1
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Loffredo M, Casciaro B, Bellavita R, Troiano C, Brancaccio D, Cappiello F, Merlino F, Galdiero S, Fabrizi G, Grieco P, Stella L, Carotenuto A, Mangoni ML. Strategic Single-Residue Substitution in the Antimicrobial Peptide Esc(1-21) Confers Activity against Staphylococcus aureus, Including Drug-Resistant and Biofilm Phenotype. ACS Infect Dis 2024; 10:2403-2418. [PMID: 38848266 PMCID: PMC11250030 DOI: 10.1021/acsinfecdis.4c00130] [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: 02/19/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024]
Abstract
Staphylococcus aureus, a bacterium resistant to multiple drugs, is a significant cause of illness and death worldwide. Antimicrobial peptides (AMPs) provide an excellent potential strategy to cope with this threat. Recently, we characterized a derivative of the frog-skin AMP esculentin-1a, Esc(1-21) (1) that is endowed with potent activity against Gram-negative bacteria but poor efficacy against Gram-positive strains. In this study, three analogues of peptide 1 were designed by replacing Gly8 with α-aminoisobutyric acid (Aib), Pro, and dPro (2-4, respectively). The single substitution Gly8 → Aib8 in peptide 2 makes it active against the planktonic form of Gram-positive bacterial strains, especially Staphylococcus aureus, including multidrug-resistant clinical isolates, with an improved biostability without resulting in cytotoxicity to mammalian cells. Moreover, peptide 2 showed a higher antibiofilm activity than peptide 1 against both reference and clinical isolates of S. aureus. Peptide 2 was also able to induce rapid bacterial killing, suggesting a membrane-perturbing mechanism of action. Structural analysis of the most active peptide 2 evidenced that the improved biological activity of peptide 2 is the consequence of a combination of higher biostability, higher α helical content, and ability to reduce membrane fluidity and to adopt a distorted helix, bent in correspondence of Aib8. Overall, this study has shown how a strategic single amino acid substitution is sufficient to enlarge the spectrum of activity of the original peptide 1, and improve its biological properties for therapeutic purposes, thus paving the way to optimize AMPs for the development of new broad-spectrum anti-infective agents.
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Affiliation(s)
- Maria
Rosa Loffredo
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Bruno Casciaro
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Rosa Bellavita
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Cassandra Troiano
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133 Rome, Italy
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Floriana Cappiello
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Francesco Merlino
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Stefania Galdiero
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Giancarlo Fabrizi
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, 00185 Rome, Italy
| | - Paolo Grieco
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Lorenzo Stella
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133 Rome, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Maria Luisa Mangoni
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
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2
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Tanada M, Tamiya M, Matsuo A, Chiyoda A, Takano K, Ito T, Irie M, Kotake T, Takeyama R, Kawada H, Hayashi R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Kage M, Hashimoto S, Nii K, Sase H, Ohara K, Ohta A, Kuramoto S, Nishimura Y, Iikura H, Shiraishi T. Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor. J Am Chem Soc 2023. [PMID: 37463267 DOI: 10.1021/jacs.3c03886] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Cyclic peptides as a therapeutic modality are attracting a lot of attention due to their potential for oral absorption and accessibility to intracellular tough targets. Here, starting with a drug-like hit discovered using an mRNA display library, we describe a chemical optimization that led to the orally available clinical compound known as LUNA18, an 11-mer cyclic peptide inhibitor for the intracellular tough target RAS. The key findings are as follows: (i) two peptide side chains were identified that each increase RAS affinity over 10-fold; (ii) physico-chemical properties (PCP) including Clog P can be adjusted by side-chain modification to increase membrane permeability; (iii) restriction of cyclic peptide conformation works effectively to adjust PCP and improve bio-activity; (iv) cellular efficacy was observed in peptides with a permeability of around 0.4 × 10-6 cm/s or more in a Caco-2 permeability assay; and (v) while keeping the cyclic peptide's main-chain conformation, we found one example where the RAS protein structure was changed dramatically through induced-fit to our peptide side chain. This study demonstrates how the chemical optimization of bio-active peptides can be achieved without scaffold hopping, much like the processes for small molecule drug discovery that are guided by Lipinski's rule of five. Our approach provides a versatile new strategy for generating peptide drugs starting from drug-like hits.
