1
|
Design of short peptides and peptide amphiphiles as collagen mimics and an investigation of their interactions with collagen using molecular dynamics simulations and docking studies. J Mol Model 2022; 29:19. [PMID: 36565373 DOI: 10.1007/s00894-022-05419-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)3 and (Ala-His-Hyp)3 formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)3 and (Ala-His-Hyp)3. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.
Collapse
|
2
|
Rani A, Sindhu A, Yao TJ, Horng JC, Venkatesu P. Profiling the impact of choline chloride on the self-assembly of collagen mimetic peptide (Pro-Hyp-Gly)10. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
3
|
Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
Collapse
Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
4
|
Kinoshita S, Mera K, Ichikawa H, Shimasaki S, Nagai M, Taga Y, Iijima K, Hattori S, Fujiwara Y, Shirakawa JI, Nagai R. Nω -(Carboxymethyl)arginine Is One of the Dominant Advanced Glycation End Products in Glycated Collagens and Mouse Tissues. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9073451. [PMID: 31583049 PMCID: PMC6754957 DOI: 10.1155/2019/9073451] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/31/2019] [Accepted: 08/16/2019] [Indexed: 01/22/2023]
Abstract
Advanced glycation end products (AGEs) accumulate in proteins during aging in humans. In particular, the AGE structure Nω -(carboxymethyl)arginine (CMA) is produced by oxidation in glycated collagen, accounting for one of the major proteins detected in biological samples. In this study, we investigated the mechanism by which CMA is generated in collagen and detected CMA in collagen-rich tissues. When various protein samples were incubated with glucose, the CMA content, detected using a monoclonal antibody, increased in a time-dependent manner only in glycated collagen, whereas the formation of Nε -(carboxymethyl)lysine (CML), a major antigenic AGE, was detected in all glycated proteins. Dominant CMA formation in glycated collagen was also observed by electrospray ionization-liquid chromatography-tandem mass spectrometry (LC-MS/MS). During incubation of glucose with collagen, CMA formation was enhanced with increasing glucose concentration, whereas it was inhibited in the presence of dicarbonyl-trapping reagents and a metal chelator. CMA formation was also observed upon incubating collagen with glyoxal, and CMA was generated in a time-dependent manner when glyoxal was incubated with type I-IV collagens. To identify hotspots of CMA formation, tryptic digests of glycated collagen were applied to an affinity column conjugated with anti-CMA. Several CMA peptides that are important for recognition by integrins were detected by LC-MS/MS and amino acid sequence analyses. CMA formation on each sequence was confirmed by incubation of the synthesized peptides with glyoxal and ribose. LC-MS detected CMA in the mouse skin at a higher level than other AGEs. Furthermore, CMA accumulation was greater in the human aorta of older individuals. Overall, our study provides evidence that CMA is a representative AGE structure that serves as a useful index to reflect the oxidation and glycation of collagen.
Collapse
Affiliation(s)
- Sho Kinoshita
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| | - Katsumi Mera
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroko Ichikawa
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| | - Satoko Shimasaki
- Department of Food and Nutrition, Laboratory of Nutritional Science and Biochemistry, Japan Women's University, Tokyo, Japan
| | - Mime Nagai
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| | - Yuki Taga
- Nippi Research Institute of Biomatrix, Tokyo, Japan
| | | | | | - Yukio Fujiwara
- Department of Cell Pathology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun-ichi Shirakawa
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| | - Ryoji Nagai
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| |
Collapse
|
5
|
Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
Collapse
Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
| |
Collapse
|
6
|
Kubyshkin V, Budisa N. Promotion of the collagen triple helix in a hydrophobic environment. Org Biomol Chem 2019; 17:2502-2507. [DOI: 10.1039/c9ob00070d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The collagen triple helix is better suited for octanol than for water.
Collapse
Affiliation(s)
| | - Nediljko Budisa
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
- University of Manitoba
| |
Collapse
|
7
|
The Characteristics of Intrinsic Fluorescence of Type I Collagen Influenced by Collagenase I. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8101947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The triple helix structure of collagen can be degraded by collagenase. In this study, we explored how the intrinsic fluorescence of type I collagen was influenced by collagenase I. We found that tyrosine was the main factor that could successfully excite the collagen fluorescence. Initially, self-assembly behavior of collagen resulted in a large amount of tyrosine wrapped with collagen, which decreased the fluorescence intensity of type I collagen. After collagenase cleavage, some wrapped-tyrosine could be exposed and thereby the intrinsic fluorescence intensity of collagen increased. By observation and analysis, the influence of collagenase to intrinsic fluorescence of collagen was investigated and elaborated. Furthermore, collagenase cleavage to the special triple helix structure of collagen would result in a slight improvement of collagen thermostability, which was explained by the increasing amount of terminal peptides. These results are helpful and effective for reaction mechanism research related to collagen, which can be observed by fluorescent technology. Meantime, the reaction behaviors of both collagenase and collagenolytic proteases can also be analyzed by fluorescent technology. In conclusion, this research provides a foundation for the further investigation of collagen reactions in different areas, such as medicine, nutrition, food and agriculture.
Collapse
|