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Berger E, Niemelä J, Lampela O, Juffer AH, Komsa HP. Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities. J Chem Inf Model 2024. [PMID: 38829726 DOI: 10.1021/acs.jcim.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.
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Affiliation(s)
- Ethan Berger
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
| | - Juha Niemelä
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Outi Lampela
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - André H Juffer
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Hannu-Pekka Komsa
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
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2
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Frolov NE, Shishkina AV, Vener MV. Specific Proton-Donor Properties of Glycine Betaine. Metric Parameters and Enthalpy of Noncovalent Interactions in its Dimer, Water Complexes and Crystalline Hydrate. Int J Mol Sci 2023; 24:12971. [PMID: 37629150 PMCID: PMC10455243 DOI: 10.3390/ijms241612971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Trimethylglycine (glycine betaine, GB) is an important organic osmolyte that accumulates in various plant species in response to environmental stresses and has significant potential as a bioactive agent with low environmental impact. It is assumed that the hydration of GB is playing an important role in the protective mechanism. The hydration and aggregation properties of GB have not yet been studied in detail at the atomistic level. In this work, noncovalent interactions in the GB dimer and its complexes with water and crystalline monohydrate are studied. Depending on the object, periodic and non-periodic DFT calculations are used. Particular attention is paid to the metric parameters and enthalpies of intermolecular hydrogen bonds. The identification of noncovalent interactions is carried out by means of the Bader analysis of periodic or non-periodic electron density. The enthalpy of hydrogen bonds is estimated using the Rosenberg formula (PCCP 2 (2000) 2699). The specific proton donor properties of glycine betaine are due to its ability to form intermolecular C-H∙∙∙O bonds with the oxygen atom of a water molecule or the carboxylate group of a neighboring GB. The enthalpy of these bonds can be significantly greater than 10 kJ/mol. The water molecule that forms a hydrogen bond with the carboxylate group of GB also interacts with its CH groups through lone pairs of electrons. The C-H∙∙∙O bonds contribute up to 40% of the total entropy of the GB-water interaction, which is about 45 kJ/mol. The possibility of identifying C-H∙∙∙O bonds by the proton nuclear magnetic resonance method is discussed.
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Affiliation(s)
- Nikita E. Frolov
- V. M. Gorbatov Federal Research Center for Food Systems, Talalikhina St., 26, Moscow 109316, Russia;
| | - Anastasia V. Shishkina
- Department of Physics and Engineering Environmental Protection, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163001, Russia;
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
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3
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Shim JH, Gwak S, Ahn BK, Han H, Hong Y, Shin OS. Investigation of d-Amino Acid-Based Surfactants and Nanocomposites with Gold and Silica Nanoparticles as against Multidrug-Resistant Bacteria Agents. ACS OMEGA 2022; 7:46146-46155. [PMID: 36570237 PMCID: PMC9773340 DOI: 10.1021/acsomega.2c04220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
d-amino acid-based surfactants (d-AASs) were synthesized and their antimicrobial activity was evaluated. N-α-lauroyl-d-arginine ethyl ester hydrochloride (d-LAE), d-proline dodecyl ester (d-PD), and d-alanine dodecyl ester (d-AD) were found to have antibacterial activity against both Gram-positive and -negative bacteria, but less efficacy against Gram-negative bacteria. For these reasons, combining antimicrobial agents with nanoparticles is a promising technique for improving their antibacterial properties to eliminate drug-resistant pathogens. d-LAE coated on gold (AuNP) and silica (SiNP) nanoparticles has more efficient antibacterial activity than that of d-LAE alone. However, unlike d-LAE, d-PD has enhanced antibacterial activity upon being coated on AuNP. The antibacterial d-AASs and their nanocomposites with nanoparticles were synthesized in an environmentally friendly manner and are expected to be valuable new antimicrobial agents against multidrug-resistant (MDR) pathogens.
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Affiliation(s)
- Jae Ho Shim
- Department
of Anatomy, Korea University College of
Medicine, Seoul 02842, Korea
| | - Sungduk Gwak
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Byung Kook Ahn
- Department
of Anatomy, Korea University College of
Medicine, Seoul 02842, Korea
| | - Hogyu Han
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Yeonsun Hong
- Department
of Microbiology and Immunology, David H. Smith Center for Vaccine
Biology and Immunology, University of Rochester, Rochester, New York 14642, United States
| | - Ok Sarah Shin
- BK21
Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
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4
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Abadian H, Cornette P, Costa D, Mezzetti A, Gervais C, Lambert JF. Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8038-8053. [PMID: 35737817 DOI: 10.1021/acs.langmuir.2c00841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO2 together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.