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Affiliation(s)
- Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
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3
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Athiyarath V, Mathew LA, Zhao Y, Khazeber R, Ramamurty U, Sureshan KM. Rational design and topochemical synthesis of polymorphs of a polymer. Chem Sci 2023; 14:5132-5140. [PMID: 37206383 PMCID: PMC10189859 DOI: 10.1039/d3sc00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Packing a polymer in different ways can give polymorphs of the polymer having different properties. β-Turn forming peptides such as 2-aminoisobutyric acid (Aib)-rich peptides adopt several conformations by varying the dihedral angles. Aiming at this, a β-turn-forming peptide monomer would give different polymorphs and these polymorphs upon topochemical polymerization would yield polymorphs of the polymer, we designed an Aib-rich monomer N3-(Aib)3-NHCH2-C[triple bond, length as m-dash]CH. This monomer crystallizes as two polymorphs and one hydrate. In all forms, the peptide adopts β-turn conformations and arranges in a head-to-tail manner with their azide and alkyne units proximally placed in a ready-to-react alignment. On heating, both the polymorphs undergo topochemical azide-alkyne cycloaddition polymerization. Polymorph I polymerized in a single-crystal-to-single-crystal (SCSC) fashion and the single-crystal X-ray diffraction analysis of the polymer revealed its screw-sense reversing helical structure. Polymorph II maintains its crystallinity during polymerization but gradually becomes amorphous upon storage. The hydrate III undergoes a dehydrative transition to polymorph II. Nanoindentation studies revealed that different polymorphs of the monomer and the corresponding polymers exhibited different mechanical properties, in accordance with their crystal packing. This work demonstrates the promising future of the marriage of polymorphism and topochemistry for obtaining polymorphs of polymers.
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Affiliation(s)
- Vignesh Athiyarath
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Liby Ann Mathew
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Yakai Zhao
- School of Mechanical and Aerospace Engineering, Nanyang Technological University 639798 Singapore
| | - Ravichandran Khazeber
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Upadrasta Ramamurty
- School of Mechanical and Aerospace Engineering, Nanyang Technological University 639798 Singapore
| | - Kana M Sureshan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
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4
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Coppa C, Bazzoli A, Barkhordari M, Contini A. Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models. J Chem Inf Model 2023; 63:3030-3042. [PMID: 37163419 DOI: 10.1021/acs.jcim.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.
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Affiliation(s)
- Crescenzo Coppa
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Andrea Bazzoli
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Maral Barkhordari
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
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5
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Yang X, Chen M, Zhang Z, Li Y, Wang P, Luo X, Lv S. Alpha-aminoisobutyric acid incorporated peptides for the construction of electrochemical biosensors with high stability and low fouling in serum. Anal Chim Acta 2022; 1238:340646. [DOI: 10.1016/j.aca.2022.340646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
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6
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Dutta A, Das S, Das P, Maity S, Ghosh P, Biswas SS. Unique supramolecular assembly of a synthetic achiral α, γ-hybrid tripeptide. Z KRIST-CRYST MATER 2022. [DOI: 10.1515/zkri-2022-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
An achiral tripeptide, namely, Boc-γ-Abu-m-ABA-Aib-OMe (γ-Abu: γ−amino butyric acid; m-ABA: meta-aminobenzoic acid) was synthesized by solution phase procedure. The α, γ-hybrid peptide was designed in such a way that two dissimilar γ−amino acids, one flexible and another rigid, were positioned sidewise along with α-amino isobutyric acid (Aib) as C-terminal residue. The single crystal X-ray diffraction analysis revealed that two kinks were generated around centrally placed m-ABA. Interestingly, the peptide self-assembled via three intermolecular N–H···O and one intermolecular C–H···O hydrogen bonding interactions to supramlecular helical architecture.
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Affiliation(s)
- Arpita Dutta
- Department of Chemistry , Rishi Bankim Chandra Evening College , Naihati , 24-Parganas (N), Pin-743165 , India
| | - Suven Das
- Department of Chemistry , Rishi Bankim Chandra College for Women , Naihati , 24-Parganas (N), Pin-743165 , India
| | - Purak Das
- Department of Chemistry , Rishi Bankim Chandra College for Women , Naihati , 24-Parganas (N), Pin-743165 , India
| | - Suvendu Maity
- Department of Chemistry , R K Mission Residential College , Narendrapur , Kolkata 700103 , India
| | - Prasanta Ghosh
- Department of Chemistry , R K Mission Residential College , Narendrapur , Kolkata 700103 , India
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7
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Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
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Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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8
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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9
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019; 58:17351-17358. [PMID: 31539186 PMCID: PMC6900064 DOI: 10.1002/anie.201907901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/19/2019] [Indexed: 12/17/2022]
Abstract
Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.
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Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
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10
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine‐Tuned Flexibility Inhibit NF‐Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
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11
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Das S, Ben Haj Salah K, Djibo M, Inguimbert N. Peptaibols as a model for the insertions of chemical modifications. Arch Biochem Biophys 2018; 658:16-30. [DOI: 10.1016/j.abb.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
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12
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Marik T, Tyagi C, Racić G, Rakk D, Szekeres A, Vágvölgyi C, Kredics L. New 19-Residue Peptaibols from Trichoderma Clade Viride. Microorganisms 2018; 6:microorganisms6030085. [PMID: 30103563 PMCID: PMC6165201 DOI: 10.3390/microorganisms6030085] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Abstract
Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.
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Affiliation(s)
- Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary.
| | - Gordana Racić
- Faculty of Environmental Protection, Educons University, Vojvode Putnika 87, 21208 Sremska Kamenica, Serbia.
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary.
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
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13
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Elenewski JE, Velizhanin KA, Zwolak M. A spin-1 representation for dual-funnel energy landscapes. J Chem Phys 2018; 149:035101. [PMID: 30037251 PMCID: PMC7723752 DOI: 10.1063/1.5036677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model-left, right, and unstructured-can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.
