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Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
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Affiliation(s)
- Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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2
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Zhu Z, Bian Y, Zhang X, Zeng R, Yang B. Examination of proline, hydroxyproline and pyroglutamic acid with different polar groups by terahertz spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120539. [PMID: 34742154 DOI: 10.1016/j.saa.2021.120539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/08/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Hydroxyproline (HYP) and pyroglutamic acid (PGA), as amino acid derivatives, are highly similar in structure to proline (Pro). However, their low-frequency vibrations show significant differences in the range of 0.25-2.6 THz. Therefore, this study investigated the reasons for the differences combined with terahertz time domain spectroscopy (THz-TDS) and density functional theory (DFT). The results show that HYP and PGA have stronger absorption of terahertz waves due to the existence of polar substituents. Furthermore, the absorption peaks of HYP and PGA are significant red shifted and blue shifted, respectively. We believe that this is caused by the change in the strength of intermolecular hydrogen bonds. Our findings demonstrate that dipole and hydrogen bond effects play a significant role in low-frequency vibrations.
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Affiliation(s)
- Zhenqi Zhu
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yujing Bian
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xun Zhang
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Ruonan Zeng
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Bin Yang
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China; Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
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3
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13C NMR Spectroscopic Studies of Intra- and Intermolecular Interactions of Amino Acid Derivatives and Peptide Derivatives in Solutions. ORGANICS 2022. [DOI: 10.3390/org3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
13C NMR spectroscopic investigations were conducted for various amino acid derivatives and peptides. It was observed that 13C NMR chemical shifts of the carbonyl carbons are correlated with the solvent polarities, but the extent depends on the structures. The size of the functional groups and inter- and intra-molecular hydrogen bonding appear to be the major contributors for this tendency.
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4
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Arcoria PJ, Ware RI, Makwana SV, Troya D, Etzkorn FA. Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic Collagen. J Phys Chem B 2021; 126:217-228. [PMID: 34968406 DOI: 10.1021/acs.jpcb.1c09180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
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Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rachel I Ware
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sunny V Makwana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Diego Troya
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Felicia A Etzkorn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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5
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Varma S, Orgel JPRO, Schieber JD. Contrasting Local and Macroscopic Effects of Collagen Hydroxylation. Int J Mol Sci 2021; 22:ijms22169068. [PMID: 34445791 PMCID: PMC8396666 DOI: 10.3390/ijms22169068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
Collagen is heavily hydroxylated. Experiments show that proline hydroxylation is important to triple helix (monomer) stability, fibril assembly, and interaction of fibrils with other molecules. Nevertheless, experiments also show that even without hydroxylation, type I collagen does assemble into its native D-banded fibrillar structure. This raises two questions. Firstly, even though hydroxylation removal marginally affects macroscopic structure, how does such an extensive chemical change, which is expected to substantially reduce hydrogen bonding capacity, affect local structure? Secondly, how does such a chemical perturbation, which is expected to substantially decrease electrostatic attraction between monomers, affect collagen's mechanical properties? To address these issues, we conduct a benchmarked molecular dynamics study of rat type I fibrils in the presence and absence of hydroxylation. Our simulations reproduce the experimental observation that hydroxylation removal has a minimal effect on collagen's D-band length. We also find that the gap-overlap ratio, monomer width and monomer length are minimally affected. Surprisingly, we find that de-hydroxylation also has a minor effect on the fibril's Young's modulus, and elastic stress build up is also accompanied by tightening of triple-helix windings. In terms of local structure, de-hydroxylation does result in a substantial drop (23%) in inter-monomer hydrogen bonding. However, at the same time, the local structures and inter-monomer hydrogen bonding networks of non-hydroxylated amino acids are also affected. It seems that it is this intrinsic plasticity in inter-monomer interactions that preclude fibrils from undergoing any large changes in macroscopic properties. Nevertheless, changes in local structure can be expected to directly impact collagen's interaction with extra-cellular matrix proteins. In general, this study highlights a key challenge in tissue engineering and medicine related to mapping collagen chemistry to macroscopic properties but suggests a path forward to address it using molecular dynamics simulations.
