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Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
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Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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2
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Code C, Qiu D, Solov’yov IA, Lee JG, Shin HC, Roland C, Sagui C, Houde D, Rand KD, Jørgensen TJD. Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties. J Am Chem Soc 2023; 145:23925-23938. [PMID: 37883679 PMCID: PMC10636759 DOI: 10.1021/jacs.3c04068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.
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Affiliation(s)
- Christian Code
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Danwen Qiu
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department
of Physics, Carl von Ossietzky University
Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Jung-Goo Lee
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Hyeon-Cheol Shin
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Christopher Roland
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Damian Houde
- Department
of Protein Pharmaceutical Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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3
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Liu M, Abdelmouleh M, Giuliani A, Nahon L, Poully JC. UV-VUV Photofragmentation Spectroscopy of Isolated Neutral Fragile Macromolecules: A Proof-of-Principle Based on a Deprotonated Vancomycin-Peptide Noncovalent Complex. J Phys Chem A 2022; 126:9042-9050. [PMID: 36442079 DOI: 10.1021/acs.jpca.2c07744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase offers the possibility to analyze organic molecules by ultraviolet-vacuum ultraviolet (UV-VUV) spectroscopy without any solvent effect or limitation in terms of spectral range due to absorption by the solvent. Up to now, the size and chemical composition of neutral molecular systems under study have been limited by the use of vaporization methods based on thermal heating. Soft sources of gas-phase thermolabile molecular systems such as electrospray or matrix-assisted laser desorption ionization are appealing alternatives to heating-based techniques, but they lead to the production of ions. In such cases, UV-VUV action spectroscopy is then the method of choice to study the electronic structure and corresponding photodynamics of these gas-phase molecular ions. However, previous investigations have shown that the UV-VUV action spectrum of a given molecular ion depends on the charge state, which in many cases might be a caveat. Here, by means of synchrotron radiation coupled to mass spectrometry and through the test case of the glycopeptide antibiotic vancomycin noncovalently bound to a deprotonated small peptide, we show that the UV-VUV photofragmentation spectrum of neutral thermally fragile organic molecules can be obtained via charge-tagging action spectroscopy.
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Affiliation(s)
- Min Liu
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
| | - Marwa Abdelmouleh
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
| | - Alexandre Giuliani
- SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192Gif sur Yvette, Cedex, France.,INRAE, UAR1008, Transform Department, Rue de la Géraudière, BP 71627, 44316Nantes, France
| | - Laurent Nahon
- SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192Gif sur Yvette, Cedex, France
| | - Jean-Christophe Poully
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
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Abdelmouleh M, Lalande M, Vizcaino V, Schlathölter T, Poully J. Photoinduced Processes within Noncovalent Complexes Involved in Molecular Recognition. Chemistry 2020; 26:2243-2250. [DOI: 10.1002/chem.201904786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/28/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Marwa Abdelmouleh
- CIMAP UMR 6252 Unicaen/CEA/CNRS/ENSICAEN, Bd Becquerel 14070 Caen Cedex 5 France
| | - Mathieu Lalande
- CIMAP UMR 6252 Unicaen/CEA/CNRS/ENSICAEN, Bd Becquerel 14070 Caen Cedex 5 France
| | - Violaine Vizcaino
- CIMAP UMR 6252 Unicaen/CEA/CNRS/ENSICAEN, Bd Becquerel 14070 Caen Cedex 5 France
| | - Thomas Schlathölter
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
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5
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Schwob L, Lalande M, Rangama J, Egorov D, Hoekstra R, Pandey R, Eden S, Schlathölter T, Vizcaino V, Poully JC. Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range. Phys Chem Chem Phys 2017; 19:18321-18329. [DOI: 10.1039/c7cp02527k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By monitoring ionization and fragmentation after single-photon absorption, we show that an isolated collagen triple helix model is stabilized by proline hydroxylation.
