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Saccuzzo EG, Robang AS, Gao Y, Chen B, Lieberman RL, Paravastu AK. Evidence for S 331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.606901. [PMID: 39149386 PMCID: PMC11326258 DOI: 10.1101/2024.08.09.606901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Myocilin-associated glaucoma is a protein-conformational disorder associated with formation of a toxic amyloid-like aggregate. Numerous destabilizing single point variants, distributed across the myocilin olfactomedin β-propeller (OLF, myocilin residues 245-504, 30 kDa) are associated with accelerated disease progression. In vitro, wild type (WT) OLF can be promoted to form thioflavin T (ThT)-positive fibrils under mildly destabilizing (37°C, pH 7.2) conditions. Consistent with the notion that only a small number of residues within a protein are responsible for amyloid formation, 3D 13C-13C solid-state NMR spectra show that OLF fibrils are likely to be composed of only about one third of the overall sequence. Here, we probe the residue composition of fibrils formed de novo from purified full-length OLF. We were able to make sequential assignments consistent with the sequence S331-G-S-L334. This sequence appears once within a previously identified amyloid-prone region (P1, G326AVVYSGSLYFQ) internal to OLF. Since nearly half of the pairs of adjacent residues (di-peptides) in OLF occur only once in the primary structure and almost all the 3-residue sequences (tri-peptides) are unique, remarkably few sequential assignments are necessary to uniquely identify specific regions of the amyloid core. This assignment approach could be applied to other systems to expand our molecular comprehension of how folded proteins undergo fibrillization.
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Affiliation(s)
- Emily G Saccuzzo
- School of Chemistry & Biochemistry and Georgia Institute of Technology, Atlanta, GA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, FL
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry and Georgia Institute of Technology, Atlanta, GA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
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2
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Mathes TG, Monirizad M, Ermis M, de Barros NR, Rodriguez M, Kraatz HB, Jucaud V, Khademhosseini A, Falcone N. Effects of amyloid-β-mimicking peptide hydrogel matrix on neuronal progenitor cell phenotype. Acta Biomater 2024; 183:89-100. [PMID: 38801867 PMCID: PMC11239292 DOI: 10.1016/j.actbio.2024.05.020] [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: 11/23/2023] [Revised: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Self-assembling peptide-based hydrogels have become a highly attractive scaffold for three-dimensional (3D) in vitro disease modeling as they provide a way to create tunable matrices that can resemble the extracellular matrix (ECM) of various microenvironments. Alzheimer's disease (AD) is an exceptionally complex neurodegenerative condition; however, our understanding has advanced due to the transition from two-dimensional (2D) to 3D in vitro modeling. Nonetheless, there is a current gap in knowledge regarding the role of amyloid structures, and previously developed models found long-term difficulty in creating an appropriate model involving the ECM and amyloid aggregates. In this report, we propose a multi-component self-assembling peptide-based hydrogel scaffold to mimic the amyloid-beta (β) containing microenvironment. Characterization of the amyloid-β-mimicking hydrogel (Col-HAMA-FF) reveals the formation of β-sheet structures as a result of the self-assembling properties of phenylalanine (Phe, F) through π-π stacking of the residues, thus mimicking the amyloid-β protein nanostructures. We investigated the effect of the amyloid-β-mimicking microenvironment on healthy neuronal progenitor cells (NPCs) compared to a natural-mimicking matrix (Col-HAMA). Our results demonstrated higher levels of neuroinflammation and apoptosis markers when NPCs were cultured in the amyloid-like matrix compared to a natural brain matrix. Here, we provided insights into the impact of amyloid-like structures on NPC phenotypes and behaviors. This foundational work, before progressing to more complex plaque models, provides a promising scaffold for future investigations on AD mechanisms and drug testing. STATEMENT OF SIGNIFICANCE: In this study, we engineered two multi-component hydrogels: one to mimic the natural extracellular matrix (ECM) of the brain and one to resemble an amyloid-like microenvironment using a self-assembling peptide hydrogel. The self-assembling peptide mimics β-amyloid fibrils seen in amyloid-β protein aggregates. We report on the culture of neuronal progenitor cells within the amyloid-mimicking ECM scaffold to study the impact through marker expressions related to inflammation and DNA damage. This foundational work, before progressing to more complex plaque models, offers a promising scaffold for future investigations on AD mechanisms and drug testing.
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Affiliation(s)
- Tess Grett Mathes
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA
| | - Mahsa Monirizad
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA
| | - Menekse Ermis
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA; BIOMATEN, Center of Excellence in Biomaterials and Tissue Engineering Middle East Technical University, Ankara 06800, Turkey
| | - Natan Roberto de Barros
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA
| | - Marco Rodriguez
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA
| | - Heinz-Bernhard Kraatz
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 2E4, Canada; Department of Physical and Environmental Science, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA.
| | - Natashya Falcone
- Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, CA, USA.
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3
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Thapa S, Clark F, Schneebeli ST, Li J. Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study. J Chem Theory Comput 2024; 20:375-384. [PMID: 38013425 PMCID: PMC11070933 DOI: 10.1021/acs.jctc.3c00699] [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] [Indexed: 11/29/2023]
Abstract
Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.
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Affiliation(s)
- Subhadra Thapa
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Finley Clark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Severin. T. Schneebeli
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
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4
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Sasselli IR, Coluzza I. Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly. J Chem Theory Comput 2024; 20:224-238. [PMID: 38113378 PMCID: PMC10782451 DOI: 10.1021/acs.jctc.3c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.
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Affiliation(s)
- Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Ivan Coluzza
- Ikerbasque,
Basque Foundation for Science, Plaza de Euskadi 5, 48009 Bilbao, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48940 Leioa, Spain
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5
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Dai K, Pol MD, Saile L, Sharma A, Liu B, Thomann R, Trefs JL, Qiu D, Moser S, Wiesler S, Balzer BN, Hugel T, Jessen HJ, Pappas CG. Spontaneous and Selective Peptide Elongation in Water Driven by Aminoacyl Phosphate Esters and Phase Changes. J Am Chem Soc 2023; 145:26086-26094. [PMID: 37992133 DOI: 10.1021/jacs.3c07918] [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: 11/24/2023]
Abstract
Nature chose phosphates to activate amino acids, where reactive intermediates and complex machinery drive the construction of polyamides. Outside of biology, the pathways and mechanisms that allow spontaneous and selective peptide elongation in aqueous abiotic systems remain unclear. Herein we work to uncover those pathways by following the systems chemistry of aminoacyl phosphate esters, synthetic counterparts of aminoacyl adenylates. The phosphate esters act as solubility tags, making hydrophobic amino acids and their oligomers soluble in water and enabling selective elongation and different pathways to emerge. Thus, oligomers up to dodecamers were synthesized in one flask and on the minute time scale, where consecutive additions activated autonomous phase changes. Depending on the pathway, the resulting phases initially carry nonpolar peptides and amphiphilic oligomers containing phosphate esters. During elongation and phosphate release, shorter oligomers dominate in solution, while the aggregated phase favors the presence of longer oligomers due to their self-assembly propensity. Furthermore we demonstrated that the solution phases can be isolated and act as a new environment for continuous elongation, by adding various phosphate esters. These findings suggest that the systems chemistry of aminoacyl phosphate esters can activate a selection mechanism for peptide bond formation by merging aqueous synthesis and self-assembly.
