 31784535 PMCID: PMC6884462 DOI: 10.1038/s41467-019-13469-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/07/2019] [Indexed: 01/07/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) is involved in both intracellular membraneless organelles and extracellular tissues. Despite growing understanding of LLPS, molecular-level mechanisms behind this process are still not fully established. Here, we use histidine-rich squid beak proteins (HBPs) as model IDPs to shed light on molecular interactions governing LLPS. We show that LLPS of HBPs is mediated though specific modular repeats. The morphology of separated phases (liquid-like versus hydrogels) correlates with the repeats' hydrophobicity. Solution-state NMR indicates that LLPS is a multistep process initiated by deprotonation of histidine residues, followed by transient hydrogen bonding with tyrosine, and eventually by hydrophobic interactions. The microdroplets are stabilized by aromatic clustering of tyrosine residues exhibiting restricted molecular mobility in the nano-to-microsecond timescale according to solid-state NMR experiments. Our findings provide guidelines to rationally design pH-responsive peptides with LLPS ability for various applications, including bioinspired protocells and smart drug-delivery systems.
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Affiliation(s)
- Bartosz Gabryelczyk
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Hao Cai
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, NTU, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yue Sun
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Piet J M Swinkels
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE, Wageningen, Netherlands
| | - Stefan Salentinig
- Laboratory for Biointerfaces, Department Materials Meet Life, EMPA, CH-9014, St-Gallen, Switzerland
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700, Fribourg, Switzerland
| | - Konstantin Pervushin
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Ali Miserez
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore.
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45
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Nguyen DT, Jeon BJ, Abraham GR, Saleh OA. Length-Dependence and Spatial Structure of DNA Partitioning into a DNA Liquid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14849-14854. [PMID: 31638820 DOI: 10.1021/acs.langmuir.9b02098] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cells can spatially and temporally control biochemistry using liquid-liquid phase separation to form membrane-less organelles. Synthetic biomolecular liquids offer a means to study the mechanisms of this process, as well as offering a route to the creation of functional biomimetic materials. With these goals in mind, we here examine the partitioning of long double-stranded DNA linkers into a liquid composed of small DNA particles ("nanostars") whose phase separation is driven by base pairing. We find that linker partitioning is length-dependent because of a confinement penalty of inserting long strands within the liquid's characteristic mesh size. We quantify this entropic-confinement effect using a simple partitioning theory and show that its magnitude is consistent with classic Odijk pictures of confined worm-like chains. Linker partitioning can also lead to inhomogeneous structures: long linkers excluded from the liquid interior tend to preferentially accumulate on the surface of liquid droplets (i.e., acting as surfactants), while linkers forced at high concentrations into the liquid undergo a secondary phase separation, forming metastable droplet-in-droplet structures. Altogether, our work demonstrates the ability to rationally engineer the composition and structure of a model biomolecular liquid.
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46
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Levenson R, Bracken C, Sharma C, Santos J, Arata C, Malady B, Morse DE. Calibration between trigger and color: Neutralization of a genetically encoded coulombic switch and dynamic arrest precisely tune reflectin assembly. J Biol Chem 2019; 294:16804-16815. [PMID: 31558609 DOI: 10.1074/jbc.ra119.010339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Indexed: 12/28/2022] Open
Abstract
Reflectin proteins are widely distributed in reflective structures in cephalopods. However, only in loliginid squids are they and the subwavelength photonic structures they control dynamically tunable, driving changes in skin color for camouflage and communication. The reflectins are block copolymers with repeated canonical domains interspersed with cationic linkers. Neurotransmitter-activated signal transduction culminates in catalytic phosphorylation of the tunable reflectins' cationic linkers; the resulting charge neutralization overcomes coulombic repulsion to progressively allow condensation, folding, and assembly into multimeric spheres of tunable well-defined size and low polydispersity. Here, we used dynamic light scattering, transmission EM, CD, atomic force microscopy, and fluorimetry to analyze the structural transitions of reflectins A1 and A2. We also analyzed the assembly behavior of phosphomimetic, deletion, and other mutants in conjunction with pH titration as an in vitro surrogate of phosphorylation. Our experiments uncovered a previously unsuspected, precisely predictive relationship between the extent of neutralization of a reflectin's net charge density and the size of resulting multimeric protein assemblies of narrow polydispersity. Comparisons of mutants revealed that this sensitivity to neutralization resides in the linkers and is spatially distributed along the protein. Imaging of large particles and analysis of sequence composition suggested that assembly may proceed through a dynamically arrested liquid-liquid phase-separated intermediate. Intriguingly, it is this dynamic arrest that enables the observed fine-tuning by charge and the resulting calibration between neuronal trigger and color in the squid. These results offer insights into the basis of reflectin-based biophotonics, opening paths for the design of new materials with tunable properties.
