1
|
Britton D, Christians LF, Liu C, Legocki J, Xiao Y, Meleties M, Yang L, Cammer M, Jia S, Zhang Z, Mahmoudinobar F, Kowalski Z, Renfrew PD, Bonneau R, Pochan DJ, Pak AJ, Montclare JK. Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure. Biomacromolecules 2024; 25:258-271. [PMID: 38110299 PMCID: PMC10777397 DOI: 10.1021/acs.biomac.3c00968] [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: 09/12/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled-coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled-coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled-coil fiber formation.
Collapse
Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Luc F. Christians
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Lin Yang
- National
Synchrotron Light Source-II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Michael Cammer
- Microscopy
Laboratory, New York University Langone
Health, New York, New York 10016, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Zihan Zhang
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Farbod Mahmoudinobar
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center for
Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
| | - Zuzanna Kowalski
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - P. Douglas Renfrew
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Richard Bonneau
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center
for Genomics and Systems Biology, New York
University, New York, New York 10003, United States
- Courant
Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Darrin J. Pochan
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Alexander J. Pak
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomedical Engineering, New
York University, New York, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department
of Radiology, New York University School
of Medicine, New York, New York 10016, United States
- Department of Biomaterials, New York University
College of Dentistry, New York, New York 10010, United States
| |
Collapse
|
2
|
Eslami H, Materzok T, Müller-Plathe F. Molecular Structure and Dynamics in Wet Gecko β-Keratin. ACS Biomater Sci Eng 2023; 9:257-268. [PMID: 36525337 DOI: 10.1021/acsbiomaterials.2c01022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular dynamics simulations are performed to investigate the molecular picture of water sorption in gecko keratin and the influence of relative humidity (RH) on the local structure and dynamics in water-swollen keratin. At low RHs, water sorption occurs through hydrogen bonding of water with the hydrophilic groups of keratin. At high RHs (>80%), additional water molecules connect to the first "layer" of amide-connected water molecules (multimolecular sorption) through hydrogen bonds, giving rise to a sigmoidal shape of the sorption isotherm. This causes the formation of large chain-like clusters surrounding the hydrophilic groups of keratin, which upon a further increase of the RH form a percolating water network. An examination of the dynamics of water molecules sorbed in keratin demonstrates that there are two states, bound and free, for water. The dynamics of water in these states depends on the RH. At low RHs, large-scale translational motions of tightly bound water molecules to keratin are needed to remake the entire hydration shell of the keratin. At high RHs (>80%), the water molecules more quickly exchange between the two states. The center-of-mass mean-square displacement of water molecules indicates a hopping motion of water molecules in the keratin solvation shell. The hopping mechanism is more pronounced at RHs < 80%. At higher RHs, water translation through water clusters (water network) dominates. We have observed two regimes for the dependence of dynamical properties on the RH: a regime of gradual increase of the dynamics over 10% < RH < 80% and a regime of drastic dynamic acceleration at RH > 80%. The latter regime begins exactly where the water uptake and the volume swelling also increase much more and where a drastic change in the elastic properties of gecko keratin has been observed. A nearly linear relation between the relaxation times for all dynamical processes and the water content of gecko keratin is observed.