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Affiliation(s)
- Kun Dai
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Mahesh D Pol
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Lenard Saile
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Arti Sharma
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bin Liu
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang, Hubei 443002, China
| | - Ralf Thomann
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
| | - Johanna L Trefs
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sandra Moser
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Bizan N Balzer
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thorsten Hugel
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Charalampos G Pappas
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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6
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Monti M, Scarel E, Hassanali A, Stener M, Marchesan S. Diverging conformations guide dipeptide self-assembly into crystals or hydrogels. Chem Commun (Camb) 2023; 59:10948-10951. [PMID: 37605851 DOI: 10.1039/d3cc02682e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The prediction of dipeptide assembly into crystals or gels is challenging. This work reveals the diverging conformational landscape that guides self-organization towards different outcomes. In silico and experimental data enabled deciphering of the electronic circular dichroism (ECD) spectra of self-assembling dipeptides to reveal folded or extended conformers as key players.
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Affiliation(s)
- M Monti
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - E Scarel
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - A Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - M Stener
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - S Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
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7
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Hu T, Xu Y, Xu G. Dipeptide-polysaccharides hydrogels through co-assembly. Food Chem 2023; 422:136272. [PMID: 37141751 DOI: 10.1016/j.foodchem.2023.136272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Self-assembling dipeptide hydrogels are attracting attention in food, materials, and biomedicine. However, there are still limitations such as weak hydrogel properties. Herein, we introduced two types of polysaccharides (Arabic gum and citrus pectin) into an alkyl-chain modified dipeptide (C13-tryptophan-tyrosine (C13-WY)) to generate co-assembled C13-WY-arabic gum and C13-WY-pectin hydrogels. The co-assembled hydrogels exhibited enhanced mechanical properties and stability. The G' value of C13-WY-arabic gum and C13-WY-pectin hydrogels was 3 and 10 times larger than that of C13-WY hydrogel, respectively. The addition of Arabic gum and citrus pectin led to the co-assembly and molecular rearrangement. Moreover, co-assembled hydrogels showed more β-sheet structure and hydrogen bonds. Importantly, the self-/co-assembled hydrogels showed low cytotoxicity. We utilized these hydrogels for the encapsulation of docetaxel and they showed a high embedding rate and slow-release. Our findings provide a novel strategy for the development of stable supramolecular peptide hydrogels with good biocompatibility through simple co-assembly.
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Affiliation(s)
- Tan Hu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China.
| | - Yang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China
| | - Gang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China
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8
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La Manna S, Florio D, Panzetta V, Roviello V, Netti PA, Di Natale C, Marasco D. Hydrogelation tunability of bioinspired short peptides. SOFT MATTER 2022; 18:8418-8426. [PMID: 36300826 DOI: 10.1039/d2sm01385a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Supramolecular assemblies of short peptides are experiencing a stimulating flowering. Herein, we report a novel class of bioinspired pentapeptides, not bearing Phe, that form hydrogels with fibrillar structures. The inherent sequence comes from the fragment 269-273 of nucleophosmin 1 protein, that is normally involved in liquid-liquid phase separation processes into the nucleolus. By means of rheology, spectroscopy, and scanning microscopy the crucial roles of the extremities in the modulation of the mechanical properties of hydrogels were elucidated. Three of four peptide showed a typical shear-thinning profile and a self-assembly into hierarchical nanostructures fibers and two of them resulted biocompatible in MCF7 cells. The presence of an amide group at C-terminal extremity caused the fastest aggregation and the major content of structured intermediates during gelling process. The tunable mechanical and structural features of this class of hydrogels render derived supramolecular systems versatile and suitable for future biomedical applications.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
| | - Valeria Panzetta
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples "Federico II", 80125, Naples, Italy
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", 80125, Naples, Italy
- Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Valentina Roviello
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", 80125, Naples, Italy
| | - Paolo Antonio Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples "Federico II", 80125, Naples, Italy
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", 80125, Naples, Italy
- Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Concetta Di Natale
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples "Federico II", 80125, Naples, Italy
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", 80125, Naples, Italy
- Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
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9
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Self-Assembly and Gelation Study of Dipeptide Isomers with Norvaline and Phenylalanine. CHEMISTRY 2022. [DOI: 10.3390/chemistry4040093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dipeptides have emerged as attractive building blocks for supramolecular materials thanks to their low-cost, inherent biocompatibility, ease of preparation, and environmental friendliness as they do not persist in the environment. In particular, hydrophobic amino acids are ideal candidates for self-assembly in polar and green solvents, as a certain level of hydrophobicity is required to favor their aggregation and reduce the peptide solubility. In this work, we analyzed the ability to self-assemble and the gel of dipeptides based on the amino acids norvaline (Nva) and phenylalanine (Phe), studying all their combinations and not yielding to enantiomers, which display the same physicochemical properties, and hence the same self-assembly behavior in achiral environments as those studied herein. A single-crystal X-ray diffraction of all the compounds revealed fine details over their molecular packing and non-covalent interactions.
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10
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The dynamic landscape of peptide activity prediction. Comput Struct Biotechnol J 2022; 20:6526-6533. [DOI: 10.1016/j.csbj.2022.11.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
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11
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Shen X, Qu F, Pei Y, Lei S, Xia S, Liang J, Li S, Sun X, Liu L. Repairing sciatic nerve injury with self-assembling peptide nanofiber scaffold-containing chitosan conduit. Front Neurol 2022; 13:867711. [PMID: 36313506 PMCID: PMC9612716 DOI: 10.3389/fneur.2022.867711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background An increasing number of nerve guide scaffolds have been used to replace the “gold-standard” autologous nerve graft for repairing peripheral nerve defects, but nerve regeneration is usually far from complete. Methods Here, we designed and prepared two functionalized self-assembling peptides (SAP) with the IKVAV and KLT sequences, which were derived from the combination of laminin and VEGF, respectively. Their mixtures were also obtained to combine the effects of neuroprotective and neurotrophic and proangiogenic factors. Results The beneficial effect of peptide gels on nerve regeneration was evaluated in vitro using Schwann cells (SCs). As a useful intraluminal filling, a three-dimensional (3D) functionalized self-assembling peptide (SAP) nanofiber hydrogel was formed in the hollow lumen of chitosan conduits under physiological conditions. In vivo, the combination of the two functionalized SAP gels containing a chitosan nerve conduit significantly accelerated nerve healing and enhanced morphological repair. Conclusion Based on the current findings, the combined application of two functionalized SAP gels with chitosan nerve conduit is a promising therapy for the engineering of peripheral nerve regeneration.