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Affiliation(s)
- Hagop Abadian
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Pauline Cornette
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Dominique Costa
- Institut de Recherche de Chimie Paris (IRCP, UMR8247 CNRS), 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Kour P, Afzal S, Gani A, Zargar MI, Nabi Tak U, Rashid S, Dar AA. Effect of nanoemulsion-loaded hybrid biopolymeric hydrogel beads on the release kinetics, antioxidant potential and antibacterial activity of encapsulated curcumin. Food Chem 2021; 376:131925. [PMID: 34973641 DOI: 10.1016/j.foodchem.2021.131925] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 12/16/2022]
Abstract
Nanoemulsion encapsulated in the hydrogel beads are important entrants for loading hydrophobic active ingredients for enhancing their bioavailability and biological activities relevant in the pharmaceutical, food and cosmetic industries. Herein, we report the formulation of curcumin-loaded nanoemulsion encapsulated in ionotropic hybrid hydrogel beads of alginate, chitosan, gelatin and polyethylene oxide for effective delivery of curcumin. The release behaviour in simulated gastric and intestinal fluids (SGF and SIF) at 37 °C showed faster release in SGF which could be explained on the basis of mesh size, the extent of hydration and the complexation of the curcumin with the Ca2+ ions present within the hydrogel network. The free radical scavenging and antibacterial activities of the released curcumin in SGF were significantly greater than in SIF. This study shows promises of such hybrid systems, ignored so far, for proper encapsulation, protection and delivery of curcumin for the development of functional foods and pharmaceutics. The high structural stability of these nanoemulsion carriers and their effective delivery of curcumin provide a novel and tailored formulation out of existing polymers with plethora of advantages for oral drug delivery. Moreover, this study opens new door for different possibilities to improve the physicochemical characteristics and delivery of bioactive molecules like curcumin.
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Affiliation(s)
- Pawandeep Kour
- Soft Matter Research Group, Physical Chemistry Section, Department of Chemistry, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Saima Afzal
- Soft Matter Research Group, Physical Chemistry Section, Department of Chemistry, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Adil Gani
- Department of Food Science and Technology, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Mohammed Iqbal Zargar
- Department of Pharmaceutical Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Umar Nabi Tak
- Soft Matter Research Group, Physical Chemistry Section, Department of Chemistry, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Showkat Rashid
- Soft Matter Research Group, Physical Chemistry Section, Department of Chemistry, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Aijaz Ahmad Dar
- Soft Matter Research Group, Physical Chemistry Section, Department of Chemistry, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India.
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6
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Riedel S, Ward D, Kudláčková R, Mazur K, Bačáková L, Kerns JG, Allinson SL, Ashton L, Koniezcny R, Mayr SG, Douglas TEL. Electron Beam-Treated Enzymatically Mineralized Gelatin Hydrogels for Bone Tissue Engineering. J Funct Biomater 2021; 12:jfb12040057. [PMID: 34698221 PMCID: PMC8544455 DOI: 10.3390/jfb12040057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/25/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022] Open
Abstract
Biological hydrogels are highly promising materials for bone tissue engineering (BTE) due to their high biocompatibility and biomimetic characteristics. However, for advanced and customized BTE, precise tools for material stabilization and tuning material properties are desired while optimal mineralisation must be ensured. Therefore, reagent-free crosslinking techniques such as high energy electron beam treatment promise effective material modifications without formation of cytotoxic by-products. In the case of the hydrogel gelatin, electron beam crosslinking further induces thermal stability enabling biomedical application at physiological temperatures. In the case of enzymatic mineralisation, induced by Alkaline Phosphatase (ALP) and mediated by Calcium Glycerophosphate (CaGP), it is necessary to investigate if electron beam treatment before mineralisation has an influence on the enzymatic activity and thus affects the mineralisation process. The presented study investigates electron beam-treated gelatin hydrogels with previously incorporated ALP and successive mineralisation via incubation in a medium containing CaGP. It could be shown that electron beam treatment optimally maintains enzymatic activity of ALP which allows mineralisation. Furthermore, the precise tuning of material properties such as increasing compressive modulus is possible. This study characterizes the mineralised hydrogels in terms of mineral formation and demonstrates the formation of CaP in dependence of ALP concentration and electron dose. Furthermore, investigations of uniaxial compression stability indicate increased compression moduli for mineralised electron beam-treated gelatin hydrogels. In summary, electron beam-treated mineralized gelatin hydrogels reveal good cytocompatibility for MG-63 osteoblast like cells indicating a high potential for BTE applications.
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Affiliation(s)
- Stefanie Riedel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; (R.K.); (S.G.M.)
- Division of Surface Physics, Faculty of Physics and Earth Science, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
- Correspondence: (S.R.); (T.E.L.D.)
| | - Daniel Ward
- Division of Biomedical and Life Sciences (BLS), Faculty of Health and Medicine, Furness College, Lancaster University, Lancaster LA1 4YG, UK; (D.W.); (S.L.A.)
| | - Radmila Kudláčková
- Department of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic; (R.K.); (L.B.)
| | - Karolina Mazur
- Faculty of Materials Engineering and Physics, Institute of Materials Engineering, Tadeusz Kosciuszko Cracow University of Technology, al. Jana Pawła II 37, 31-864 Cracow, Poland;
| | - Lucie Bačáková
- Department of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic; (R.K.); (L.B.)
| | - Jemma G. Kerns
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK;
| | - Sarah L. Allinson
- Division of Biomedical and Life Sciences (BLS), Faculty of Health and Medicine, Furness College, Lancaster University, Lancaster LA1 4YG, UK; (D.W.); (S.L.A.)
| | - Lorna Ashton
- Chemistry Department, Lancaster University, Lancaster LA1 4YB, UK;
| | - Robert Koniezcny
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; (R.K.); (S.G.M.)
| | - Stefan G. Mayr
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; (R.K.); (S.G.M.)
- Division of Surface Physics, Faculty of Physics and Earth Science, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
| | - Timothy E. L. Douglas
- Engineering Department, Lancaster University, Lancaster LA1 4YW, UK
- Materials Science Institute (MSI), Lancaster University, Lancaster LA1 4YW, UK
- Correspondence: (S.R.); (T.E.L.D.)