Collapse
Affiliation(s)
- Hossein Eslami
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, Darmstadt64287, Germany.,Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr75168, Iran
| | - Tobias Materzok
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, Darmstadt64287, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, Darmstadt64287, Germany
| |
Collapse
|
3
|
Fast and reversible crosslinking of a silk elastin-like polymer. Acta Biomater 2022; 141:14-23. [PMID: 34971785 PMCID: PMC8898266 DOI: 10.1016/j.actbio.2021.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Elastin-like polymers (ELPs) and their chimeric subfamily the silk elastin-like polymers (SELPs) exhibit a lower critical solvation temperature (LCST) behavior in water which has been extensively studied from theoretical, computational and experimental perspectives. The inclusion of silk domains in the backbone of the ELPs effects the molecular dynamics of the elastin-like domains in response to increased temperature above its transition temperature and confers gelation ability. This response has been studied in terms of initial and long-term changes in structures, however, intermediate transition states have been less investigated. Moreover, little is known about the effects of reversible hydration on the elastin versus silk domains in the physical crosslinks. We used spectroscopic techniques to analyze initial, intermediate and long-term states of the crosslinks in SELPs. A combination of thermoanalytical and rheological measurements demonstrated that the fast reversible rehydration of the elastin motifs adjacent to the relatively small silk domains was capable of breaking the silk physical crosslinks. This feature can be exploited to tailor the dynamics of these types of crosslinks in SELPs. STATEMENT OF SIGNIFICANCE: The combination of silk and elastin in a single molecule results in synergy via their interactions to impact the protein polymer properties. The ability of the silk domains to crosslink affects the thermoresponsive properties of the elastin domains. These interactions have been studied at early and late states of the physical crosslinking, while the intermediate states were the focus of the present study to understand the reversible phase-transitions of the elastin domains over the silk physical crosslinking. The thermoresponsive properties of the elastin domains at the initial, intermediate and late states of silk crosslinking were characterized to demonstrate that reversible hydration of the elastin domains influenced the reversibility of the silk crosslinks.
Collapse
|
4
|
Gonzalez-Obeso C, Backlund FG, Kaplan DL. Charge-Modulated Accessibility of Tyrosine Residues for Silk-Elastin Copolymer Cross-Linking. Biomacromolecules 2022; 23:760-765. [PMID: 35113522 PMCID: PMC9211056 DOI: 10.1021/acs.biomac.1c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The modulation of reaction kinetics with horseradish peroxidase (HRP)-catalyzed cross-linking of proteins remains a useful strategy to modulate hydrogel formation. Here, we demonstrate that the presence of positively charged lysines in silk-elastin-like polymers impacts the thermal transition temperature of these proteins, while the location in the primary sequence modulates the reactivity of the tyrosines. The positively charged lysine side chains decreased π-π interactions among the tyrosines and reduced the rate of formation and number of HRP-mediated dityrosine bonds, dependent on the proximity of the charged group to the tyrosine. The results suggest that the location of repulsive charges can be used to tailor the reaction kinetics for enzymatic cross-linking, providing further control of gelation rates for in situ gel formation and the resulting protein-based gel characteristics.
Collapse
Affiliation(s)
- Constancio Gonzalez-Obeso
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
| | - Fredrik G Backlund
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
| |
Collapse
|
5
|
Shi H, Ji T, Zhai C, Lu J, Huang W, Yeo J. Thermo- and Ion-responsive Silk-elastin-like Proteins and Their Multiscale Mechanisms. J Mater Chem B 2022; 10:6133-6142. [DOI: 10.1039/d2tb01002j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silk-elastin-like protein (SELP) is an excellent biocompatible and biodegradable material for hydrogels with tunable properties that can respond to multiple external stimuli. By integrating fully atomistic, replica exchange molecular dynamics...
Collapse
|
6
|
Rodriguez-Cabello JC, Gonzalez De Torre I, González-Pérez M, González-Pérez F, Montequi I. Fibrous Scaffolds From Elastin-Based Materials. Front Bioeng Biotechnol 2021; 9:652384. [PMID: 34336798 PMCID: PMC8323661 DOI: 10.3389/fbioe.2021.652384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022] Open
Abstract
Current cutting-edge strategies in biomaterials science are focused on mimicking the design of natural systems which, over millions of years, have evolved to exhibit extraordinary properties. Based on this premise, one of the most challenging tasks is to imitate the natural extracellular matrix (ECM), due to its ubiquitous character and its crucial role in tissue integrity. The anisotropic fibrillar architecture of the ECM has been reported to have a significant influence on cell behaviour and function. A new paradigm that pivots around the idea of incorporating biomechanical and biomolecular cues into the design of biomaterials and systems for biomedical applications has emerged in recent years. Indeed, current trends in materials science address the development of innovative biomaterials that include the dynamics, biochemistry and structural features of the native ECM. In this context, one of the most actively studied biomaterials for tissue engineering and regenerative medicine applications are nanofiber-based scaffolds. Herein we provide a broad overview of the current status, challenges, manufacturing methods and applications of nanofibers based on elastin-based materials. Starting from an introduction to elastin as an inspiring fibrous protein, as well as to the natural and synthetic elastin-based biomaterials employed to meet the challenge of developing ECM-mimicking nanofibrous-based scaffolds, this review will follow with a description of the leading strategies currently employed in nanofibrous systems production, which in the case of elastin-based materials are mainly focused on supramolecular self-assembly mechanisms and the use of advanced manufacturing technologies. Thus, we will explore the tendency of elastin-based materials to form intrinsic fibers, and the self-assembly mechanisms involved. We will describe the function and self-assembly mechanisms of silk-like motifs, antimicrobial peptides and leucine zippers when incorporated into the backbone of the elastin-based biomaterial. Advanced polymer-processing technologies, such as electrospinning and additive manufacturing, as well as their specific features, will be presented and reviewed for the specific case of elastin-based nanofiber manufacture. Finally, we will present our perspectives and outlook on the current challenges facing the development of nanofibrous ECM-mimicking scaffolds based on elastin and elastin-like biomaterials, as well as future trends in nanofabrication and applications.