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Affiliation(s)
- Xuezhen Shen
- Department of Orthopedics, Beijing Luhe Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Feng Qu
- Foot and Ankle Surgery Center, Beijing Tongren Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Yilun Pei
- Department of Orthopedics, Beijing Luhe Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Simeng Lei
- Department of Orthopedics, Beijing Luhe Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Suhang Xia
- Department of Orthopedics, Beijing Luhe Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Jing Liang
- Department of Pediatrics, Tianjin Hospital, Tianjin University, Tianjin, China
| | - Shan Li
- Department of Pediatrics, Tianjin Hospital, Tianjin University, Tianjin, China
| | - Xun Sun
- Department of Orthopedics, Tianjin Hospital, Tianjin University, Tianjin, China
- *Correspondence: Xun Sun
| | - Liang Liu
- Department of Orthopedics, Beijing Luhe Hospital, Affiliated to Capital Medical University, Beijing, China
- Liang Liu
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12
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Biswas S, Vasudevan A, Yadav N, Yadav S, Rawal P, Kaur I, Tripathi DM, Kaur S, Chauhan VS. Chemically Modified Dipeptide Based Hydrogel Supports Three-Dimensional Growth and Functions of Primary Hepatocytes. ACS APPLIED BIO MATERIALS 2022; 5:4354-4365. [PMID: 35994753 DOI: 10.1021/acsabm.2c00526] [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] [Indexed: 11/29/2022]
Abstract
A huge shortage of organ donors, particularly in the case of liver, has necessitated the development of alternative therapeutic strategies. Primary hepatocytes (pHCs) transplantation has made a considerable transition from bench to bedside, but the short-term viability and functionality of pHCs in in vitro limit their use for clinical applications. Different cell culture strategies are required to maintain the proliferation of pHCs for extended periods. Here, we described the formation of a hybrid scaffold based on a modified dipeptide for the culture of pHCs. First, the dipeptide (Dp), isoleucine-α,β-dehydrophenylalanine (IΔF) was synthesized, purified, and fully characterized. IΔF readily formed a highly stable hydrogel, which was also characterized by CD, TEM, and thioflavin T assay. The addition of soluble liver extracellular matrix (sLEM) to the dipeptide readily formed a hybrid scaffold that was characterized by TEM, and its mechanical strength was determined by rheology experiments. The hybrid scaffold was translucent, biocompatible, and proteolytically stable and, with its mechanical strength, closely mimicked that of the native liver. LEM1-Dp matrix exhibited high biocompatibility in the readily available adherent liver cell line Huh7 and primary rat hepatocyte cells (pHCs). pHCs cultured on LEM1-Dp matrix also maintained significantly higher cell viability and an escalated expression of markers related to the hepatocytes such as albumin as compared to that observed in cells cultured on collagen type I (Col I)-coated substrate plate (col-TCTP). Z-stacking of confocal laser microscopy's volume view clearly indicated pHCs seeded on top of the hydrogel matrix migrated toward the Z direction showing 3D growth. Our results indicated that low molecular weight dipeptide hydrogel along with sLEM can resemble biomimetic 3D-like microenvironments for improved pHCs proliferation, differentiation, and function. This hybrid scaffold is also easy to scale up, which makes it suitable for several downstream applications of hepatocytes, including drug development, pHCs transplantation, and liver regeneration.
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Affiliation(s)
- Saikat Biswas
- International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi 110067, India
| | - Ashwini Vasudevan
- Institute of Liver and Biliary Sciences, New Delhi, Delhi 110070, India
| | - Nitin Yadav
- International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi 110067, India
| | - Saurabh Yadav
- International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi 110067, India
| | - Preety Rawal
- Institute of Liver and Biliary Sciences, New Delhi, Delhi 110070, India
| | - Impreet Kaur
- Institute of Liver and Biliary Sciences, New Delhi, Delhi 110070, India
| | - Dinesh M Tripathi
- Institute of Liver and Biliary Sciences, New Delhi, Delhi 110070, India
| | - Savneet Kaur
- Institute of Liver and Biliary Sciences, New Delhi, Delhi 110070, India
| | - Virander Singh Chauhan
- International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi 110067, India
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13
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Hu T, Xu Y, Xu G, Pan S. Sequence-Selected C 13-Dipeptide Self-Assembled Hydrogels for Encapsulation of Lemon Essential Oil with Antibacterial Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7148-7157. [PMID: 35657010 DOI: 10.1021/acs.jafc.2c02385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Supramolecular self-assembling peptide hydrogels are attracting attention. The switching of even one amino acid may lead to differences in structure and functions of peptide hydrogels. Herein, we investigate the effect of substitution of a single amino acid residue on the gelation properties of C13-dipeptide hydrogels. We show that four C13-R1Y (C13-VY, C13-FY, C13-WY, and C13-YY) can form hydrogels with drastically tunable rigidity (the G' values were 5.74, 0.16, 27.74, and 67.90 KPa, respectively). Moreover, C13-WY and C13-YY hydrogels with high stability and excellent mechanical properties formed β-sheet nanofiber cross-linked networks. Furthermore, we applied four hydrogels into encapsulation of lemon essential oil (LEO). The peptide hydrogels had a high encapsulation rate and slowly released the LEO. Importantly, the LEO-loaded hydrogels showed enhanced antibacterial activity than free LEO. Our results clearly demonstrate the significance of side-chain interactions in determining hydrogel properties and their potential application in encapsulation for nutrition agents and hydrophobic drugs.
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Affiliation(s)
- Tan Hu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Yang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Gang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
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14
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Bellotto O, Pierri G, Rozhin P, Polentarutti M, Kralj S, D'Andrea P, Tedesco C, Marchesan S. Dipeptide self-assembly into water-channels and gel biomaterial. Org Biomol Chem 2022; 20:6211-6218. [PMID: 35575102 DOI: 10.1039/d2ob00622g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dipeptides are convenient building blocks for supramolecular gel biomaterials that can be produced on a large scale at low cost and do not persist in the environment. In the case of unprotected sequences, hydrophobicity is a key requirement to enable gelation, with Phe-Phe standing out for its self-assembling ability. Conversely, more hydrophilic sequences such as homochiral dipeptides Phe-Val and Val-Phe neither fibrillate nor gel aqueous buffers and their crystal structures reveal amphipathic layers. In this work, we test emerging rules for the design of self-assembling dipeptides using heterochiral Phe-Val and Val-Phe. Each dipeptide is characterized by 1H- and 13C-NMR, LC-MS, circular dichroism, infrared and Raman spectroscopies, rheology, electron microscopy, and single-crystal X-ray diffraction. In particular, D-Phe-L-Val is the first heterochiral dipeptide to self-assemble into supramolecular water-channels whose cavity is defined by four peptide molecules arranged head-to-tail. This minimalistic sequence is devoid of amyloid character as probed by thioflavin T fluorescence and it displays excellent biocompatibility in vitro. The dataset provided, through comparison with the literature, significantly advances the definition of molecular design rules for minimalistic unprotected dipeptides that self-assemble into water-channels and biocompatible gels, to assist with the future development of supramolecular biomaterials with fine control over nanomorphological features for a variety of applications.
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Affiliation(s)
- Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Giovanni Pierri
- University of Salerno, Dept. of Chemistry & Biologi "A. Zambelli", Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy.
| | - Petr Rozhin
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | | | - Slavko Kralj
- Jožef Stefan Institute, Materials Synthesis Dept., Jamova 39, 1000 Ljubljana, Slovenia.,University of Ljubljana, Pharmaceutical Technology Dept., Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Paola D'Andrea
- University of Trieste, Life Sciences Dept., Via L. Giorgieri 5, 34127 Trieste, Italy
| | - Consiglia Tedesco
- University of Salerno, Dept. of Chemistry & Biologi "A. Zambelli", Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy.
| | - Silvia Marchesan
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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15
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Scarel E, Bellotto O, Rozhin P, Kralj S, Tortora M, Vargiu AV, De Zorzi R, Rossi B, Marchesan S. Single-atom substitution enables supramolecular diversity from dipeptide building blocks. SOFT MATTER 2022; 18:2129-2136. [PMID: 35179536 DOI: 10.1039/d1sm01824h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by 1H- and 13C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.