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7
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Williams AE, Hammer NI, Fortenberry RC, Reinemann DN. Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study. Molecules 2021; 26:4790. [PMID: 34443382 PMCID: PMC8399447 DOI: 10.3390/molecules26164790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.
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Affiliation(s)
- Ashley E. Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Nathan I. Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Dana N. Reinemann
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, USA
- Department of Chemical Engineering, University of Mississippi, University, MS 38677, USA
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8
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Vesga MJ, McKechnie D, Laing S, Kearns H, Faulds K, Johnston K, Sefcik J. Effect of glycine on aggregation of citrate-functionalised gold nanoparticles and SERS measurements. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:641-651. [PMID: 33558954 PMCID: PMC8189991 DOI: 10.1007/s00249-021-01507-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 01/25/2023]
Abstract
Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system.
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10
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Williams AE, Davis JE, Reynolds JE, Fortenberry RC, Hammer NI, Reinemann DN. Determination of vibrational band positions in the E-hook of β-tubulin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118895. [PMID: 32919160 DOI: 10.1016/j.saa.2020.118895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/22/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Raman spectral characterization of the β-TUBB2A E-hook hexapeptide, EGEDEA, is determined through experimental analysis combined with full geometry optimizations and corresponding harmonic vibrational frequency computations employing DFT methods. The hexapeptide is first broken down into di- and tetrapeptide fragments which are analyzed both quantum chemically and experimentally, and then combined to achieve an energetic minimum of the large EGEDEA hexapeptide. The Raman spectral characterization of EGEDEA band positions are then verified via the literature and comparison to the small fragment's similarly located band positions. The approach employed provides further evidence for the use of fragments as a helpful tool in characterization of the vibrational band positions of large peptides. STATEMENT OF SIGNIFICANCE: To investigate β-TUBB2A E-hook hexapeptide, a unique approach is employed whereby the hexapeptide is broken into fragments, EG, ED, EA, EGED, and EDEA and analyzed via experimental Raman spectroscopy of the crystalline solids. The experimentally observed vibrational band positions are compared to those computed using and scaled from DFT methods and Pople's 6-311+G(2df,2pd) basis set. The reported vibrational band positions are also confirmed by previously reported bands of similar peptides in the literature. This methodology facilitates differentiation between the behaviors of various side chains and their influence on the structure of the hexapeptide, providing insight into not only the nature of the peptide but also defining regions for potential protein and cytoplasmic interactions, without requiring excessive computing resources or overly-sensitive experimental methods.
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Affiliation(s)
- Ashley E Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Juliana E Davis
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America
| | - Justin E Reynolds
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Dana N Reinemann
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America; Department of Chemical Engineering, University of Mississippi, University, MS 38677, United States of America.
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11
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Terpugov EL, Kondratyev MS, Degtyareva OV. Light-induced effects in glycine aqueous solution studied by Fourier transform infrared-emission spectroscopy and ultraviolet-visible spectroscopy. J Biomol Struct Dyn 2020; 39:108-117. [PMID: 31948354 DOI: 10.1080/07391102.2020.1717628] [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: 10/25/2022]
Abstract
Although amino acids are insensitive to visible light, as is generally accepted, we show that particular light-matter interaction can break this obviousness. Using sensitive (FT-IR)-technique in a combination of a broadband visible light source, we registered emission spectra of glycine in the range 2500-500 cm-1. Sensitivity of the infrared emission spectrum to the exciting power -induced changes in the glycine structure was demonstrated experimentally.Vibrational spectra of glycine displayed the prominent spectral features of CH2, COO-, COOH, NH+3 groups in the "fingerprint region". Simultaneous appearance of ionised COO- and unionised COOH forms of glycine in solution at neutral pH clearly indicated that visible light induces the partial protonation of COO- groups; if so, visible light irradiation should lead to occurrence of dimers or dimeric hydrogen - bonded structures. Spectroscopic and microscopic evidence of visible light-mediated formation of aggregates and nucleus in aqueous solution was presented.Electronic absorption/emission spectra of glycine in aqueous solution were primarily characterized in the near ultraviolet-visible region (240-600 nm). Negligible absorption near 270 nm was observed for a 1.0 M solution and dramatically enhanced with its "aging". Moreover, an extension of the absorption edge into the region above 400 nm could be seen. Due to the visible light irradiation, we observed modification of electronic structure or occurrence of additional species causing changes in absorption of glycine amino acid. For "aged" solution, it was shown that excitation spectra corresponding to the different emission wavelengths were entirely different, at that each excitation-spectral band had a characteristic emission band.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Evgeni L Terpugov
- Institute of Cell Biophysics Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Maxim S Kondratyev
