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Synytsya A, Janstová D, Šmidová M, Synytsya A, Petrtýl J. Evaluation of IR and Raman spectroscopic markers of human collagens: Insides for indicating colorectal carcinogenesis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 296:122664. [PMID: 36996519 DOI: 10.1016/j.saa.2023.122664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/26/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Vibrational spectroscopic methods are widely used in the molecular diagnostics of carcinogenesis. Collagen, a component of connective tissue, plays a special role as a biochemical marker of pathological changes in tissues. The vibrational bands of collagens are very promising to distinguish between normal colon tissue, benign and malignant colon polyps. Differences in these bands indicate changes in the amount, structure, conformation and the ratio between the individual structural forms (subtypes) of this protein. The screening of specific collagen markers of colorectal carcinogenesis was carried out based on the FTIR and Raman (λex 785 nm) spectra of colon tissue samples and purified human collagens. It was found that individual types of human collagens showed significant differences in their vibrational spectra, and specific spectral markers were found for them. These collagen bands were assigned to specific vibrations in the polypeptide backbone, amino acid side chains and carbohydrate moieties. The corresponding spectral regions for colon tissues and colon polyps were investigated for the contribution of collagen vibrations. Mentioned spectral differences in collagen spectroscopic markers could be of interest for early ex vivo diagnosis of colorectal carcinoma if combine vibrational spectroscopy and colonoscopy.
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Affiliation(s)
- Alla Synytsya
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic.
| | - Daniela Janstová
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Miroslava Šmidová
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Andriy Synytsya
- Department of Carbohydrates and Cereals, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Jaromír Petrtýl
- 4th Internal Clinic-Gastroenterology and Hepatology, 1(st) Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, U Nemocnice 2, 128 00 Prague 2, Czech Republic
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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Knapinska AM, Tokmina-Roszyk D, Amar S, Tokmina-Roszyk M, Mochalin VN, Gogotsi Y, Cosme P, Terentis AC, Fields GB. Solid-phase synthesis, characterization, and cellular activities of collagen-model nanodiamond-peptide conjugates. Biopolymers 2016; 104:186-95. [PMID: 25753561 DOI: 10.1002/bip.22636] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/24/2015] [Accepted: 02/24/2015] [Indexed: 01/10/2023]
Abstract
Nanodiamonds (NDs) have received considerable attention as potential drug delivery vehicles. NDs are small (∼5 nm diameter), can be surface modified in a controllable fashion with a variety of functional groups, and have little observed toxicity in vitro and in vivo. However, most biomedical applications of NDs utilize surface adsorption of biomolecules, as opposed to covalent attachment. Covalent modification provides reliable and reproducible ND-biomolecule ratios, and alleviates concerns over biomolecule desorption prior to delivery. The present study has outlined methods for the efficient solid-phase conjugation of ND to peptides and characterization of ND-peptide conjugates. Utilizing collagen-derived peptides, the ND was found to support or even enhance the cell adhesion and viability activities of the conjugated sequence. Thus, NDs can be incorporated into peptides and proteins in a selective manner, where the presence of the ND could potentially enhance the in vivo activities of the biomolecule it is attached to.
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Affiliation(s)
- Anna M Knapinska
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, 34987
| | - Dorota Tokmina-Roszyk
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, 34987
| | - Sabrina Amar
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, 34987
| | - Michal Tokmina-Roszyk
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, 34987
| | - Vadym N Mochalin
- Department of Materials Science and Engineering and A.J. Drexel Nanotechnology Institute, Drexel University, Philadelphia, PA, 19104
| | - Yury Gogotsi
- Department of Materials Science and Engineering and A.J. Drexel Nanotechnology Institute, Drexel University, Philadelphia, PA, 19104
| | - Patrick Cosme
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458
| | - Gregg B Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, 33458.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, 34987.,Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL, 33458
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Shepherd D, Shepherd J, Ghose S, Kew S, Cameron R, Best S. The process of EDC-NHS Cross-linking of reconstituted collagen fibres increases collagen fibrillar order and alignment. APL MATERIALS 2015; 3:014902. [PMID: 25506518 PMCID: PMC4262854 DOI: 10.1063/1.4900887] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe the production of collagen fibre bundles through a multi-strand, semi-continuous extrusion process. Cross-linking using an EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide), NHS (N-hydroxysuccinimide) combination was considered. Atomic Force Microscopy (AFM) and Raman spectroscopy focused on how cross-linking affected the collagen fibrillar structure. In the cross-linked fibres, a clear fibrillar structure comparable to native collagen was observed which was not observed in the non-cross-linked fibre. The amide III doublet in the Raman spectra provided additional evidence of alignment in the cross-linked fibres. Raman spectroscopy also indicated no residual polyethylene glycol (from the fibre forming buffer) or water in any of the fibres.