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Affiliation(s)
- Erica Scarel
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Petr Rozhin
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Slavko Kralj
- Jožef Stefan Institute, Materials Synthesis Dept., Jamova 39, 1000 Ljubljana, Slovenia
- University of Ljubljana, Pharmaceutical Technology Dept., Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Mariagrazia Tortora
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Attilio V Vargiu
- University of Cagliari, Physics Dept., 09042 Monserrato, Cagliari, Italy
| | - Rita De Zorzi
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Silvia Marchesan
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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16
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Sivagnanam S, Das K, Basak M, Mahata T, Stewart A, Maity B, Das P. Self-assembled dipeptide based fluorescent nanoparticles as a platform for developing cellular imaging probes and targeted drug delivery chaperones. NANOSCALE ADVANCES 2022; 4:1694-1706. [PMID: 36134376 PMCID: PMC9417502 DOI: 10.1039/d1na00885d] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/13/2022] [Indexed: 06/16/2023]
Abstract
Self-assembled peptide-based nanostructures, comprised of naturally occurring amino acids, display excellent biocompatibility, biodegradability, flexible responsiveness, and synthetic feasibility and can be customized for various biomedical applications. However, the lack of inherent optical properties of peptide-based nanoparticles is a limitation on their use as imaging probes or drug delivery vehicles. To overcome this impediment, we generated Boc protected tyrosine-tryptophan dipeptide-based nanoparticles (DPNPs) with structure rigidification by Zn(ii), which shifted the peptide's intrinsic fluorescent properties from the ultraviolet to the visible range. These DPNPs are photostable, biocompatible and have visible fluorescence signals that allow for real-time monitoring of their entry into cells. We further show that two DPNPs (PS1-Zn and PS2-Zn) can encapsulate the chemotherapeutic drug doxorubicin (Dox) and facilitate intracellular drug delivery resulting in cancer cell killing actions comparable to the unencapsulated drug. Finally, we chemically modified our DPNPs with an aptamer directed toward the epithelial cell surface marker EPCAM, which improved Dox delivery to the lung cancer epithelial cell line A549. In contrast, the aptamer conjugated DPNPs failed to deliver Dox into the cardiomyocyte cell line AC16. Theoretically, this strategy could be employed in vivo to specifically deliver Dox to cancer cells while sparing the myocardium, a major source of dose-limiting adverse events in the clinic. Our work represents an important proof-of-concept exercise demonstrating that ultra-short peptide-based fluorescent nanostructures have great promise for the development of new imaging probes and targeted drug delivery vehicles.
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Affiliation(s)
- Subramaniyam Sivagnanam
- Department of Chemistry, SRM Institute of Science and Technology SRM Nagar, Potheri, Kattankulathur Tamil Nadu 603203 India
| | - Kiran Das
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGI) Campus Raebareli Road Lucknow Uttar Pradesh 226014 India
| | - Madhuri Basak
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGI) Campus Raebareli Road Lucknow Uttar Pradesh 226014 India
| | - Tarun Mahata
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGI) Campus Raebareli Road Lucknow Uttar Pradesh 226014 India
| | - Adele Stewart
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University Jupiter FL 33458 USA
| | - Biswanath Maity
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGI) Campus Raebareli Road Lucknow Uttar Pradesh 226014 India
| | - Priyadip Das
- Department of Chemistry, SRM Institute of Science and Technology SRM Nagar, Potheri, Kattankulathur Tamil Nadu 603203 India
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17
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Multifunctional building elements for the construction of peptide drug conjugates. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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18
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Bao Y, Li Z, Li Y, Chen T, Cheng Y, Xu M. Recent Advances of Biomedical Materials for Prevention of Post-ESD Esophageal Stricture. Front Bioeng Biotechnol 2021; 9:792929. [PMID: 35004652 PMCID: PMC8727907 DOI: 10.3389/fbioe.2021.792929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Esophageal stricture commonly occurs in patients that have suffered from endoscopic submucosal dissection (ESD), and it makes swallowing difficult for patients, significantly reducing their life qualities. So far, the prevention strategies applied in clinical practice for post-ESD esophageal stricture usually bring various inevitable complications, which drastically counteract their effectiveness. Nowadays, with the widespread investigation and application of biomedical materials, lots of novel approaches have been devised in terms of the prevention of esophageal stricture. Biomedical polymers and biomedical-derived materials are the most used biomedical materials to prevent esophageal stricture after ESD. Both of biomedical polymers and biomedical-derived materials possess great physicochemical properties such as biocompatibility and biodegradability. Moreover, some biomedical polymers can be used as scaffolds to promote cell growth, and biomedical-derived materials have biological functions similar to natural organisms, so they are important in tissue engineering. In this review, we have summarized the current approaches for preventing esophageal stricture and put emphasis on the discussion of the roles biomedical polymers and biomedical-derived materials acted in esophageal stricture prevention. Meanwhile, we proposed several potential methods that may be highly rational and feasible in esophageal stricture prevention based on other researches associated with biomedical materials. This review is expected to offer a significant inspiration from biomedical materials to explore more effective, safer, and more economical strategies to manage post-ESD esophageal stricture.
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Affiliation(s)
- Yuchen Bao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhenguang Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yingze Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tao Chen
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu Cheng
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Meidong Xu
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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19
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Galzitskaya OV, Selivanova OM, Gorbunova EY, Mustaeva LG, Azev VN, Surin AK. Mechanism of Amyloid Gel Formation by Several Short Amyloidogenic Peptides. NANOMATERIALS 2021; 11:nano11113129. [PMID: 34835893 PMCID: PMC8621528 DOI: 10.3390/nano11113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022]
Abstract
Under certain conditions, many proteins/peptides are capable of self-assembly into various supramolecular formations: fibrils, films, amyloid gels. Such formations can be associated with pathological phenomena, for example, with various neurodegenerative diseases in humans (Alzheimer’s, Parkinson’s and others), or perform various functions in the body, both in humans and in representatives of other domains of life. Recently, more and more data have appeared confirming the ability of many known and, probably, not yet studied proteins/peptides, to self-assemble into quaternary structures. Fibrils, biofilms and amyloid gels are promising objects for the developing field of research of nanobiotechnology. To develop methods for obtaining nanobiomaterials with desired properties, it is necessary to study the mechanism of such structure formation, as well as the influence of various factors on this process. In this work, we present the results of a study of the structure of biogels formed by four 10-membered amyloidogenic peptides: the VDSWNVLVAG peptide (AspNB) and its analogue VESWNVLVAG (GluNB), which are amyloidogenic fragments of the glucantransferase Bgl2p protein from a yeast cell wall, and amyloidogenic peptides Aβ(31–40), Aβ(33–42) from the Aβ(1–42) peptide. Based on the analysis of the data, we propose a possible mechanism for the formation of amyloid gels with these peptides.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence: ; Tel.: +7-903-675-0156
| | - Olga M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
| | - Elena Y. Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Leila G. Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Viacheslav N. Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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20
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Bellotto O, Kralj S, Melchionna M, Pengo P, Kisovec M, Podobnik M, De Zorzi R, Marchesan S. Self-Assembly of Unprotected Dipeptides into Hydrogels: Water-Channels Make the Difference. Chembiochem 2021; 23:e202100518. [PMID: 34784433 PMCID: PMC9299199 DOI: 10.1002/cbic.202100518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Indexed: 12/24/2022]
Abstract
Unprotected dipeptides are attractive building blocks for environmentally friendly hydrogel biomaterials by virtue of their low‐cost and ease of preparation. This work investigates the self‐assembling behaviour of the distinct stereoisomers of Ile‐Phe and Phe‐Ile in phosphate buffered saline (PBS) to form hydrogels, using transmission electron microscopy (TEM), attenuated total reflectance infrared spectroscopy (ATR‐IR), circular dichroism (CD), and oscillatory rheometry. Each peptide purity and identity was also confirmed by 1H‐ and 13C‐NMR spectroscopy and HPLC‐MS. Finally, single‐crystal XRD data allowed the key interactions responsible for the supramolecular packing into amphipathic layers or water‐channels to be revealed. The presence of the latter in the crystal structure is a distinctive feature of the only gelator of this work that self‐organizes into stable hydrogels, with fast kinetics and the highest elastic modulus amongst its structural isomers and stereoisomers.