- Institute of Cell Biophysics Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Olga V Degtyareva
- Institute of Cell Biophysics Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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12
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Biswas A, Mallik BS. Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell. RSC Adv 2020. [DOI: 10.1039/c9ra10521b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
| | - Bhabani S. Mallik
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
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13
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Ettah I, Ashton L. Determination of Phosphorylation and Deprotonation Induced Higher Order Structural Transitions in αs-Caseins. Anal Chem 2019; 91:13940-13946. [DOI: 10.1021/acs.analchem.9b03457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ilokugbe Ettah
- Department of Chemistry, Lancaster University, Lancaster, Lancashire LA1 4YB, United Kingdom
| | - Lorna Ashton
- Department of Chemistry, Lancaster University, Lancaster, Lancashire LA1 4YB, United Kingdom
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14
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pH-dependent adsorption of α-amino acids, lysine, glutamic acid, serine and glycine, on TiO2 nanoparticle surfaces. J Colloid Interface Sci 2019; 554:362-375. [DOI: 10.1016/j.jcis.2019.06.086] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/28/2022]
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15
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Koyambo-Konzapa SJ, Dhaouadi Z, Nsangou M. Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method. J Mol Graph Model 2019; 88:194-202. [DOI: 10.1016/j.jmgm.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022]
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16
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Bajaj N, Bhatt H, Vishwakarma SR, Deo MN. Orientational Adaptations Leading to Plausible Phase Transitions in l-Leucine at Low Temperatures: Revealed by Infrared Spectroscopy. J Phys Chem B 2019; 123:561-570. [PMID: 30605334 DOI: 10.1021/acs.jpcb.8b09590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonding is essential for the stability of amino acids. A change in the geometry and conformation of hydrogen bonds in such molecular systems, for example, under varying thermodynamic conditions of temperature/pressure, may lead to subtle or drastic phase transitions. We demonstrate here the mechanism of temperature-induced phase transitions in the polycrystalline solid sample of l-leucine [(CH3)2-C(4)H-C(3)H2-C(2)H(C(1)OO-)(NH3+)], an "essential" amino acid, using in situ Fourier transform infrared spectroscopy in the temperature range 300-4.3 K. Unambiguous spectral signatures of preferred microstructural changes have been reported, which are linked to phase transitions at ∼150 and ∼240 K. The transition at 150 K is found to be associated with a sudden change in reorientation dynamics of the torsional vibrations of the (C3C4) group. In contrast, the transition at 240 K is associated with the conformational distortions in the NH3 group, which causes strengthening of the hydrogen bonds in the ac-plane forming two-dimensional sheets, well separated from each other in the b-direction. These findings pave the way toward settling the long-standing debate on the temperature-induced behavior of l-leucine as well as harnessing its physicochemical properties.
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Affiliation(s)
- Naini Bajaj
- High Pressure & Synchrotron Radiation Physics Division , Bhabha Atomic Research Centre , Mumbai 400085 , India.,Homi Bhabha National Institute , Anushakti Nagar , Mumbai 400094 , India
| | - Himal Bhatt
- High Pressure & Synchrotron Radiation Physics Division , Bhabha Atomic Research Centre , Mumbai 400085 , India
| | - S R Vishwakarma
- High Pressure & Synchrotron Radiation Physics Division , Bhabha Atomic Research Centre , Mumbai 400085 , India
| | - M N Deo
- High Pressure & Synchrotron Radiation Physics Division , Bhabha Atomic Research Centre , Mumbai 400085 , India.,Homi Bhabha National Institute , Anushakti Nagar , Mumbai 400094 , India
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17
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Sakhno Y, Battistella A, Mezzetti A, Jaber M, Georgelin T, Michot L, Lambert JF. One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica. Chemistry 2019; 25:1275-1285. [PMID: 30284764 DOI: 10.1002/chem.201803845] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 12/17/2022]
Abstract
Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.
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Affiliation(s)
- Yuriy Sakhno
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alice Battistella
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Maguy Jaber
- Laboratoire d'Archéologie Moléculaire et Structurale, UMR 8220, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Thomas Georgelin
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France.,Temporary address: Centre de Biophysique Moléculaire, UPR 4301, CNRS, Rue Charles Sadron CS 80054, 45071, Orléans CEDEX 2, France
| | - Laurent Michot
- Laboratoire de Physicochimie des Electrolytes et Nanosystèmes Interfaciaux, UMR 8234, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
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18
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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19
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Fang H, Liu X, Sun CQ, Huang Y. Phonon Spectrometric Evaluation of the Solute-Solvent Interface in Solutions of Glycine and Its N-Methylated Derivatives. J Phys Chem B 2018; 122:7403-7408. [PMID: 29965768 DOI: 10.1021/acs.jpcb.8b05373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
From the perspective of O:H-O bond cooperativity, we analyzed the solute capability of transiting the O:H-O bond from the mode of ordinary water to the hydration state and its consequence on the solution viscosity and surface stress. Phonon spectrometric results suggest that glycine and its N-methyl derivatives strongly affect the surrounding solvent molecules through H ↔ H repulsion and dipolar polarization. The H ↔ H interproton repulsion disrupts the surface stress, and the polarization enhances the solution viscosity.