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Affiliation(s)
- Robert Levenson
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Colton Bracken
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Cristian Sharma
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Jerome Santos
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Claire Arata
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Brandon Malady
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Daniel E Morse
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
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47
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Cinar H, Fetahaj Z, Cinar S, Vernon RM, Chan HS, Winter RHA. Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications. Chemistry 2019; 25:13049-13069. [PMID: 31237369 DOI: 10.1002/chem.201902210] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
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Affiliation(s)
- Hasan Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Zamira Fetahaj
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Süleyman Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Robert M Vernon
- Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Hue Sun Chan
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada
| | - Roland H A Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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48
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Majumdar A, Dogra P, Maity S, Mukhopadhyay S. Liquid-Liquid Phase Separation Is Driven by Large-Scale Conformational Unwinding and Fluctuations of Intrinsically Disordered Protein Molecules. J Phys Chem Lett 2019; 10:3929-3936. [PMID: 31260322 DOI: 10.1021/acs.jpclett.9b01731] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Liquid-liquid phase separation occurs via a multitude of transient, noncovalent, and intermolecular interactions resulting in phase transition of intrinsically disordered proteins/regions (IDPs/IDRs) and other biopolymers into mesoscopic, dynamic, nonstoichiometric, and supramolecular condensates. Here we present a unique case to demonstrate that unusual conformational expansion events coupled with solvation and fluctuations drive phase separation of tau, an IDP associated with Alzheimer's disease. Using intramolecular excimer emission as a powerful proximity readout, we show the unraveling of polypeptide chains within the protein-rich interior environment that can promote critical interchain contacts. Using highly sensitive picosecond time-resolved fluorescence depolarization measurements, we directly capture rapid large-amplitude torsional fluctuations in the extended chains that can control the relay of making-and-breaking of noncovalent intermolecular contacts maintaining the internal fluidity. The interplay of these key molecular parameters can be of prime importance in modulating the mesoscale material property of liquid-like condensates and their maturation into pathological gel-like and solid-like aggregates.
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49
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Ibáñez-Fonseca A, Flora T, Acosta S, Rodríguez-Cabello JC. Trends in the design and use of elastin-like recombinamers as biomaterials. Matrix Biol 2019; 84:111-126. [PMID: 31288085 DOI: 10.1016/j.matbio.2019.07.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/23/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022]
Abstract
Elastin-like recombinamers (ELRs), which derive from one of the repetitive domains found in natural elastin, have been intensively studied in the last few years from several points of view. In this mini review, we discuss all the recent works related to the investigation of ELRs, starting with those that define these polypeptides as model intrinsically disordered proteins or regions (IDPs or IDRs) and its relevance for some biomedical applications. Furthermore, we summarize the current knowledge on the development of drug, vaccine and gene delivery systems based on ELRs, while also emphasizing the use of ELR-based hydrogels in tissue engineering and regenerative medicine (TERM). Finally, we show different studies that explore applications in other fields, and several examples that describe biomaterial blends in which ELRs have a key role. This review aims to give an overview of the recent advances regarding ELRs and to encourage further investigation of their properties and applications.
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Affiliation(s)
- Arturo Ibáñez-Fonseca
- BIOFORGE Lab, CIBER-BBN, University of Valladolid, Paseo de Belén 19, 47011 Valladolid, Spain
| | - Tatjana Flora
- BIOFORGE Lab, CIBER-BBN, University of Valladolid, Paseo de Belén 19, 47011 Valladolid, Spain
| | - Sergio Acosta
- BIOFORGE Lab, CIBER-BBN, University of Valladolid, Paseo de Belén 19, 47011 Valladolid, Spain
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Wunder T, Oh ZG, Mueller‐Cajar O. CO
2
‐fixing liquid droplets: Towards a dissection of the microalgal pyrenoid. Traffic 2019; 20:380-389. [DOI: 10.1111/tra.12650] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Tobias Wunder
- School of Biological SciencesNanyang Technological University Singapore
| | - Zhen Guo Oh
- School of Biological SciencesNanyang Technological University Singapore
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