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Affiliation(s)
- Ottavia Bellotto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.,Department of Pharmaceutical Technology, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Michele Melchionna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy.,Unit of Trieste, INSTM, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Matic Kisovec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy.,Unit of Trieste, INSTM, Via L. Giorgieri 1, 34127, Trieste, Italy
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21
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Li L, Xie L, Zheng R, Sun R. Self-Assembly Dipeptide Hydrogel: The Structures and Properties. Front Chem 2021; 9:739791. [PMID: 34540806 PMCID: PMC8440803 DOI: 10.3389/fchem.2021.739791] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
Self-assembly peptide-based hydrogels are well known and popular in biomedical applications due to the fact that they are readily controllable and have biocompatibility properties. A dipeptide is the shortest self-assembling motif of peptides. Due to its small size and simple synthesis method, dipeptide can provide a simple and easy-to-use method to study the mechanism of peptides' self-assembly. This review describes the design and structures of self-assembly linear dipeptide hydrogels. The strategies for preparing the new generation of linear dipeptide hydrogels can be divided into three categories based on the modification site of dipeptide: 1) COOH-terminal and N-terminal modified dipeptide, 2) C-terminal modified dipeptide, and 3) uncapped dipeptide. With a deeper understanding of the relationship between the structures and properties of dipeptides, we believe that dipeptide hydrogels have great potential application in preparing minimal biocompatible materials.
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Affiliation(s)
- Liangchun Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Li Xie
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Renlin Zheng
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Rongqin Sun
- School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang, China
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22
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Chaker Z, Chervy P, Boulard Y, Bressanelli S, Retailleau P, Paternostre M, Charpentier T. Systematic Method for the Exploration, Representation, and Classification of the Diphenylalanine Solvatomorphic Space. J Phys Chem B 2021; 125:9454-9466. [PMID: 34382396 DOI: 10.1021/acs.jpcb.1c04203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An understanding of the conditions that govern the self-assembly process of peptides is a fundamental step toward the design of new nanostructures that possess interesting properties. In this work, we first synthesize and explore extensively diphenylalanine (FF) self-assembling crystals formed in different solvents (i.e., solvatomorphs) using polarized optical microscopy and transmission electron microscopy. Then, we develop a numerical method that allows an unambiguous classification of the solvatomorphs through a K-means automatic clustering method. In addition, we generate a two-dimensional (2D) representation of the solvatomorphic space together with the clustering results via a principal component analysis (PCA). The classification is based on structural similarities of solvatomorphs as revealed by the analysis of their respective infrared spectra. Among the 20 samples considered, 4 clear clusters are extracted within which the compounds show very similar crystalline structures. The information extracted allows us to assign many of the peaks that appear in the complex IR spectra of the samples considered. The implementation of the overall procedure we propose, i.e., "GAULOIS" and "REFRACT-R", is transferable to other types of spectra and paves the way for a systematic, fast, and accurate classification method applicable to various types of experimental spectroscopic data.
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Affiliation(s)
- Ziyad Chaker
- Université PAris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif-sur-Yvette Cedex, France
| | - Pierre Chervy
- Université PAris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif-sur-Yvette Cedex, France
| | - Yves Boulard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Pascal Retailleau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Maité Paternostre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
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23
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Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications. Molecules 2021; 26:molecules26154587. [PMID: 34361740 PMCID: PMC8348434 DOI: 10.3390/molecules26154587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/04/2021] [Accepted: 07/17/2021] [Indexed: 12/19/2022] Open
Abstract
There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.
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24
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Abstract
Hydrogels comprise a class of soft materials which are extremely useful in a number of contexts, for example as matrix-mimetic biomaterials for applications in regenerative medicine and drug delivery. One particular subclass of hydrogels consists of materials prepared through non-covalent physical crosslinking afforded by supramolecular recognition motifs. The dynamic, reversible, and equilibrium-governed features of these molecular-scale motifs often transcend length-scales to endow the resulting hydrogels with these same properties on the bulk scale. In efforts to engineer hydrogels of all types with more precise or application-specific uses, inclusion of stimuli-responsive sol-gel transformations has been broadly explored. In the context of biomedical uses, temperature is an interesting stimulus which has been the focus of numerous hydrogel designs, supramolecular or otherwise. Most supramolecular motifs are inherently temperature-sensitive, with elevated temperatures commonly disfavoring motif formation and/or accelerating its dissociation. In addition, supramolecular motifs have also been incorporated for physical crosslinking in conjunction with polymeric or macromeric building blocks which themselves exhibit temperature-responsive changes to their properties. Through molecular-scale engineering of supramolecular recognition, and selection of a particular motif or polymeric/macromeric backbone, it is thus possible to devise a number of supramolecular hydrogel materials to empower a variety of future biomedical applications.
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Affiliation(s)
- Sijie Xian
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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25
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Fu K, Wu H, Su Z. Self-assembling peptide-based hydrogels: Fabrication, properties, and applications. Biotechnol Adv 2021; 49:107752. [PMID: 33838284 DOI: 10.1016/j.biotechadv.2021.107752] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/02/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023]
Abstract
The hierarchical formation of self-assembling peptide-based hydrogels (SAPHs) starts from peptide to nanofibers, following with the entanglement into hydrogels with nanofibrous network. Such characteristic structure and extraordinary biocompatibility, and the peptide components endow the SAPHs with diverse applications in biotechnological field. Therefore, the thorough comprehension of SAPHs is significant to broadening their application. In this review, fabrication, properties, and biological applications of the SAPHs are introduced, and the factors influencing the synthesis process as well as the properties of the SAPHs products are also systematically explained. Meanwhile, we conclude the problems to be solved and provide our perspective to the future development of SAPHs in the biotechnology.
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Affiliation(s)
- Kun Fu
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Advanced Functional Polymer Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanguang Wu
- Beijing Key Laboratory of Clothing Materials R & D and Assessment, Beijing Institute of Fashion Technology, 100029 Beijing, China.
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Advanced Functional Polymer Composites, Beijing University of Chemical Technology, Beijing 100029, China.
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26
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Hu T, Zhang Z, Euston SR, Geng M, Pan S. Coassembly of C 13-Dipeptides: Gelations from Solutions and Precipitations. Biomacromolecules 2020; 21:5256-5268. [PMID: 33201680 DOI: 10.1021/acs.biomac.0c01325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C13-dipeptides that did not gel on their own were found to form hydrogels when combined with mixtures (coassembly). At pH = 4.6, by mixing negatively charged C13-WD (C13-WD2- and/or C13-WD-) with C13-KW or C13-YK, where the side chain of K carried positive charge, two composite hydrogels with different mechanical properties were formed. The gels exhibited various fiber structures that would account for their individual functionalities. According to molecular dynamics computer simulations, the composite systems formed spherical micelles through hydrophobic interactions that further aggregate to form gels through electrostatic interactions. The electrostatic repulsions between C13-WD molecules were interfered by insertions of C13-KW or C13-YK molecules, which result in gel formation in the composite systems. The results of computer simulations well explained the experimental observations, which provided new insights into the design and selection strategies for peptide gelators.
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Affiliation(s)
- Tan Hu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Zhuo Zhang
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Stephen Robert Euston
- Institute of Mechanical, Process & Energy Engineering School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K
| | - Mengjie Geng
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
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27
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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28
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Bellotto O, Kralj S, De Zorzi R, Geremia S, Marchesan S. Supramolecular hydrogels from unprotected dipeptides: a comparative study on stereoisomers and structural isomers. SOFT MATTER 2020; 16:10151-10157. [PMID: 32935720 DOI: 10.1039/d0sm01191f] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amino acid stereoconfiguration has been shown to play a key role in the self-assembly of unprotected tripeptides into hydrogels under physiological conditions. Dramatic changes were noted for hydrophobic sequences based on the diphenylalanine motif from the formation of amorphous aggregates in the case of homochiral peptides to nanostructured and stable hydrogels in the case of heterochiral stereoisomers. Herein, we report that by further shortening the sequence to a dipeptide, the overall differences between isomers are less marked, with both homo- and hetero-chiral dipeptides forming gels, although with different stability over time. The soft materials are studied by a number of spectroscopic and microcopic techniques, and single-crystal X-ray diffraction to unveil the supramolecular interactions of these hydrogel building blocks.