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Affiliation(s)
- Hengxin Fang
- School of Materials Science and Engineering , Xiangtan University , Xiangtan 411105 , China
| | - Xinjuan Liu
- CBME, College of Materials Science and Engineering , China Jiliang University , Hangzhou 310018 , China
| | - Chang Q Sun
- NOVITAS, Nanyang Technological University , 639798 Singapore
| | - Yongli Huang
- School of Materials Science and Engineering , Xiangtan University , Xiangtan 411105 , China
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20
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A Raman-spectroscopy-based approach for detection and discrimination of Streptococcus thermophilus and Lactobacillus bulgaricus phages at low titer in raw milk. Folia Microbiol (Praha) 2018; 63:627-636. [DOI: 10.1007/s12223-018-0604-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/02/2018] [Indexed: 12/11/2022]
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21
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Pazderka T, Kopecký V. Drop coating deposition Raman spectroscopy of proteinogenic amino acids compared with their solution and crystalline state. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:207-216. [PMID: 28577510 DOI: 10.1016/j.saa.2017.05.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/03/2017] [Accepted: 05/20/2017] [Indexed: 06/07/2023]
Abstract
The Raman spectra of 20 proteinogenic amino acids were recorded in the solution, glass phase (as drop coating deposition Raman (DCDR) samples) and crystalline forms in the wide spectral range of 200-3200cm-1. The most apparent spectral differences between the Raman spectra of the crystalline forms, glass phases and aqueous solutions of amino acids were briefly discussed and described in the frame of published works. The possible density dependencies of spectral bands were noted. In some cases, a strong influence of the sample density, as well as of the organization of the water envelope, was observed. The most apparent changes were observed for Ser and Thr. Nevertheless, for the majority of amino acids, the DCDR sample form is an intermediate between the solution and crystalline forms. In contrast, aromatic amino acids have only a small sensitivity to the form of the sample. Our reference set of Raman spectra is useful for revealing discrepancies between the SERS and solid/solution spectra of amino acids. We also found that some previously published Raman spectra of polycrystalline samples resemble glassy state rather than crystalline spectra. Therefore, this reference set of spectra will find application in every branch of Raman spectroscopy where the spectra of biomolecules are collected from coatings.
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Affiliation(s)
- Tomáš Pazderka
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic.
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22
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Numata Y, Otsuka M, Yamagishi K, Tanaka H. Quantitative Determination of Glycine, Alanine, Aspartic Acid, Glutamic Acid, Phenylalanine, and Tryptophan by Raman Spectroscopy. ANAL LETT 2017. [DOI: 10.1080/00032719.2016.1193189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yasushi Numata
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Japan
| | - Maria Otsuka
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Japan
| | - Kenji Yamagishi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Japan
| | - Hiroyuki Tanaka
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Japan
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23
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Jannone JM, Grigg JI, Aguirre LM, Jones EM. Electrostatic Interactions at N- and C-Termini Determine Fibril Polymorphism in Serum Amyloid A Fragments. J Phys Chem B 2016; 120:10258-10268. [PMID: 27632709 DOI: 10.1021/acs.jpcb.6b07672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid polymorphism presents a challenge to physical theories of amyloid formation and stability. The amyloidogenic protein serum amyloid A (SAA) exhibits complex and unexplained structural polymorphism in its N-terminal fragments: the N-terminal 11-residue peptide (SAA1-11) forms left-handed helical fibrils, while extension by one residue (SAA1-12) produces a rare right-handed amyloid. In this study, we use a combination of vibrational spectroscopy and ultramicroscopy to examine fibrils of these peptides and their terminally acetylated and amidated variants, in an effort to uncover the physical basis for this effect. Raman spectroscopy and atomic force microscopy provide evidence that SAA1-12 forms a β-helical fibril architecture, while SAA1-11 forms more typical stacked β-sheets. Importantly, N-terminal acetylation blocks fibril formation by SAA1-12 with no effect on SAA1-11, while C-terminal amidation has nearly the opposite effect. Together, these data suggest distinct electrostatic interactions at the N- and C-termini stabilize the two fibril structures; we propose model fibril structures in which C-terminal extension changes the favored intermolecular interaction between peptide monomers from an Arg1-C-terminus charge pair to an N-terminus-C-terminus charge pair. This model suggests a general mechanism for charge-mediated amyloid polymorphism and may inform strategies for design of peptide-based nanomaterials stabilized by engineered intermolecular contacts.
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Affiliation(s)
- Justine M Jannone
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - James I Grigg
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - Lauren M Aguirre
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - Eric M Jones
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
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24
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Meng L, Wu W, Lin Z. Electronic structures of intermolecular hydrogen bond contacts with solute in aqueous solution: glycine as a working prototype. Phys Chem Chem Phys 2016; 18:15894-8. [PMID: 27243041 DOI: 10.1039/c5cp07968c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intermolecular hydrogen bond (H-bond) interactions play vital roles in many biological systems. Despite continued interest, the nature of their electronic structures has remained elusive. Based on the unique features of aqueous solution, a simple model depicting the H-bond electronic states by orbital hybridizations is developed. The model is demonstrated by reproducing the experimental IR data and yielding favorable solute-solvent interactions for the prototype glycine. The H-bond state for solute H, O and N atoms is found to be characterized by sp(1), sp(2), and sp(3) hybridizations, respectively. The model provides a new way for probing the intricate solute-solvent contacts.
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Affiliation(s)
- Lingbiao Meng
- Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900, China.
