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Tolmachev DA, Malkamäki M, Linder MB, Sammalkorpi M. Spidroins under the Influence of Alcohol: Effect of Ethanol on Secondary Structure and Molecular Level Solvation of Silk-Like Proteins. Biomacromolecules 2023; 24:5638-5653. [PMID: 38019577 PMCID: PMC10716855 DOI: 10.1021/acs.biomac.3c00637] [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: 06/29/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
Future sustainable materials based on designer biomolecules require control of the solution assembly, but also interfacial interactions. Alcohol treatments of protein materials are an accessible means to this, making understanding of the process at the molecular level of seminal importance. We focus here on the influence of ethanol on spidroins, the main proteins of silk. By large-scale atomistically detailed molecular dynamics (MD) simulations and interconnected experiments, we characterize the protein aggregation, secondary structure changes, molecular level origins of them, and solvation environment changes for the proteins, as induced by ethanol as a solvation additive. The MD and circular dichoroism (CD) findings jointly show that ethanol promotes ordered structure in the protein molecules, leading to an increase of helix content and turns but also increased aggregation, as revealed by dynamic light scattering (DLS) and light microscopy. The structural changes correlate at the molecular level with increased intramolecular hydrogen bonding. The simulations reveal that polar amino acids, such as glutamine and serine, are most influenced by ethanol, whereas glycine residues are most prone to be involved in the ethanol-induced secondary structure changes. Furthermore, ethanol engages in interactions with the hydrophobic alanine-rich regions of the spidroin, significantly decreasing the hydrophobic interactions of the protein with itself and its surroundings. The protein solutes also change the microstructure of water/ethanol mixtures, essentially decreasing the level of larger local clustering. Overall, the work presents a systematic characterization of ethanol effects on a widely used, common protein type, spidroins, and generalizes the findings to other intrinsically disordered proteins by pinpointing the general features of the response. The results can aid in designing effective alcohol treatments for proteins, but also enable design and tuning of protein material properties by a relatively controllable solvation handle, the addition of ethanol.
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Affiliation(s)
- Dmitry A. Tolmachev
- Department
of Chemistry and Materials Science, Aalto
University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maaria Malkamäki
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Markus B. Linder
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department
of Chemistry and Materials Science, Aalto
University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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2
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Fedorov D, Roas-Escalona N, Tolmachev D, Harmat AL, Scacchi A, Sammalkorpi M, Aranko AS, Linder MB. Triblock Proteins with Weakly Dimerizing Terminal Blocks and an Intrinsically Disordered Region for Rational Design of Condensate Properties. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2306817. [PMID: 37964343 DOI: 10.1002/smll.202306817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Condensates are molecular assemblies that are formed through liquid-liquid phase separation and play important roles in many biological processes. The rational design of condensate formation and their properties is central to applications, such as biosynthetic materials, synthetic biology, and for understanding cell biology. Protein engineering is used to make a triblock structure with varying terminal blocks of folded proteins on both sides of an intrinsically disordered mid-region. Dissociation constants are determined in the range of micromolar to millimolar for a set of proteins suitable for use as terminal blocks. Varying the weak dimerization of terminal blocks leads to an adjustable tendency for condensate formation while keeping the intrinsically disordered region constant. The dissociation constants of the terminal domains correlate directly with the tendency to undergo liquid-liquid phase separation. Differences in physical properties, such as diffusion rate are not directly correlated with the strength of dimerization but can be understood from the properties and interplay of the constituent blocks. The work demonstrates the importance of weak interactions in condensate formation and shows a principle for protein design that will help in fabricating functional condensates in a predictable and rational way.
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Affiliation(s)
- Dmitrii Fedorov
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Nelmary Roas-Escalona
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Dmitry Tolmachev
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Adam L Harmat
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Alberto Scacchi
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Applied Physics, Aalto University, P.O. Box 11000, Aalto, FI-00076, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
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3
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Gabir H, Gupta M, Meier M, Heide F, Koch M, Stetefeld J, Demeler B. Investigation of dynamic solution interactions between NET-1 and UNC-5B by multi-wavelength analytical ultracentrifugation. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:473-481. [PMID: 36939874 PMCID: PMC10509325 DOI: 10.1007/s00249-023-01644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/21/2023]
Abstract
NET-1 is a key chemotropic ligand that signals commissural axon migration and change in direction. NET-1 and its receptor UNC-5B switch axon growth cones from attraction to repulsion. The biophysical properties of the NET-1 + UNC-5B complex have been poorly characterized. Using multi-wavelength-AUC by adding a fluorophore to UNC-5B, we were able to separate the UNC-5B sedimentation from NET-1. Using both multi-wavelength- and single-wavelength AUC, we investigated NET-1 and UNC-5B hydrodynamic parameters and complex formation. The sedimentation velocity experiments show that NET-1 exists in a monomer-dimer equilibrium. A close study of the association shows that NET-1 forms a pH-sensitive dimer that interacts in an anti-parallel orientation. UNC-5B can form equimolar NET-1 + UNC-5B heterocomplexes with both monomeric and dimeric NET-1.