Collapse
Affiliation(s)
- Jose Carlos Rodriguez-Cabello
- BIOFORGE, University of Valladolid, Valladolid, Spain
- Center for Biomedical Research in the Network in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Israel Gonzalez De Torre
- BIOFORGE, University of Valladolid, Valladolid, Spain
- Center for Biomedical Research in the Network in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Miguel González-Pérez
- BIOFORGE, University of Valladolid, Valladolid, Spain
- Center for Biomedical Research in the Network in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Fernando González-Pérez
- BIOFORGE, University of Valladolid, Valladolid, Spain
- Center for Biomedical Research in the Network in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Irene Montequi
- BIOFORGE, University of Valladolid, Valladolid, Spain
- Center for Biomedical Research in the Network in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| |
Collapse
|
7
|
López Barreiro D, Minten IJ, Thies JC, Sagt CMJ. Structure-Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies. ACS Biomater Sci Eng 2021. [PMID: 34251181 DOI: 10.1021/acsbiomaterials.1c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor tropoelastin, a 60-72 kDa water-soluble and temperature-responsive protein that coacervates at physiological temperature, undergoing a phenomenon termed lower critical solution temperature (LCST). Inspired by this behavior, many scientists and engineers are developing recombinantly produced elastin-inspired biopolymers, usually termed elastin-like polypeptides (ELPs). These ELPs are generally comprised of repetitive motifs with the sequence VPGXG, which corresponds to repeats of a small part of the tropoelastin sequence, X being any amino acid except proline. ELPs display LCST and mechanical properties similar to tropoelastin, which renders them promising candidates for the development of elastic and stimuli-responsive protein-based materials. Unveiling the structure-property relationships of ELPs can aid in the development of these materials by establishing the connections between the ELP amino acid sequence and the macroscopic properties of the materials. Here we present a review of the structure-property relationships of ELPs and ELP-based materials, with a focus on LCST and mechanical properties and how experimental and computational studies have aided in their understanding.
Collapse
Affiliation(s)
- Diego López Barreiro
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Inge J Minten
- DSM Materials Science Center - Applied Science Center, DSM, Urmonderbaan 22, 6160 BB, Geleen, The Netherlands
| | - Jens C Thies
- DSM Biomedical, DSM, Koestraat 1, 6167 RA, Geleen, The Netherlands
| | - Cees M J Sagt
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| |
Collapse
|
8
|
Zhou S, Jin K, Buehler MJ. Understanding Plant Biomass via Computational Modeling. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2003206. [PMID: 32945027 DOI: 10.1002/adma.202003206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Plant biomass, especially wood, has been used for structural materials since ancient times. It is also showing great potential for new structural materials and it is the major feedstock for the emerging biorefineries for building a sustainable society. The plant cell wall is a hierarchical matrix of mainly cellulose, hemicellulose, and lignin. Herein, the structure, properties, and reactions of cellulose, lignin, and wood cell walls, studied using density functional theory (DFT) and molecular dynamics (MD), which are the widely used computational modeling approaches, are reviewed. Computational modeling, which has played a crucial role in understanding the structure and properties of plant biomass and its nanomaterials, may serve a leading role on developing new hierarchical materials from biomass in the future.