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Affiliation(s)
- D.V. Shepherd
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK
| | - J.H. Shepherd
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK
| | - S. Ghose
- Tigenix Ltd, Byron House, Cambridge, UK
| | - S.J. Kew
- Tigenix Ltd, Byron House, Cambridge, UK
| | - R.E. Cameron
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK
| | - S.M. Best
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK
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Liu YY, Zhang Y, Zeng XA, El-Mashad H, Pan ZL, Wang QJ. Effect of Pulsed Electric Field on Microstructure of Some Amino Acid Group of Soy Protein Isolates. INTERNATIONAL JOURNAL OF FOOD ENGINEERING 2014. [DOI: 10.1515/ijfe-2013-0033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The effect of a pulsed electric field (PEF) on the microstructure of some amino acids was studied. Raman spectrum was used to determine the effect of PEF on tyrosine, tryptophan, proline residues, histidine, arginine, aliphatic amino acid, disulfide bond, and polypeptide backbone in soy protein isolates (SPI). Results suggested that increasing the intensity of PEF gradually to 50 kV cm−1 led to a reduction in gauche C–S conformation of CCSSCC dihedral angles. The increase of the PEF intensity caused an increase in the gauche–gauche–gauche conformation of the disulfide bond accompanying a decrease in α-helix and β-sheet and an increase in antiparallel β-sheet and disorder structure. A critical pulse intensity of 30 kV cm−1 was observed for unfolding and reassembling of SPI, which was verified in our previous study (Liu et al., Eur Food Res Technol 233:841–50). When the pulse intensity gradually increased to around 30 kV cm−1, the exposure of tyrosine and tryptophan, the vibration of CH2 wagging in proline and CH2 in the midazole ring of histidine, the vibration of C—H bending and C—N stretching inside a charged arginine, and asymmetric H—C—H bending deformation vibration in CH2 and CH3 groups in aromatic and aliphatic amino acids gradually increased, suggesting an unfolding of protein molecules. When the pulse intensity continually increased from 30 to 50 kV cm−1, the microstructure of all above amino acids decreased due to the reassembly of unfolding proteins.
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Ronda L, Merlino A, Bettati S, Verde C, Balsamo A, Mazzarella L, Mozzarelli A, Vergara A. Role of tertiary structures on the Root effect in fish hemoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1885-93. [PMID: 23376186 DOI: 10.1016/j.bbapap.2013.01.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
Abstract
Many fish hemoglobins exhibit a marked dependence of oxygen affinity and cooperativity on proton concentration, called Root effect. Both tertiary and quaternary effects have been evoked to explain the allosteric regulation brought about by protons in fish hemoglobins. However, no general rules have emerged so far. We carried out a complementary crystallographic and microspectroscopic characterization of ligand binding to crystals of deoxy-hemoglobin from the Antarctic fish Trematomus bernacchii (HbTb) at pH6.2 and pH8.4. At low pH ligation has negligible structural effects, correlating with low affinity and absence of cooperativity in oxygen binding. At high pH, ligation causes significant changes at the tertiary structural level, while preserving structural markers of the T state. These changes mainly consist in a marked displacement of the position of the switch region CD corner towards an R-like position. The functional data on T-state crystals validate the relevance of the crystallographic observations, revealing that, differently from mammalian Hbs, in HbTb a significant degree of cooperativity in oxygen binding is due to tertiary conformational changes, in the absence of the T-R quaternary transition. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma, Parma, Italy
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