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Affiliation(s)
- Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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29
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Abraham JN, Joseph S, Trivedi R, Karle M. Injectable
dextran‐fluorenylmethoxycarbonyl
phenylalanine composite hydrogels with improved mechanical properties. POLYM INT 2020. [DOI: 10.1002/pi.6118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jancy N Abraham
- Polymer Science and Engineering Division CSIR‐National Chemical Laboratory Pune India
| | - Seena Joseph
- Polymer Science and Engineering Division CSIR‐National Chemical Laboratory Pune India
| | - Rishabh Trivedi
- Polymer Science and Engineering Division CSIR‐National Chemical Laboratory Pune India
| | - Mrunal Karle
- Polymer Science and Engineering Division CSIR‐National Chemical Laboratory Pune India
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30
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Pappas CG, Wijerathne N, Sahoo JK, Jain A, Kroiss D, Sasselli IR, Pina AS, Lampel A, Ulijn RV. Spontaneous Aminolytic Cyclization and Self‐Assembly of Dipeptide Methyl Esters in Water. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Charalampos G. Pappas
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Nadeesha Wijerathne
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Hunter CollegeDepartment of Chemistry CUNY 695 Park Avenue New York 10065 USA
- Ph.D. Program in Chemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
| | - Jugal Kishore Sahoo
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Ph.D. Program in Biochemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
| | - Ivan R. Sasselli
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
| | - Ana Sofia Pina
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Ayala Lampel
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Rein V. Ulijn
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Hunter CollegeDepartment of Chemistry CUNY 695 Park Avenue New York 10065 USA
- Ph.D. Program in Chemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
- Ph.D. Program in Biochemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
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31
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Garcia AM, Lavendomme R, Kralj S, Kurbasic M, Bellotto O, Cringoli MC, Semeraro S, Bandiera A, De Zorzi R, Marchesan S. Self-Assembly of an Amino Acid Derivative into an Antimicrobial Hydrogel Biomaterial. Chemistry 2020; 26:1880-1886. [PMID: 31868256 DOI: 10.1002/chem.201905681] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 02/06/2023]
Abstract
N-(4-Nitrobenzoyl)-Phe self-assembled into a transparent supramolecular hydrogel, which displayed high fibroblast and keratinocyte cell viability. The compound showed a mild antimicrobial activity against E. coli both as a hydrogel and in solution. Single-crystal XRD data revealed packing details, including protonation of the C-terminus due to an apparent pKa shift, as confirmed by pH titrations. MicroRaman analysis revealed almost identical features between the gel and crystal states, although more disorder in the former. The hydrogel is thermoreversible and disassembles within a range of temperatures that can be fine-tuned by experimental conditions, such as gelator concentration. At the minimum gelling concentration of 0.63 wt %, the hydrogel disassembles in a physiological temperature range of 39-42 °C, thus opening the way to its potential use as a biomaterial.
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Affiliation(s)
- Ana M Garcia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Roy Lavendomme
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Marina Kurbasic
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Ottavia Bellotto
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Maria C Cringoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Sabrina Semeraro
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Antonella Bandiera
- Dipartimento di Scienze della Vita, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Rita De Zorzi
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Silvia Marchesan
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
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32
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Datta D, Nagaraj R, Chaudhary N. Water-Alcohol Bigels from Fatty Acylated Dipeptides. J Phys Chem B 2020; 124:577-588. [PMID: 31880938 DOI: 10.1021/acs.jpcb.9b10002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Peptide-based gels are emerging as an interesting class of biocompatible soft materials. 9-Fluorenylmethoxycarbonyl-protected amino acids and short peptides have gained considerable attention as promising gelators. Peptide amphiphiles, wherein an alkyl chain is appended to a polar peptidic moiety, are another important class of peptide-based gelators. Here, we report the alcohol/water bigels formed by the rather simple fatty acylated dipeptides wherein the peptidic moiety is made up of hydrophobic amino acids, viz., Val, Ile, and Leu. Lauroyl, myristoyl, and palmitoyl were investigated as the N-terminal fatty acyl groups. None of the lauroylated peptides caused gelation of methanol/water and ethanol/water mixtures up to 2 wt % peptide concentration. Eight out of the 27 peptides resulted in distinct bigels. The gels are composed of fibrous aggregates as characterized by electron microscopy. Infrared spectroscopy suggests the β-sheet conformation of the peptidic region in the gels. Using the Ma-IV ethanol/water bigel as the representative gel, entrapment and steady release of the anticancer drug docetaxel are demonstrated. Such bigels from rather simple amphipathic peptides that are easily synthesized and purified through solvent extraction could be attractive gelator candidates with potential application in drug delivery.
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Affiliation(s)
- Debika Datta
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781 039 , India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology , Uppal Road , Hyderabad 500 007 , India
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781 039 , India
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33
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Ziganshin MA, Larionov RA, Gerasimov AV, Ziganshina SA, Klimovitskii AE, Khayarov KR, Mukhametzyanov TA, Gorbatchuk VV. Thermally induced cyclization of L -isoleucyl- L -alanine in solid state: Effect of dipeptide structure on reaction temperature and self-assembly. J Pept Sci 2019; 25:e3177. [PMID: 31317614 DOI: 10.1002/psc.3177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
Thermal treatment of short-chain oligopeptides is able to initiate the process of their self-assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of L -isoleucyl-L -alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self-assembly changes to chemical reaction. The differences in self-assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self-assembly of dipeptides was shown. The new information obtained on the thermal properties and self-assembly of linear and cyclic forms of L -isoleucyl-L -alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.
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Affiliation(s)
- Marat A Ziganshin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - Radik A Larionov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | | | - Sufia A Ziganshina
- Zavoisky Physical-Technical Institute of FRC Kazan Scientific Center of RAS, Kazan, Russia
| | | | - Khasan R Khayarov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | | | - Valery V Gorbatchuk
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
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34
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Yadav N, Chauhan MK, Chauhan VS. Short to ultrashort peptide-based hydrogels as a platform for biomedical applications. Biomater Sci 2019; 8:84-100. [PMID: 31696870 DOI: 10.1039/c9bm01304k] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Short peptides have attracted significant attention from researchers in the past few years due to their easy design, synthesis and characterization, diverse functionalisation possibilities, low cost, possibility to make a large range of hierarchical nanostructures and most importantly their high biocompatibility and biodegradability. Generally, short peptides are also relatively more stable than their longer variants, non-immunogenic in nature and many of them self-assemble to provide an exciting range of nanostructures, including hydrogels. Thus, the development of short peptide-based hydrogels has become an area of intense investigation. Although these hydrogels have a water content of greater than 90%, they are surprisingly highly stable structures, and thus have been used for various biomedical applications, including cell therapeutics, drug delivery, tissue engineering and regeneration, contact lenses, biosensors, and wound healing, by different researchers. Herein, we review the progress of research in the rapidly expanding field of short to ultrashort peptide-based hydrogels and their possible applications. Special attention is paid to address and review this field with regard to the stability of peptide-based hydrogels, particularly to enzymatic degradation.