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25
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Timón V, Gálvez Ó, Maté B, Tanarro I, Herrero VJ, Escribano R. Theoretical model of the interaction of glycine with hydrogenated amorphous carbon (HAC). Phys Chem Chem Phys 2015; 17:28966-76. [PMID: 26456640 DOI: 10.1039/c5cp03938j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical model of hydrogenated amorphous carbon (HAC) is developed and applied to study the interaction of glycine with HAC surfaces at astronomical temperatures. Two models with different H content are tried for the HAC surface. The theory is applied at the Density Functional Theory (DFT) level, including a semiempirical dispersion correlation potential, d-DFT or Grimme DFT-D2. The level of theory is tested on glycine adsorption on a Si(001) surface. Crystalline glycine is also studied in its two stable phases, α and β, and the metastable γ phase. For the adsorption on Si or HAC surfaces, molecular glycine is introduced in the neutral and zwitterionic forms, and the most stable configurations are searched. All theoretical predictions are checked against experimental observations. HAC films are prepared by plasma enhanced vapor deposition at room temperature. Glycine is deposited at 20 K into a high vacuum, cold temperature chamber, to simulate astronomical conditions. Adsorption takes place through the acidic group COO(-) and when several glycine molecules are present, they form H-bond chains among them. Comparison between experiments and predictions suggests that a possible way to improve the theoretical model would require the introduction of aliphatic chains or a polycyclic aromatic core. The lack of previous models to study the interaction of amino-acids with HAC surfaces provides a motivation for this work.
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Affiliation(s)
- Vicente Timón
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Óscar Gálvez
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Belén Maté
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Isabel Tanarro
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Víctor J Herrero
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Rafael Escribano
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
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26
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Koyambo-Konzapa SJ, Minguirbara A, Nsangou M. Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine. J Mol Model 2015; 21:189. [DOI: 10.1007/s00894-015-2718-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 06/01/2015] [Indexed: 11/24/2022]
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27
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Gaillard T, Trivella A, Stote RH, Hellwig P. Far infrared spectra of solid state L-serine, L-threonine, L-cysteine, and L-methionine in different protonation states. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:301-307. [PMID: 26056980 DOI: 10.1016/j.saa.2015.05.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 06/04/2023]
Abstract
In this study, experimental far infrared measurements of L-serine, L-threonine, L-cysteine, and L-methionine are presented showing the spectra for the 1.0-13.0 pH range. In parallel, solid state DFT calculations were performed on the amino acid zwitterions in the crystalline form. We focused on the lowest frequency far infrared normal modes, which required the most precision and convergence of the calculations. Analysis of the computational results, which included the potential energy distribution of the vibrational modes, permitted a detailed and almost complete assignment of the experimental spectrum. In addition to characteristic signals of the two main acid-base couples, CO2H/CO2(-) and NH3(+)/NH2, specific side chain contributions for these amino acids, including CCO and CCS vibrational modes were analyzed. This study is in line with the growing application of FIR measurements to biomolecules.
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Affiliation(s)
- Thomas Gaillard
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
| | - Aurélien Trivella
- Laboratoire de bio électrochimie et spectroscopie, UMR7140, Chimie de la Matière complexe, Université de Strasbourg, CNRS, 1 rue Blaise Pascal, F-67070 Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch CEDEX, France
| | - Petra Hellwig
- Laboratoire de bio électrochimie et spectroscopie, UMR7140, Chimie de la Matière complexe, Université de Strasbourg, CNRS, 1 rue Blaise Pascal, F-67070 Strasbourg, France.
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28
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
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Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
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29
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Gómez de la Cuesta R, Goodacre R, Ashton L. Monitoring antibody aggregation in early drug development using Raman spectroscopy and perturbation-correlation moving windows. Anal Chem 2014; 86:11133-40. [PMID: 25329604 DOI: 10.1021/ac5038329] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we demonstrate the sensitivity of two-dimensional perturbation-correlation moving windows (PCMW) to characterize conformational transitions in antibodies. An understanding of how physiochemical properties affect protein stability and instigate aggregation is essential for the engineering of antibodies. In order to establish the potential of PCMW as a technique for early identification of aggregation mechanisms during antibody development, five antibodies with varying propensity to aggregate were compared. Raman spectra were acquired, using a 532 nm excitation wavelength as the protein samples were heated from 56 to 78 °C and analyzed with PCMW. Initial principal component analysis confirmed a trend between the observed spectral variations and increasing temperature for all five samples. Analysis using PCMW revealed that when spectral variations were directly related to temperature, distinct differences in conformational changes could be determined between samples related to protein stability, providing a greater understanding of the aggregation mechanisms of problematic antibody variants.
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30
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Sjöberg B, Foley S, Cardey B, Enescu M. An experimental and theoretical study of the amino acid side chain Raman bands in proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:300-11. [PMID: 24681316 DOI: 10.1016/j.saa.2014.02.080] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 05/15/2023]
Abstract
The Raman spectra of a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was tryptophan, tyrosine, phenylalanine, glycine, methionine, histidine, lysine and leucine were measured in H2O. The theoretical Raman spectra obtained using density functional theory (DFT) calculations at the B3LYP/6-311+G(2df,2pd) level of theory allows a precise attribution of the vibrational bands. The experimental results show that there is a blue shift in the frequencies of several bands of the amino acid side chains in tripeptides compared to free amino acids, especially in the case of AAs containing aromatic rings. On the other hand, a very good agreement was found between the Raman bands of AA residues in tripeptides and those measured on three model proteins: bovine serum albumin, β-lactoglobulin and lysozyme. The present analysis contributes to an unambiguous interpretation of the protein Raman spectra that is useful in monitoring the biological reactions involving AA side chains alteration.