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Affiliation(s)
- Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, Department of Physics, University of South Florida, Tampa, FL 33620, USA
- Correspondence:
| | - Joseph P. R. O. Orgel
- Department of Biology, Department of Physics, Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Jay D. Schieber
- Department of Chemical and Biological Engineering, Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA;
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6
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Mabesoone MFJ, Ter Huurne GM, Palmans ARA, Meijer EW. How Water in Aliphatic Solvents Directs the Interference of Chemical Reactivity in a Supramolecular System. J Am Chem Soc 2020; 142:12400-12408. [PMID: 32543841 PMCID: PMC7366503 DOI: 10.1021/jacs.0c04962] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Water is typically considered to be insoluble in alkanes. Recently, however, monomerically dissolved water in alkanes has been shown to dramatically impact the structure of hydrogen-bonded supramolecular polymers. Here, we report that water in methylcyclohexane (MCH) also determines the outcome of combining a Michael reaction with a porphyrin-based supramolecular system. In dry conditions, the components of the reaction do not affect or destabilize the supramolecular polymer, whereas in ambient or wet conditions the polymers are rapidly destabilized. Although spectroscopic investigations show no effect of water on the molecular structure of the supramolecular polymer, light scattering and atomic force microscopy experiments show that water increases the flexibility of the supramolecular polymer and decreases the polymer length. Through a series of titrations, we show that a cooperative interaction, involving the coordination of the amine catalyst to the porphyrin and complexation of the substrates to the flexible polymers invokes the depolymerization of the aggregates. Water crucially stabilizes these cooperative interactions to cause complete depolymerization in humid conditions. Additionally, we show that the humidity-controlled interference in the polymer stability occurs with various substrates, indicating that water may play a ubiquitous role in supramolecular polymerizations in oils. By controlling the amount of water, the influence of a covalent chemical process on noncovalent aggregates can be mediated, which holds great potential to forge a connection between chemical reactivity and supramolecular material structure. Moreover, our findings highlight that understanding cooperative interactions in multicomponent noncovalent systems is crucial to design complex molecular systems.
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Affiliation(s)
- Mathijs F J Mabesoone
- Institute for Complex Molecular Systems and the Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Gijs M Ter Huurne
- Institute for Complex Molecular Systems and the Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems and the Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems and the Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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7
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Harris T, Chenoweth DM. Sterics and Stereoelectronics in Aza-Glycine: Impact of Aza-Glycine Preorganization in Triple Helical Collagen. J Am Chem Soc 2019; 141:18021-18029. [DOI: 10.1021/jacs.9b05524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trevor Harris
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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8
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Sorushanova A, Delgado LM, Wu Z, Shologu N, Kshirsagar A, Raghunath R, Mullen AM, Bayon Y, Pandit A, Raghunath M, Zeugolis DI. The Collagen Suprafamily: From Biosynthesis to Advanced Biomaterial Development. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1801651. [PMID: 30126066 DOI: 10.1002/adma.201801651] [Citation(s) in RCA: 498] [Impact Index Per Article: 99.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/03/2018] [Indexed: 05/20/2023]
Abstract
Collagen is the oldest and most abundant extracellular matrix protein that has found many applications in food, cosmetic, pharmaceutical, and biomedical industries. First, an overview of the family of collagens and their respective structures, conformation, and biosynthesis is provided. The advances and shortfalls of various collagen preparations (e.g., mammalian/marine extracted collagen, cell-produced collagens, recombinant collagens, and collagen-like peptides) and crosslinking technologies (e.g., chemical, physical, and biological) are then critically discussed. Subsequently, an array of structural, thermal, mechanical, biochemical, and biological assays is examined, which are developed to analyze and characterize collagenous structures. Lastly, a comprehensive review is provided on how advances in engineering, chemistry, and biology have enabled the development of bioactive, 3D structures (e.g., tissue grafts, biomaterials, cell-assembled tissue equivalents) that closely imitate native supramolecular assemblies and have the capacity to deliver in a localized and sustained manner viable cell populations and/or bioactive/therapeutic molecules. Clearly, collagens have a long history in both evolution and biotechnology and continue to offer both challenges and exciting opportunities in regenerative medicine as nature's biomaterial of choice.
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Affiliation(s)
- Anna Sorushanova
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Luis M Delgado
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Zhuning Wu
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Naledi Shologu
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Aniket Kshirsagar
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Rufus Raghunath
- Centre for Cell Biology and Tissue Engineering, Competence Centre Tissue Engineering for Drug Development (TEDD), Department Life Sciences and Facility Management, Institute for Chemistry and Biotechnology (ICBT), Zürich University of Applied Sciences, Wädenswil, Switzerland
| | | | - Yves Bayon
- Sofradim Production-A Medtronic Company, Trevoux, France
| | - Abhay Pandit
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Michael Raghunath
- Centre for Cell Biology and Tissue Engineering, Competence Centre Tissue Engineering for Drug Development (TEDD), Department Life Sciences and Facility Management, Institute for Chemistry and Biotechnology (ICBT), Zürich University of Applied Sciences, Wädenswil, Switzerland
| | - Dimitrios I Zeugolis
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), Galway, Ireland
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9
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Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest. Biochem J 2018; 475:3123-3140. [PMID: 30315001 DOI: 10.1042/bcj20180482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022]
Abstract
The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.