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Affiliation(s)
- Nitin Yadav
- Molecular Medicine Group, International Centre for Genetic Engineering & Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India. and Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli-Badarpur Road, Sector-3, Pushpvihar, New Delhi-110017, India
| | - Meenakshi K Chauhan
- Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli-Badarpur Road, Sector-3, Pushpvihar, New Delhi-110017, India
| | - Virander S Chauhan
- Molecular Medicine Group, International Centre for Genetic Engineering & Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
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35
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Rezaei-Ghaleh N, Munari F, Becker S, Assfalg M, Griesinger C. A facile oxygen-17 NMR method to determine effective viscosity in dilute, molecularly crowded and confined aqueous media. Chem Commun (Camb) 2019; 55:12404-12407. [PMID: 31566648 DOI: 10.1039/c9cc06124j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present an NMR method based on natural abundance 17O relaxation of water to determine effective viscosity in biological aqueous samples. The method accurately captures viscosity of dilute and crowded protein solutions and offers a fairly simple way to quantify the internal fluidity of biological condensates formed through phase separation.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany. and Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Francesca Munari
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for Their Prediction and Characterization. Methods Mol Biol 2019. [PMID: 30945222 DOI: 10.1007/978-1-4939-9161-7_12] [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: 09/08/2023]
Abstract
Proteins with prion-like behavior are attracting an increasing interest, since accumulating evidences indicate that they play relevant roles both in health and disease. The self-assembly of these proteins into insoluble aggregates is associated with severe neuropathological processes such as amyotrophic lateral sclerosis (ALS). However, in normal conditions, they are known to accomplish a wide range of functional roles. The conformational duality of prion-like proteins is often encoded in specific protein regions, named prion-like domains (PrLDs). PrLDs are usually long and disordered regions of low complexity. We have shown that PrLDs might contain soft-amyloid cores that contribute significantly to trigger their aggregation, as well as to support their propagation. Further exploration of the role of these sequences in the conformational conversion of prion-like proteins might provide novel insights into the mechanism of action and regulation of these polypeptides, enabling the future development of therapeutic strategies. Here, we describe a set of methodologies aimed to identify and characterize these short amyloid stretches in a protein or proteome of interest, ranging from in silico detection to in vitro and in vivo evaluation and validation.
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Tang JD, Mura C, Lampe KJ. Stimuli-Responsive, Pentapeptide, Nanofiber Hydrogel for Tissue Engineering. J Am Chem Soc 2019; 141:4886-4899. [PMID: 30830776 DOI: 10.1021/jacs.8b13363] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Short peptides are uniquely versatile building blocks for self-assembly. Supramolecular peptide assemblies can be used to construct functional hydrogel biomaterials-an attractive approach for neural tissue engineering. Here, we report a new class of short, five-residue peptides that form hydrogels with nanofiber structures. Using rheology and spectroscopy, we describe how sequence variations, pH, and peptide concentration alter the mechanical properties of our pentapeptide hydrogels. We find that this class of seven unmodified peptides forms robust hydrogels from 0.2-20 kPa at low weight percent (less than 3 wt %) in cell culture media and undergoes shear-thinning and rapid self-healing. The peptides self-assemble into long fibrils with sequence-dependent fibrillar morphologies. These fibrils exhibit a unique twisted ribbon shape, as visualized by transmission electron microscopy (TEM) and Cryo-EM imaging, with diameters in the low tens of nanometers and periodicities similar to amyloid fibrils. Experimental gelation behavior corroborates our molecular dynamics simulations, which demonstrate peptide assembly behavior, an increase in β-sheet content, and patterns of variation in solvent accessibility. Our rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels are syringe-injectable and support cytocompatible encapsulation of oligodendrocyte progenitor cells (OPCs), as well as their proliferation and three-dimensional process extension. Furthermore, RAPID gels protect OPCs from mechanical membrane disruption and acute loss of viability when ejected from a syringe needle, highlighting the protective capability of the hydrogel as potential cell carriers for transplantation therapies. The tunable mechanical and structural properties of these supramolecular assemblies are shown to be permissive to cell expansion and remodeling, making this hydrogel system suitable as an injectable material for cell delivery and tissue engineering applications.
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38
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Vardhishna MV, Srinivasulu G, Harikrishna A, Thakur SS, Chatterjee B. Simultaneous Occurrence of Nanospheres and Nanofibers Self-Assembled from Achiral Tripeptides. ChemistryOpen 2019; 8:266-270. [PMID: 30868048 PMCID: PMC6398100 DOI: 10.1002/open.201800258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/28/2018] [Indexed: 11/24/2022] Open
Abstract
The achiral tripeptide Boc‐Aib‐MABA‐Aib‐OMe has the ability to co‐exist as nanospheres and as a network of nanofibers in methanol. Furthermore, AFM and TEM images show the presence of bulges in the network of nanofibers. Interestingly, the formation of nanofibers is seen to emerge from the outer boundary of the spherical structures. Some of the nanofibers curl up at the tip and later result in the formation of hollow nanospheres with thick boundaries. The presence of β‐turn‐like structures with hydrogen bonding is observed using FT‐IR studies. The presence of hydrogen bonding is also demonstrated by using NMR studies.
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Affiliation(s)
- Malapaka Venkata Vardhishna
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
| | - Gannoju Srinivasulu
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
| | - Adicherl Harikrishna
- Proteomics and Cell Signaling, Lab E409 Centre for Cellular and Molecular Biology Uppal Road Hyderabad - 500007 India
| | - Suman Siddharth Thakur
- Proteomics and Cell Signaling, Lab E409 Centre for Cellular and Molecular Biology Uppal Road Hyderabad - 500007 India
| | - Bhaswati Chatterjee
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
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39
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Li Q, Jia Y, Li J. Controlled Assembly of Chiral Structure of Diphenylalanine Peptide. ACTA CHIMICA SINICA 2019. [DOI: 10.6023/a19060241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Anderson J, Lake PT, McCullagh M. Initial Aggregation and Ordering Mechanism of Diphenylalanine from Microsecond All-Atom Molecular Dynamics Simulations. J Phys Chem B 2018; 122:12331-12341. [PMID: 30511861 DOI: 10.1021/acs.jpcb.8b10335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-assembled diphenylalanine (FF) nanostructures have recently been demonstrated to be interesting materials for antibacterial and anticancer applications. These applications, among others, seek to take advantage of the high-order and resulting appealing physical properties of FF nanostructures by modifying the peptide in some way to achieve specific functionality. To rationally design modifications to the dipeptide that allow for this behavior, the driving forces of FF self-assembly must be understood. Molecular simulations have been utilized to assess these properties but have yielded conflicting conclusions due to inconsistencies in models chosen as well as the lack of quantitative analyses on the specific driving forces. Here, we present an all-atom explicit solvent molecular dynamics-based study on different length scales of FF aggregation. We utilize a free energy decomposition analysis as well as a dimer cluster analysis to identify the initial aggregation driving force to be FF intermolecular electrostatics, whereas solvent-mediated forces drive crystal growth. These data are consistent with the hypothesis that all hydrophobic dipeptides will have a similar initial aggregation mechanism until a critical aggregate size is reached, at which point crystallization occurs and subsequent crystal growth is dominated by solvent-mediated forces. We demonstrate that this proposed mechanism is testable by infrared spectroscopy focusing on the blueshift of the amide I peak as well as the ordering of the carboxylate peak.
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Affiliation(s)
- Jakob Anderson
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Peter T Lake
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
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41
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Galzitskaya OV, Lobanov MY. Proteome-scale understanding of relationship between homo-repeat enrichments and protein aggregation properties. PLoS One 2018; 13:e0206941. [PMID: 30399196 PMCID: PMC6219797 DOI: 10.1371/journal.pone.0206941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023] Open
Abstract
Expansion of homo-repeats is a molecular basis for human neurological diseases. We are the first who studied the influence of homo-repeats with lengths larger than four amino acid residues on the aggregation properties of 1449683 proteins across 122 eukaryotic and bacterial proteomes. Only 15% of proteins (215481) include homo-repeats of such length. We demonstrated that RNA-binding proteins with a prion-like domain are enriched with homo-repeats in comparison with other non-redundant protein sequences and those in the PDB. We performed a bioinformatics analysis for these proteins and found that proteins with homo-repeats are on average two times longer than those in the whole database. Moreover, we are first to discover that as a rule, homo-repeats appear in proteins not alone but in pairs: hydrophobic and aromatic homo-repeats appear with similar ones, while homo-repeats with small, polar and charged amino acids appear together with different preferences. We elaborated a new complementary approach to demonstrate the influence of homo-repeats on their host protein aggregation properties. We have shown that addition of artificial homo-repeats to natural and random proteins results in intensification of aggregation properties of the proteins. The maximal effect is observed for the insertion of artificial homo-repeats with 5–6 residues, which is consistent with the minimal length of an amyloidogenic region. We have also demonstrated that the ability of proteins with homo-repeats to aggregate cannot be explained only by the presence of long homo-repeats in them. There should be other characteristics of proteins intensifying the aggregation property including such as the appearance of homo-repeats in pairs in the same protein. We are the first who elaborated a new approach to study the influence of homo-repeats present in proteins on their aggregation properties and performed an appropriate analysis of the large number of proteomes and proteins.