Collapse
Affiliation(s)
- Shengfei Zhou
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave 1-290, Cambridge, MA, 02139, USA
| | - Kai Jin
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave 1-290, Cambridge, MA, 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave 1-290, Cambridge, MA, 02139, USA
| |
Collapse
|
9
|
Wang Y, Huang W, Wang Y, Mu X, Ling S, Yu H, Chen W, Guo C, Watson MC, Yu Y, Black LD, Li M, Omenetto FG, Li C, Kaplan DL. Stimuli-responsive composite biopolymer actuators with selective spatial deformation behavior. Proc Natl Acad Sci U S A 2020; 117:14602-14608. [PMID: 32522869 PMCID: PMC7322001 DOI: 10.1073/pnas.2002996117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bioinspired actuators with stimuli-responsive and deformable properties are being pursued in fields such as artificial tissues, medical devices and diagnostics, and intelligent biosensors. These applications require that actuator systems have biocompatibility, controlled deformability, biodegradability, mechanical durability, and stable reversibility. Herein, we report a bionic actuator system consisting of stimuli-responsive genetically engineered silk-elastin-like protein (SELP) hydrogels and wood-derived cellulose nanofibers (CNFs), which respond to temperature and ionic strength underwater by ecofriendly methods. Programmed site-selective actuation can be predicted and folded into three-dimensional (3D) origami-like shapes. The reversible deformation performance of the SELP/CNF actuators was quantified, and complex spatial transformations of multilayer actuators were demonstrated, including a biomimetic flower design with selective petal movements. Such actuators consisting entirely of biocompatible and biodegradable materials will offer an option toward constructing stimuli-responsive systems for in vivo biomedicine soft robotics and bionic research.
Collapse
Affiliation(s)
- Yushu Wang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Wenwen Huang
- Department of Orthopedics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- The Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Xuan Mu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Shengjie Ling
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Haipeng Yu
- Key laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Wenshuai Chen
- Key laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Chengchen Guo
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Matthew C Watson
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Yingjie Yu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Lauren D Black
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Meng Li
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | | | - Chunmei Li
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155;
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155;
| |
Collapse
|
10
|
Katyal P, Mahmoudinobar F, Montclare JK. Recent trends in peptide and protein-based hydrogels. Curr Opin Struct Biol 2020; 63:97-105. [PMID: 32512499 DOI: 10.1016/j.sbi.2020.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
Hydrogels are classic examples of biomaterials that have found its niche in biomedical and allied fields. Here, we describe examples of peptide-based and protein-based hydrogels with a focus on smart gels that respond to various stimuli including temperature, pH, light, and ionic strength. With the recent advancements in computational modeling, it has been possible to predict as well as design peptide and protein sequences that can assemble into hydrogels with unique and improved properties. We briefly discuss coarse grained and atomistic simulations in designing peptides that can form hydrogels. In addition, we highlight the trends that will influence the future design and applications of hydrogels, with emphasis on bioadhesion, exosomes delivery, tissue and organoids engineering, and even intracellular production of gels.
Collapse
Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA; Department of Radiology, New York University Langone Health, New York, NY, 10016, USA; Department of Biomaterials, New York University College of Dentistry, New York, NY, 10010, USA; Department of Chemistry, New York University, New York, NY 10003, USA.