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10
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Stantchev RI, Mansfield JC, Edginton RS, Hobson P, Palombo F, Hendry E. Subwavelength hyperspectral THz studies of articular cartilage. Sci Rep 2018; 8:6924. [PMID: 29720708 PMCID: PMC5932036 DOI: 10.1038/s41598-018-25057-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Abstract
Terahertz-spectroscopy probes dynamics and spectral response of collective vibrational modes in condensed phase, which can yield insight into composition and topology. However, due to the long wavelengths employed (λ = 300 μm at 1THz), diffraction limited imaging is typically restricted to spatial resolutions around a millimeter. Here, we demonstrate a new form of subwavelength hyperspectral, polarization-resolved THz imaging which employs an optical pattern projected onto a 6 μm-thin silicon wafer to achieve near-field modulation of a co-incident THz pulse. By placing near-field scatterers, one can measure the interaction of object with the evanescent THz fields. Further, by measuring the temporal evolution of the THz field a sample's permittivity can be extracted with 65 μm spatial resolution due to the presence of evanescent fields. Here, we present the first application of this new approach to articular cartilage. We show that the THz permittivity in this material varies progressively from the superficial zone to the deep layer, and that this correlates with a change in orientation of the collagen fibrils that compose the extracellular matrix (ECM) of the tissue. Our approach enables direct interrogation of the sample's biophysical properties, in this case concerning the structure and permittivity of collagen fibrils and their anisotropic organisation in connective tissue.
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Affiliation(s)
- Rayko I Stantchev
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK.
| | | | - Ryan S Edginton
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Peter Hobson
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
- QinetiQ Limited, Cody Technology Park, Ively Road, Farnborough, GU14 0LX, UK
| | - Francesca Palombo
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Euan Hendry
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
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11
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Gu LS, Huang XQ, Griffin B, Bergeron BR, Pashley DH, Niu LN, Tay FR. Primum non nocere - The effects of sodium hypochlorite on dentin as used in endodontics. Acta Biomater 2017; 61:144-156. [PMID: 28801267 DOI: 10.1016/j.actbio.2017.08.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/28/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
The medical literature is replete with the maxim 'primum non nocere', cautioning health care providers to avoid doing any harm to human subjects in their delivery of medical care. Sodium hypochlorite (NaOCl) is a well-established irrigant for root canal treatment because of its antimicrobial and organic tissue remnant dissolution capability. However, little is known about the deleterious effect of this strong oxidizing agent on the integrity of human mineralized dentin. Iatrogenically-induced loss of dentin integrity may precipitate post-treatment root fracture and has potential medico-legal complications. In the present work, transmission electron microscopy provided evidence for collagen destruction in the surface/subsurface of dentin treated with high NaOCl concentrations and long contact times. Size exclusion chromatography showed that the hypochlorite anion, because of its small size, penetrated the water compartments of apatite-encapsulated collagen fibrils, degraded the collagen molecules and produced a 25-35µm thick, non-uniform "ghost mineral layer" with enlarged, coalesced dentinal tubules and their lateral branches. Fourier transform-infrared spectroscopy identified increases in apatite/collagen ratio in NaOCl-treated dentin. The apatite-rich, collagen-sparse dentin matrix that remained after NaOCl treatment is more brittle, as shown by the reductions in flexural strength. Understanding the deleterious effects of NaOCl on mineralized dentin enables one to balance the risks and benefits in using high NaOCl concentrations for lengthy periods in root canal debridement. Delineating the mechanism responsible for such a phenomenon enables high molecular weight, polymeric antimicrobial and tissue dissolution irrigants to be designed that abides by the maxim of 'primum non nocere' in contemporary medical practices. STATEMENT OF SIGNIFICANCE The antimicrobial and tissue-dissolution capacities of NaOCl render it a well-accepted agent for root canal debridement. These highly desirable properties, however, appear to be intertwined with the untoward effect of collagen matrix degradation within mineralized dentin. Because of its small size, the hypochlorite anion is capable of infiltrating mineralized collagen and destroying the collagen fibrils, producing a mineral-rich, collagen sparse ghost mineral matrix with reduced flexural strength. Findings from the present work challenge the biosafety of NaOCl when it is used in high concentrations and for lengthy time periods during root canal treatment, and laid the background work for future biomaterials design in debridement of the canal space.
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12
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Yang W, Li L, Su G, Zhang Z, Cao Y, Li X, Shi Y, Zhang Q. A collagen telopeptide binding peptide shows potential in aiding collagen bundle formation and fibril orientation. Biomater Sci 2017. [DOI: 10.1039/c6bm00574h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A double-armed CTBP-PEG-CTBP derivative of a collagen telopeptide binding peptide (CTBP), shows potential in aiding collagen bundle formation and fibril orientation by interacting with fibrils.