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Affiliation(s)
- Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | | | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Manuel Koch
- Medical Faculty, Institute for Dental Research and Oral Musculoskeletal Biology, University of Cologne, Cologne, Germany
| | - Joerg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA.
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4
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Lemetti L, Scacchi A, Yin Y, Shen M, Linder MB, Sammalkorpi M, Aranko AS. Liquid-Liquid Phase Separation and Assembly of Silk-like Proteins is Dependent on the Polymer Length. Biomacromolecules 2022; 23:3142-3153. [PMID: 35796676 PMCID: PMC9364312 DOI: 10.1021/acs.biomac.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Phase transitions
have an essential role in the assembly of nature’s
protein-based materials into hierarchically organized structures,
yet many of the underlying mechanisms and interactions remain to be
resolved. A central question for designing proteins for materials
is how the protein architecture and sequence affects the nature of
the phase transitions and resulting assembly. In this work, we produced
82 kDa (1×), 143 kDa (2×), and 204 kDa (3×) silk-mimicking
proteins by taking advantage of protein ligation by SpyCatcher/Tag
protein-peptide pair. We show that the three silk proteins all undergo
a phase transition from homogeneous solution to assembly formation.
In the assembly phase, a length- and concentration-dependent transition
between two distinct assembly morphologies, one forming aggregates
and another coacervates, exists. The coacervates showed properties
that were dependent on the protein size. Computational modeling of
the proteins by a bead-spring model supports the experimental results
and provides us a possible mechanistic origin for the assembly transitions
based on architectures and interactions.
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Affiliation(s)
- Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Alberto Scacchi
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland.,Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Department of Applied Physics, School of Science, Aalto University, Otakaari 1, Espoo 02150, Finland
| | - Yin Yin
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Mengjie Shen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, Department of Chemistry and Materials Science, and Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), School of Chemical Engineering, Aalto University, Espoo, 02150, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
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5
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Jayawardena HSN, Liyanage SH, Rathnayake K, Patel U, Yan M. Analytical Methods for Characterization of Nanomaterial Surfaces. Anal Chem 2021; 93:1889-1911. [PMID: 33434434 PMCID: PMC7941215 DOI: 10.1021/acs.analchem.0c05208] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- H Surangi N Jayawardena
- Department of Chemistry, The University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
| | - Sajani H Liyanage
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Kavini Rathnayake
- Department of Chemistry, The University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
| | - Unnati Patel
- Department of Chemistry, The University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
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6
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Batys P, Fedorov D, Mohammadi P, Lemetti L, Linder MB, Sammalkorpi M. Self-Assembly of Silk-like Protein into Nanoscale Bicontinuous Networks under Phase-Separation Conditions. Biomacromolecules 2021; 22:690-700. [PMID: 33406825 DOI: 10.1021/acs.biomac.0c01506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liquid-liquid phase separation of biomacromolecules is crucial in various inter- and extracellular biological functions. This includes formation of condensates to control, e.g., biochemical reactions and structural assembly. The same phenomenon is also found to be critically important in protein-based high-performance biological materials. Here, we use a well-characterized model triblock protein system to demonstrate the molecular level formation mechanism and structure of its condensate. Large-scale molecular modeling supported by analytical ultracentrifuge characterization combined with our earlier high magnification precision cryo-SEM microscopy imaging leads to deducing that the condensate has a bicontinuous network structure. The bicontinuous network rises from the proteins having a combination of sites with stronger mutual attraction and multiple weakly attractive regions connected by flexible, multiconfigurational linker regions. These attractive sites and regions behave as stickers of varying adhesion strength. For the examined model triblock protein construct, the β-sheet-rich end units are the stronger stickers, while additional weaker stickers, contributing to the condensation affinity, rise from spring-like connections in the flexible middle region of the protein. The combination of stronger and weaker sticker-like connections and the flexible regions between the stickers result in a versatile, liquid-like, self-healing structure. This structure also explains the high flexibility, easy deformability, and diffusion of the proteins, decreasing only 10-100 times in the bicontinuous network formed in the condensate phase in comparison to dilute protein solution. The here demonstrated structure and condensation mechanism of a model triblock protein construct via a combination of the stronger binding regions and the weaker, flexible sacrificial-bond-like network as well as its generalizability via polymer sticker models provide means to not only understand intracellular organization, regulation, and cellular function but also to identify direct control factors for and to enable engineering improved protein and polymer constructs to enhance control of advanced fiber materials, smart liquid biointerfaces, or self-healing matrices for pharmaceutics or bioengineering materials.
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Affiliation(s)
- Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Dmitrii Fedorov
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., FI-02044 Espoo, Finland
| | - Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.,Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
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