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Affiliation(s)
- Béatrice Sjöberg
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| | - Sarah Foley
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France.
| | - Bruno Cardey
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| | - Mironel Enescu
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
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31
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Mojibola A, Dongmo-Momo G, Mohammed M, Aslan K. Crystal Engineering of l-Alanine with l-Leucine Additive using Metal-Assisted and Microwave-Accelerated Evaporative Crystallization. CRYSTAL GROWTH & DESIGN 2014; 14:2494-2501. [PMID: 24839404 PMCID: PMC4018178 DOI: 10.1021/cg500204t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/21/2014] [Indexed: 05/04/2023]
Abstract
In this work, we demonstrated that the change in the morphology of l-alanine crystals can be controlled with the addition of l-leucine using the metal-assisted and microwave accelerated evaporative crystallization (MA-MAEC) technique. Crystallization experiments, where an increasing stoichiometric amount of l-leucine is added to initial l-alanine solutions, were carried out on circular poly(methyl methacrylate) (PMMA) disks modified with a 21-well capacity silicon isolator and silver nanoparticle films using microwave heating (MA-MAEC) and at room temperature (control experiments). The use of the MA-MAEC technique afforded for the growth of l-alanine crystals with different morphologies up to ∼10-fold faster than those grown at room temperature. In addition, the length of l-alanine crystals was systematically increased from ∼380 to ∼2000 μm using the MA-MAEC technique. Optical microscope images revealed that the shape of l-alanine crystals was changed from tetragonal shape (without l-leucine additive) to more elongated and wire-like structures with the addition of the l-leucine additive. Further characterization of l-alanine crystals was undertaken by Fourier transform infrared (FT-IR) spectroscopy, Raman spectroscopy and powder X-ray diffraction (PXRD) measurements. In order to elucidate the growth mechanism of l-alanine crystals, theoretical simulations of l-alanine's morphology with and without l-leucine additive were carried out using Materials Studio software in conjunction with our experimental data. Theoretical simulations revealed that the growth of l-alanine's {011} and {120} crystal faces were inhibited due to the incorporation of l-leucine into these crystal faces in selected positions.
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Wei Z, Chen D, Zhao H, Li Y, Zhu J, Liu B. Ab initio investigation of the first hydration shell of protonated glycine. J Chem Phys 2014; 140:085103. [DOI: 10.1063/1.4862985] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Singh S, Srivastava SK, Donfack P, Schlücker S, Materny A, Asthana BP. Molecular interactions of 2'-deoxyguanosine 5'-monophosphate with glycine in aqueous media probed via concentration and pH dependent Raman spectroscopic investigations and DFT study. Phys Chem Chem Phys 2013; 14:14315-24. [PMID: 23008833 DOI: 10.1039/c2cp41205e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to gain insights into nucleotide-protein interaction, the molecular interaction of glycine (Gly) with 2'-deoxyguanosine 5'-monophosphate (dGMP) was monitored in aqueous media through Raman spectroscopic measurements and density functional theory (DFT) calculations. Raman spectra of dGMP, glycine and their binary mixtures (dGMP + Gly) in aqueous media at 10 different concentrations corresponding to the dGMP : Gly molar ratios varying from 1 : 1 to 1 : 10 were recorded in the fingerprint region 2000-400 cm(-1). Raman spectra of the dGMP : Gly mixture with a molar ratio of 1 : 3 in aqueous media at 10 different pH values starting from 1 to 10 at an interval of 1 were also recorded. The DFT calculations were performed on dGMP, glycine and their various complexes with varying number of H(2)O molecules in gas phase as well as in solvation using hybrid functional B3LYP employing the high level basis set 6-311+G(d,p). The variations in the observed spectral features were explained in terms of calculated optimized structures of dGMP, glycine and their various complexes with water molecules and a good spectra-structure correlation was obtained. Raman spectra of glycine in 1.2 M aqueous solution were also recorded at three pH values, 2, 6 and 10, and the subtle differences in the spectral features were correlated with the calculated Raman spectra of protonated, deprotonated and zwitterionic forms of glycine. The results also give experimental evidence rather convincingly that the zwitterionic and protonated forms of glycine are formed at pH = 6 and 2, respectively, but even at pH = 10, deprotonated glycine is not formed. An important aspect of this study is the monitoring of the interaction of dGMP with the zwitterionic form of glycine giving insightful details regarding the binding site.
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Affiliation(s)
- Shweta Singh
- Department of Physics, Banaras Hindu University, Varanasi, India
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The effect of the amphoteric properties of amino acids in the zwitterionic form on the structure of iodine complex compounds in aqueous solutions. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.10.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
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Liu S, Hu AD, Lin Z. Extensive Computational Study on Conformations of Microsolvated Leucine Complexes. CHINESE J CHEM PHYS 2012. [DOI: 10.1088/1674-0068/25/04/409-418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Boeckx B, Nelissen W, Maes G. Potential Energy Surface and Matrix Isolation FT-IR Study of Isoleucine. J Phys Chem A 2012; 116:3247-58. [DOI: 10.1021/jp212240p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Wouter Nelissen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
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Takis PG, Melissas VS, Troganis AN. A “hidden” role of amino and imino groups is unveiled during the micro-solvation study of three biomolecule groups in water. NEW J CHEM 2012. [DOI: 10.1039/c2nj40390k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ganesan A, Wang F, Brunger M, Prince K. Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:733-742. [PMID: 21862853 DOI: 10.1107/s0909049511029499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/21/2011] [Indexed: 05/31/2023]
Abstract
Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP < 290 eV (where IP is the ionization potential). The two glycyl parent spectral peaks of the amide 291.0 eV [C((2))] and carboxylic 293.5 eV [C((1))] C atoms are shifted in the aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.