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Affiliation(s)
- Wenyu Yang
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Lin Li
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Guanghao Su
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Zhe Zhang
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Yiting Cao
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Xuemin Li
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
| | - Yanping Shi
- School of Chemistry and Chemical Engineering
- Tianjin University of Technology
- Tianjin
- PR China
| | - Qiqing Zhang
- The Key Laboratory of Biomedical Material of Tianjin
- Institute of Biomedical Engineering
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Tianjin
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13
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Bezerra KS, Oliveira JIN, Lima Neto JX, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Quantum binding energy features of the T3-785 collagen-like triple-helical peptide. RSC Adv 2017. [DOI: 10.1039/c6ra25206k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Structural representation of the T3-785 collagen-like triple-helical peptide depicting the 15 most and fewest energetically significant amino acids.
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Affiliation(s)
- Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | | | | | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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14
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Strauss K, Chmielewski J. Metal-Promoted Assembly of Two Collagen Mimetic Peptides into a Biofunctional "Spiraled Horn" Scaffold. MATERIALS (BASEL, SWITZERLAND) 2016; 9:E838. [PMID: 28773959 PMCID: PMC5456626 DOI: 10.3390/ma9100838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 12/27/2022]
Abstract
Biofunctional scaffolds for the delivery of living cells are of the utmost importance for regenerative medicine. Herein, a novel, robust "spiraled horn" scaffold was elucidated through the Co2+-promoted hierarchical assembly of two collagen mimetic peptides, NCoH and HisCol. Each "horn" displayed a periodic banding pattern with band lengths corresponding to the length of the collagen peptide triple helix. Strand exchange between the two peptide trimers resulted in failure to form this intricate morphology, lending support to a precise metal-ligand-based mechanism of assembly. Little change occurred to the observed morphology when the Co2+ concentration was varied from 0.5 to 4.0 mM, and the scaffold was found to be fully formed within two minutes of exposure to the metal ion. The horned network also displayed biological functionality by binding to a His-tagged fluorophore and associating with cells.
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Affiliation(s)
- Kevin Strauss
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
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Newberry RW, VanVeller B, Raines RT. Thioamides in the collagen triple helix. Chem Commun (Camb) 2016; 51:9624-7. [PMID: 25967743 DOI: 10.1039/c5cc02685g] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.
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Affiliation(s)
- Robert W Newberry
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA.
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Berisio R, Vitagliano L. Polyproline and triple helix motifs in host-pathogen recognition. Curr Protein Pept Sci 2013; 13:855-65. [PMID: 23305370 PMCID: PMC3707005 DOI: 10.2174/138920312804871157] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/10/2012] [Accepted: 08/30/2012] [Indexed: 01/18/2023]
Abstract
Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating host-pathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.
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Affiliation(s)
- Rita Berisio
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy
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Crestoni ME, Chiavarino B, Scuderi D, Di Marzio A, Fornarini S. Discrimination of 4-hydroxyproline diastereomers by vibrational spectroscopy of the gaseous protonated species. J Phys Chem B 2012; 116:8771-9. [PMID: 22764742 DOI: 10.1021/jp302382p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of proline is a prominent oxidative post-translational modification (oxPTM) in animals, characterized by site specificity and stereochemical control. The presence of this irreversible modification and the ensuing generation of a chiral center have been assayed in (2S,4R)-4-hydroxyproline and (2S,4S)-4-hydroxyproline forming the protonated species by electrospray ionization and sampling them by infrared multiple photon dissociation (IRMPD) spectroscopy. IRMPD spectra, recorded both in the 950-1950 cm(-1) (using the CLIO free electron laser) and in the 3200-3700 cm(-1) [using a tabletop parametric oscillator/amplifier (OPO/OPA) laser] regions, have been interpreted by comparison with the absorbance spectra of the lowest energy structures calculated at MP2/6-311+G** level of theory. Remarkable spectral differences have emerged in the fingerprint region, pointing to the unambiguous discrimination between S,R and S,S diastereomers. The main differences arise from the position of the carbonyl stretching mode, a signature of nonzwitterionic structures, moving from 1750 cm(-1) for the S,R form to 1770 cm(-1) for the S,S diastereomer. Furthermore, a well-defined band associated with the NH(2) wagging mode at 1333 cm(-1) is a distinct mark of the S,S isomer. Each gaseous protonated epimer comprises a population of at least three conformers, stabilized by intramolecular hydrogen bonds linking the two hydrogens of protonated secondary amine group with the 4-hydroxy substituent and with an oxygen atom of the carboxylic group, respectively. Interestingly, a tendency to adopt either C(4)-exo (up) or C(4)-endo (down) pyrrolidine puckering upon proline 4(R)- or 4(S)-hydroxylation, respectively, is observed here. The same bias is found in neutral hydroxyprolines and in collagen model peptides. In the protonated species under examination, this bias originates chirality-induced vibrational features revealed by IRMPD spectroscopy.
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Affiliation(s)
- Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, P. le A. Moro 5, I-00185 Roma, Italy.
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