| |
Collapse
|
11
|
Roberts EG, Rim NG, Huang W, Tarakanova A, Yeo J, Buehler MJ, Kaplan DL, Wong JY. Fabrication and Characterization of Recombinant Silk-Elastin-Like-Protein (SELP) Fiber. Macromol Biosci 2018; 18:e1800265. [PMID: 30417967 PMCID: PMC6960454 DOI: 10.1002/mabi.201800265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/28/2018] [Indexed: 11/06/2022]
Abstract
Silk-elastin-like-protein polymers (SELPs) are genetically engineered recombinant protein sequences consisting of repeating units of silk-like and elastin-like blocks. By combining these entities, it is shown that both the characteristic strength of silk and the temperature-dependent responsiveness of elastin can be leveraged to create an enhanced stimuli-responsive material. It is hypothesized that SELP behavior can be influenced by varying the silk-to-elastin ratio. If the responsiveness of the material at different ratios is significantly different, this would allow for the design of materials with specific temperature-based swelling and mechanical properties. This study demonstrates that SELP fiber properties can be controlled via a temperature transition dependent on the ratio of silk-to-elastin in the material. SELP fibers are experimentally wet spun from polymers with different ratios of silk-to-elastin and conditioned in either a below or above transition temperature (T t ) water bath prior to characterization. The fibers with higher elastin content showed more stimuli-responsive behavior compared to the fibers with lower elastin content in the hot (57-60 °C) versus cold (4-7 °C) environment, both computationally and experimentally. This work builds a foundation for developing SELP materials with well-characterized mechanical properties and responsive features.
Collapse
Affiliation(s)
- Erin G Roberts
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Nae-Gyune Rim
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Anna Tarakanova
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jingjie Yeo
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute of High Performance Computing, A∗STAR, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Joyce Y Wong
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| |
Collapse
|
12
|
López Barreiro D, Yeo J, Tarakanova A, Martin-Martinez FJ, Buehler MJ. Multiscale Modeling of Silk and Silk-Based Biomaterials-A Review. Macromol Biosci 2018; 19:e1800253. [PMID: 30375164 DOI: 10.1002/mabi.201800253] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/20/2018] [Indexed: 12/25/2022]
Abstract
Silk embodies outstanding material properties and biologically relevant functions achieved through a delicate hierarchical structure. It can be used to create high-performance, multifunctional, and biocompatible materials through mild processes and careful rational material designs. To achieve this goal, computational modeling has proven to be a powerful platform to unravel the causes of the excellent mechanical properties of silk, to predict the properties of the biomaterials derived thereof, and to assist in devising new manufacturing strategies. Fine-scale modeling has been done mainly through all-atom and coarse-grained molecular dynamics simulations, which offer a bottom-up description of silk. In this work, a selection of relevant contributions of computational modeling is reviewed to understand the properties of natural silk, and to the design of silk-based materials, especially combined with experimental methods. Future research directions are also pointed out, including approaches such as 3D printing and machine learning, that may enable a high throughput design and manufacturing of silk-based biomaterials.
Collapse
Affiliation(s)
- Diego López Barreiro
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA.,Institute of High Performance Computing, A*STAR, 1 Fusionopolis Way, Singapore, 138632, Singapore.,Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA, 02155, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Francisco J Martin-Martinez
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| |
Collapse
|
13
|
Huang W, Ling S, Li C, Omenetto FG, Kaplan DL. Silkworm silk-based materials and devices generated using bio-nanotechnology. Chem Soc Rev 2018; 47:6486-6504. [PMID: 29938722 PMCID: PMC6113080 DOI: 10.1039/c8cs00187a] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Silks are natural fibrous protein polymers that are spun by silkworms and spiders. Among silk variants, there has been increasing interest devoted to the silkworm silk of B. mori, due to its availability in large quantities along with its unique material properties. Silk fibroin can be extracted from the cocoons of the B. mori silkworm and combined synergistically with other biomaterials to form biopolymer composites. With the development of recombinant DNA technology, silks can also be rationally designed and synthesized via genetic control. Silk proteins can be processed in aqueous environments into various material formats including films, sponges, electrospun mats and hydrogels. The versatility and sustainability of silk-based materials provides an impressive toolbox for tailoring materials to meet specific applications via eco-friendly approaches. Historically, silkworm silk has been used by the textile industry for thousands of years due to its excellent physical properties, such as lightweight, high mechanical strength, flexibility, and luster. Recently, due to these properties, along with its biocompatibility, biodegradability and non-immunogenicity, silkworm silk has become a candidate for biomedical utility. Further, the FDA has approved silk medical devices for sutures and as a support structure during reconstructive surgery. With increasing needs for implantable and degradable devices, silkworm silk has attracted interest for electronics, photonics for implantable yet degradable medical devices, along with a broader range of utility in different device applications. This Tutorial review summarizes and highlights recent advances in the use of silk-based materials in bio-nanotechnology, with a focus on the fabrication and functionalization methods for in vitro and in vivo applications in the field of tissue engineering, degradable devices and controlled release systems.