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Affiliation(s)
- Aravindhan Ganesan
- Faculty of Life and Social Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
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Panuszko A, Śmiechowski M, Stangret J. Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its N-methylated derivatives. J Chem Phys 2011; 134:115104. [PMID: 21428668 DOI: 10.1063/1.3567202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11∕12, 80-233 Gdańsk, Poland
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Zhu G, Zhu X, Fan Q, Wan X. Raman spectra of amino acids and their aqueous solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:1187-95. [PMID: 21242101 DOI: 10.1016/j.saa.2010.12.079] [Citation(s) in RCA: 247] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/24/2010] [Accepted: 12/25/2010] [Indexed: 05/14/2023]
Abstract
Amino acids are the basic "building blocks" that combine to form proteins and play an important physiological role in all life-forms. Amino acids can be used as models for the examination of the importance of intermolecular bonding in life processes. Raman spectra serve to obtain information regarding molecular conformation, giving valuable insights into the topology of more complex molecules (peptides and proteins). In this paper, amino acids and their aqueous solution have been studied by Raman spectroscopy. Comparisons of certain values for these frequencies in amino acids and their aqueous solutions are given. Spectra of solids when compared to those of the solute in solution are invariably much more complex and almost always sharper. We present a collection of Raman spectra of 18 kinds of amino acids (L-alanine, L-arginine, L-aspartic acid, cystine, L-glutamic acid, L-glycine, L-histidine, L-isoluecine, L-leucine, L-lysine, L-phenylalanine, L-methionone, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, L-valine) and their aqueous solutions that can serve as references for the interpretation of Raman spectra of proteins and biological materials.
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Affiliation(s)
- Guangyong Zhu
- Department of Chemical Engineering, Shanghai University, Shanghai, PR China
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Ottosson N, Børve KJ, Spångberg D, Bergersen H, Sæthre LJ, Faubel M, Pokapanich W, Öhrwall G, Björneholm O, Winter B. On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq). J Am Chem Soc 2011; 133:3120-30. [PMID: 21319819 DOI: 10.1021/ja110321q] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.
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Affiliation(s)
- Niklas Ottosson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
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Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VIII. Amino Acids with Aromatic Side Chains: l-Phenylalanine, l-Tyrosine, and l-Tryptophan. J Phys Chem B 2010; 114:15319-30. [DOI: 10.1021/jp106786j] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Alain Adenier
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Sergei G. Kruglik
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
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Pflüger F, Hernández B, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VII. Energy Landscapes, Energetic and Geometrical Features of L-Histidine with Protonated and Neutral Side Chains. J Phys Chem B 2010; 114:9072-83. [DOI: 10.1021/jp103348y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Belén Hernández
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine (SMBH), Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Trivella A, Gaillard T, Stote RH, Hellwig P. Far infrared spectra of solid state aliphatic amino acids in different protonation states. J Chem Phys 2010; 132:115105. [DOI: 10.1063/1.3356027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hernández B, Pflüger F, Derbel N, De Coninck J, Ghomi M. Vibrational analysis of amino acids and short peptides in hydrated media. VI. Amino acids with positively charged side chains: L-lysine and L-arginine. J Phys Chem B 2010; 114:1077-88. [PMID: 20025231 DOI: 10.1021/jp909517r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In two recent reports of the same series (J. Phys. Chem. B 2007, 111, 1470-1477 and J. Phys. Chem. B 2009, 113, 3169-3178), we have described the geometrical and vibrational analysis of glycine and amino acids (AAs) with hydrophobic side chains through the joint use of optical spectroscopy and quantum mechanical calculations. Here, we report Raman scattering and Fourier-Transform Infrared (FT-IR) Attenuated Total Reflectance (ATR) spectra measured from the aqueous solutions (H(2)O and D(2)O) of L-lysine and L-arginine, i.e. two alpha-AAs with positively charged hydrophilic side chains. The discussion on the vibrational features of both AAs could be carried out thanks to the theoretical calculations performed by means of the Density Functional Theory (DFT) approach at the B3LYP/6-31++G* level. We have analyzed the influence of implicit (with a polarizable dielectric continuum) and explicit (by means of an H(2)O cluster interacting with H-donor and H-acceptor sites of AAs) hydration models. In addition, through the calculated geometrical parameters and vibrational wavenumbers, a discussion was performed on the effect of the Cl(-) anion interacting with the positively charged side chains of explicitly hydrated AAs.
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Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Hernández B, Pflüger F, Nsangou M, Ghomi M. Vibrational analysis of amino acids and short peptides in hydrated media. IV. Amino acids with hydrophobic side chains: L-alanine, L-valine, and L-isoleucine. J Phys Chem B 2009; 113:3169-78. [PMID: 19708268 DOI: 10.1021/jp809204d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.
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Affiliation(s)
- Belén Hernández
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), UMR CNRS 7033, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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Rimola A, Civalleri B, Ugliengo P. Neutral vs zwitterionic glycine forms at the water/silica interface: structure, energies, and vibrational features from B3LYP periodic simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:14027-14034. [PMID: 19360956 DOI: 10.1021/la8029352] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.
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Affiliation(s)
- Albert Rimola
- Dipartimento di Chimica IFM and Nanostructured Interfaces and Surfaces, Centre of Excellence and INSTM (Materials Science and Technology) National Consortium, Università di Torino, Via P. Giuria 7, 10125 Torino, Italy
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