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Affiliation(s)
- Oxana V. Galzitskaya
- Group of Bioinformatics, Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
- * E-mail:
| | - Miсhail Yu. Lobanov
- Group of Bioinformatics, Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
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42
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Macha P, Perreault L, Hamedani Y, Mayes ML, Vasudev MC. Molecular Mechanisms of Tryptophan–Tyrosine Nanostructures Formation and their Influence on PC-12 Cells. ACS APPLIED BIO MATERIALS 2018; 1:1266-1275. [DOI: 10.1021/acsabm.8b00121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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43
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Restu WK, Nishida Y, Yamamoto S, Ishii J, Maruyama T. Short Oligopeptides for Biocompatible and Biodegradable Supramolecular Hydrogels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8065-8074. [PMID: 29897242 DOI: 10.1021/acs.langmuir.8b00362] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Short Phe-rich oligopeptides, consisting of only four and five amino acids, worked as effective supramolecular hydrogelators for buffer solutions at low gelator concentrations (0.5-1.5 wt %). Among 10 different oligopeptides synthesized, peptide P1 (Ac-Phe-Phe-Phe-Gly-Lys) showed high gelation ability. Transmission electron microscopy observations suggested that the peptide molecules self-assembled into nanofibrous networks, which turned into gels. The hydrogel of peptide P1 showed reversible thermal gel-sol transition and viscoelastic properties typical of a gel. Circular dichroism spectra revealed that peptide P1 formed a β-sheetlike structure, which decreased with increasing temperature. The self-assembly of peptide P1 occurred even in the presence of nutrients in culture media and common surfactants. Escherichia coli and yeast successfully grew on the hydrogel. The hydrogel exhibited low cytotoxicity to animal cells. Finally, we demonstrated that functional compounds can be released from the hydrogel in different manners based on the interaction between the compounds and the hydrogel.
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Affiliation(s)
- Witta Kartika Restu
- Department of Chemical Science and Engineering, Graduate School of Engineering , Kobe University , 1-1 Rokkodaicho , Nada-ku, Kobe 657-8501 , Japan
- Research Center for Chemistry , Indonesian Institute of Sciences, Kawasan Puspiptek Serpong , Tangerang Selatan , Banten 15314 , Indonesia
| | - Yuki Nishida
- Department of Chemical Science and Engineering, Graduate School of Engineering , Kobe University , 1-1 Rokkodaicho , Nada-ku, Kobe 657-8501 , Japan
| | - Shota Yamamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering , Kobe University , 1-1 Rokkodaicho , Nada-ku, Kobe 657-8501 , Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation , Kobe University , 1-1 Rokkodaicho , Nada-ku, Kobe 657-8501 , Japan
| | - Tatsuo Maruyama
- Department of Chemical Science and Engineering, Graduate School of Engineering , Kobe University , 1-1 Rokkodaicho , Nada-ku, Kobe 657-8501 , Japan
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44
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Solid-State NMR Characterization of the Structure of Self-Assembled Ile–Phe–OH. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4030030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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46
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Dissection of the deep-blue autofluorescence changes accompanying amyloid fibrillation. Arch Biochem Biophys 2018; 651:13-20. [PMID: 29803394 DOI: 10.1016/j.abb.2018.05.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/02/2018] [Accepted: 05/23/2018] [Indexed: 11/21/2022]
Abstract
Pathogenesis of numerous diseases is associated with the formation of amyloid fibrils. Extrinsic fluorescent dyes, including Thioflavin T (ThT), are used to follow the fibrillation kinetics. It has recently been reported that the so-called deep-blue autofluorescence (dbAF) is changing during the aggregation process. However, the origin of dbAF and the reasons for its change remain debatable. Here, the kinetics of fibril formation in model proteins were comprehensively analyzed using fluorescence lifetime and intensity of ThT, intrinsic fluorescence of proteinaceous fluorophores, and dbAF. For all systems, intensity enhancement of the dbAF band with similar spectral parameters (∼350 nm excitation; ∼450 nm emission) was observed. Although the time course of ThT lifetime (indicative of protofibrils formation) coincided with that of tyrosine residues in insulin, and the kinetic changes in the ThT fluorescence intensity (reflecting formation of mature fibrils) coincided with changes in ThT absorption spectrum, the dbAF band started to increase from the beginning of the incubation process without a lag-phase. Our mass-spectrometry data and model experiments suggested that dbAF could be at least partially related to oxidation of amino acids. This study scrutinizes the dbAF features in the context of the existing hypotheses about the origin of this spectral band.
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47
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018; 57:7709-7713. [PMID: 29603545 PMCID: PMC6055752 DOI: 10.1002/anie.201801001] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Indexed: 01/13/2023]
Abstract
Oligopeptide‐based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control, with minor alterations in the peptide sequence significantly influencing the self‐assembly process. We explored three pentapeptide sequences with different charge distributions and discovered that they formed robust, pH‐responsive hydrogels. By altering the concentration and charge distribution of the peptide sequence, the stiffness of the hydrogels could be tuned across two orders of magnitude (2–200 kPa). Also, through reassembly of the β‐sheet interactions the hydrogels could self‐heal and they demonstrated shear‐thin behavior. Using spectroscopic and cryo‐imaging techniques, we investigated the relationship between peptide sequence and molecular structure, and how these influence the mechanical properties of the hydrogel. These pentapeptide hydrogels with tunable morphology and mechanical properties have promise in tissue engineering, injectable delivery vectors, and 3D printing applications.
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Affiliation(s)
- David E Clarke
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher D J Parmenter
- Nottingham Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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48
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David E. Clarke
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Christopher D. J. Parmenter
- Nottingham Nanoscale and Microscale Research Centre; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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Sasselli IR, Moreira IP, Ulijn RV, Tuttle T. Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries. Org Biomol Chem 2018; 15:6541-6547. [PMID: 28745772 DOI: 10.1039/c7ob01268c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
There is significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixtures of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of the DPL of mixed sequences (e.g. starting from a mixture of dileucine, L2, and diphenylalanine, F2) did not give the same outcome as the separate L2 and F2 libraries (which give rise to the formation of F6 and L6), implying that interactions between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamics (CG-MD) simulations are used to understand the DPL results for F2, L2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in the mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in the DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. This work shows that combined computational and experimental screening can be used complementarily and in combination providing a powerful means to discover new supramolecular peptide nanostructures.
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Affiliation(s)
- I R Sasselli
- Department of Pure & Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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50
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Mamone S, Glöggler S. Nuclear spin singlet states as magnetic on/off probes in self-assembling systems. Phys Chem Chem Phys 2018; 20:22463-22467. [DOI: 10.1039/c8cp04448a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear singlet states in thermo-responsive peptides are introduced as magnetic on/off switches.
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Affiliation(s)
- Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG
- 37075 Göttingen
| | - Stefan Glöggler
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG
- 37075 Göttingen
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