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Affiliation(s)
- Lucas Schwob
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Mathieu Lalande
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Jimmy Rangama
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Rahul Pandey
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Samuel Eden
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Violaine Vizcaino
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
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6
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Kopysov V, Nagornova NS, Boyarkin OV. Identification of Tyrosine-Phosphorylated Peptides Using Cold Ion Spectroscopy. J Am Chem Soc 2014; 136:9288-91. [DOI: 10.1021/ja5053544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Kopysov
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Natalia S. Nagornova
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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8
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Ketabchi A, Komm K, Miles-Rossouw M, Cassani DAD, Variola F. Nanoporous titanium surfaces for sustained elution of proteins and antibiotics. PLoS One 2014; 9:e92080. [PMID: 24633020 PMCID: PMC3954914 DOI: 10.1371/journal.pone.0092080] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
Current medically relevant metals for prosthetic reconstructions enjoy a relatively good success rate, but their performance drops significantly in patients with compromised health status, and post-surgical infections still remain an important challenge. To address these problems, different nanotechnology-based strategies have been exploited to create implantable metals with an enhanced bioactivity and antibacterial capacities. Among these, oxidative nanopatterning has emerged as a very effective approach to engender nanoporous surfaces that stimulate and guide the activity of adhering cells. The resulting nanoporosity is also attractive because it offers nanoconfined volumes that can be exploited to load bioactive compounds and modulate their release over time. Such extended elution is needed since a single exposure to growth factors and/or antibiotics, for instance, may not be adequate to further sustain bone regeneration and/or to counteract bacterial colonization. In this article, we assessed the capacities of nanoporous titanium surfaces generated by oxidative nanopatterning to provide controlled and sustained elution of proteins and antibiotic molecules. To this end, we have selected bovine serum albumin (BSA) and vancomycin to reflect commonly used compounds, and investigated their adsorption and elution by Fourier-transform infrared (FT-IR) and ultraviolet-visible (UV-VIS) spectroscopy. Our results demonstrate that while the elution of albumin is not significantly affected by the nanoporosity, in the case of vancomycin, nanoporous surfaces provided an extended release. These findings were successively correlated to the establishment of interactions with the surface and physical-entrapment effects exerted by the nanopores, ultimately highlighting their synergistic contribution to the release profiles and thus their importance in the design of nanostructured eluting platforms for applications in medicine.
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Affiliation(s)
| | - Kristopher Komm
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Canada
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, Canada
| | - Malaika Miles-Rossouw
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Canada
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, Canada
| | - Davide A. D. Cassani
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Canada
- Department of Chemistry, Material and Chemical Engineering, Politecnico di Milano, Milan, Italy
| | - Fabio Variola
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Canada
- Department of Physics, University of Ottawa, Ottawa, Canada
- * E-mail:
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Le TN, Poully JC, Lecomte F, Nieuwjaer N, Manil B, Desfrançois C, Chirot F, Lemoine J, Dugourd P, van der Rest G, Grégoire G. Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1937-49. [PMID: 24043520 DOI: 10.1007/s13361-013-0722-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/22/2013] [Accepted: 07/30/2013] [Indexed: 05/11/2023]
Abstract
The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.
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Affiliation(s)
- Thi Nga Le
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS UMR 7538, F-93430, Villetaneuse, France
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10
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Bellina B, Compagnon I, MacAleese L, Chirot F, Lemoine J, Maître P, Broyer M, Antoine R, Kulesza A, Mitrić R, Bonačić-Koutecký V, Dugourd P. Binding motifs of silver in prion octarepeat model peptides: a joint ion mobility, IR and UV spectroscopies, and theoretical approach. Phys Chem Chem Phys 2012; 14:11433-40. [DOI: 10.1039/c2cp40924k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Joshi K, Semrouni D, Ohanessian G, Clavaguéra C. Structures and IR Spectra of the Gramicidin S Peptide: Pushing the Quest for Low-Energy Conformations. J Phys Chem B 2011; 116:483-90. [DOI: 10.1021/jp207102v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaustubh Joshi
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - David Semrouni
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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12
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Schwing K, Reyheller C, Schaly A, Kubik S, Gerhards M. Structural Analysis of an Isolated Cyclic Tetrapeptide and its Monohydrate by Combined IR/UV Spectroscopy. Chemphyschem 2011; 12:1981-8. [DOI: 10.1002/cphc.201001055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/07/2011] [Indexed: 11/10/2022]
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Abstract
AbstractSix complexes of vancomycin and peptidoglycan precursors were studied via molecular dynamics simulations. The interactions between the antibiotic and peptidoglycan fragments were identified and described in detail. All six studied modifications of the peptidoglycan precursor resulted in a weakening of the interaction with vancomycin when comparing to the native D-Ala-D-Ala-terminated fragment. It was confirmed that the N-terminus of the vancomycin is directly responsible for peptidoglycan recognition and antimicrobial activity. In simulated systems, the saccharide part of the antibiotic interacts with peptide precursors, thus it could also be important for antimicrobial activity. The complex terminated with D-Lac is the only one in which there is a weak interaction with the sugar moiety in the simulated systems. Analysis of conformational changes is a major scope of this work. The lack of interactions resulting from modification of the peptidoglycan precursors (D-Lac, D-Ser or other substitution) would be counterbalanced by proper modifications of the vancomycin moiety, especially the saccharide part of vancomycin.
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