Collapse
Affiliation(s)
- Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, USA.
| | | | | | | | | |
Collapse
|
14
|
Yeo J, Huang W, Tarakanova A, Zhang YW, Kaplan DL, Buehler MJ. Unraveling the Molecular Mechanisms of Thermo-responsive Properties of Silk-Elastin-Like Proteins by Integrating Multiscale Modeling and Experiment. J Mater Chem B 2018; 6:3727-3734. [PMID: 30467524 PMCID: PMC6241539 DOI: 10.1039/c8tb00819a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Adaptive hydrogels tailor-made from silk-elastin-like proteins (SELPs) possess excellent biocompatibility and biodegradability with properties that are tunable and responsive to multiple simultaneous external stimuli. To unravel the molecular mechanisms of their physical response to external stimuli in tandem with experiments, here we predict and measure the variation in structural properties as a function of temperature through coarse-grained (CG) modeling of individual and crosslinked SE8Y and S4E8Y molecules, which have ratios of 1:8 and 4:8 of silk to elastin blocks respectively. Extensive structural reshuffling in single SE8Y molecules led to the increased compactness of the structure, whereas S4E8Y molecules did not experience any significant changes as they already adopted very compact structures at low temperatures. Crosslinking of SE8Y molecules at high concentrations impeded their structural transition at high temperatures that drastically reduced the degree of deswelling through extensive suppression of the structural shuffling and the trapping of the molecules in high potential energy states due to inter-molecular constraints. This integrative experimental and computational understanding of the thermal response in single molecules of SELPs and their crosslinked networks should lead to further improvements in the properties of SELP hydrogels through predictive designs and their wider applications in biomaterials and tissue engineering.
Collapse
Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, ASTAR, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yong-Wei Zhang
- Institute of High Performance Computing, ASTAR, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
15
|
Yeo J, Jung GS, Martín-Martínez FJ, Ling S, Gu GX, Qin Z, Buehler MJ. Materials-by-Design: Computation, Synthesis, and Characterization from Atoms to Structures. PHYSICA SCRIPTA 2018; 93:053003. [PMID: 31866694 PMCID: PMC6924929 DOI: 10.1088/1402-4896/aab4e2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In the 50 years that succeeded Richard Feynman's exposition of the idea that there is "plenty of room at the bottom" for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.
Collapse
Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Gang Seob Jung
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francisco J. Martín-Martínez
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shengjie Ling
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Grace X. Gu
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
16
|
Genin GM, Shenoy VB, Peng G, Buehler MJ. Integrated Multiscale Biomaterials Experiment and Modeling. ACS Biomater Sci Eng 2017; 3:2628-2632. [PMID: 31157296 PMCID: PMC6544164 DOI: 10.1021/acsbiomaterials.7b00821] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The integration of modeling and experimentation is an integral component of all engineering design. Developing the technologies to achieve this represents a critical challenge in biomaterials because of the hierarchical structures that comprise them and the spectra of timescales upon which they operate. Progress in integrating modeling and experiment in biomaterials represents progress towards harnessing them for engineering application. We present here a summary of the state of the art, and outlooks for the field as a whole.
Collapse
Affiliation(s)
- Guy M Genin
- Department of Mechanical Engineering and Materials Science, 1 Brookings Drive, Washington University in St. Louis, St. Louis, MO 63130 United States
- NSF Science and Technology Center for Engineering Mechanobiology, 1 Brookings Drive, Washington University in St. Louis, St. Louis, MO 63130 United States
| | - Vivek B Shenoy
- Department of Materials Science and Engineering, University of Pennsylvania, 220 South 33rd Street, Philadelphia, PA 19104-6391 United States
- NSF Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, 220 South 33rd Street, Philadelphia, PA 19104-6391 United States
| | - Grace Peng
- National Institute of Biomedical Imaging and Bioengineering, 6707 Democracy Boulevard, Suite 202, Bethesda, MD 20892-5469 United States
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|