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Affiliation(s)
- Justin E. Elenewski
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | | | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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14
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15
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Lee YS, Kupp R, Remesic MV, Ramos-Colon C, Hall SM, Chan C, Rankin D, Lai J, Porreca F, Hruby VJ. Various modifications of the amphipathic dynorphin A pharmacophore for rat brain bradykinin receptors. Chem Biol Drug Des 2016; 88:615-9. [PMID: 27203574 DOI: 10.1111/cbdd.12789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/26/2016] [Accepted: 05/14/2016] [Indexed: 12/18/2022]
Abstract
As a unique endogenous opioid ligand, dynorphin A shows paradoxical neuroexcitatory effects at bradykinin receptors, and the effects are known to be amplified by the upregulation of dynorphin A under chronic pain and inflammatory conditions. In our earlier structure-activity relationship studies, the amphipathic dynorphin A fragment, [Des-Arg(7) ]-Dyn A-(4-11), was identified as a pharmacophore for the bradykinin receptors along with key structural features. Here, further modifications of the pharmacophore showed that the position of a Pro residue is also an important feature because of its role in making (or disrupting) a β-turn or 310 helix structure which is crucial for receptor recognition.
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Affiliation(s)
- Yeon Sun Lee
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
| | - Robert Kupp
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael V Remesic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Cyf Ramos-Colon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Sara M Hall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Christopher Chan
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - David Rankin
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Josephine Lai
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Frank Porreca
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Victor J Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
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16
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Werner HM, Cabalteja CC, Horne WS. Peptide Backbone Composition and Protease Susceptibility: Impact of Modification Type, Position, and Tandem Substitution. Chembiochem 2015. [PMID: 26205791 DOI: 10.1002/cbic.201500312] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The clinical utility of peptides is limited by their rapid degradation by endogenous proteases. Modification of the peptide backbone can generate functional analogues with enhanced proteolytic stability. Existing principles for the design of such oligomers have focused primarily on effective structural mimicry. A more robust strategy would incorporate a rational approach for engineering maximal proteolytic stability with minimal unnatural residue content. We report here the systematic comparison of the proteolytic resistance imparted by four backbone modifications commonly employed in the design of protease-stable analogues of peptides with complex folding patterns. The degree of protection was quantified as a function of modification type, position, and tandem substitution in the context of a long, unstructured host sequence and a canonical serine protease. These results promise to inform ongoing work to develop biostable mimics of increasingly complex peptides and proteins.
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Affiliation(s)
- Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - Chino C Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA.
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17
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Pellegrino S, Bonetti A, Clerici F, Contini A, Moretto A, Soave R, Gelmi ML. 1H-Azepine-2-oxo-5-amino-5-carboxylic Acid: A 310 Helix Inducer and an Effective Tool for Functionalized Gold Nanoparticles. J Org Chem 2015; 80:5507-16. [DOI: 10.1021/acs.joc.5b00396] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sara Pellegrino
- Dipartimento
di Scienze Farmaceutiche- Sezione di Chimica Generale e Organica-
“A. Marchesini” Università degli Studi di Milano, Via Venezian 21 20133, Milano, Italy
| | - Andrea Bonetti
- Dipartimento
di Scienze Farmaceutiche- Sezione di Chimica Generale e Organica-
“A. Marchesini” Università degli Studi di Milano, Via Venezian 21 20133, Milano, Italy
| | - Francesca Clerici
- Dipartimento
di Scienze Farmaceutiche- Sezione di Chimica Generale e Organica-
“A. Marchesini” Università degli Studi di Milano, Via Venezian 21 20133, Milano, Italy
| | - Alessandro Contini
- Dipartimento
di Scienze Farmaceutiche- Sezione di Chimica Generale e Organica-
“A. Marchesini” Università degli Studi di Milano, Via Venezian 21 20133, Milano, Italy
| | - Alessandro Moretto
- Dipartimento
di Scienze Chimiche, Università degli Studi di Padova, Via
Marzolo 1 35131, Padova, Italy
| | - Raffaella Soave
- CNR- Istituto di Scienze e Tecnologie Molecolari, Via Golgi 19 20133, Milano, Italy
| | - Maria Luisa Gelmi
- Dipartimento
di Scienze Farmaceutiche- Sezione di Chimica Generale e Organica-
“A. Marchesini” Università degli Studi di Milano, Via Venezian 21 20133, Milano, Italy
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18
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Castro TG, Micaêlo NM. Conformational and thermodynamic properties of non-canonical α,α-dialkyl glycines in the peptaibol Alamethicin: molecular dynamics studies. J Phys Chem B 2014; 118:9861-70. [PMID: 25091499 DOI: 10.1021/jp505400q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we investigate the structure, dynamic and thermodynamic properties of noncanonical disubstituted amino acids (α,α-dialkyl glycines), also known as non-natural amino acids, in the peptaibol Alamethicin. The amino acids under study are Aib (α-amino isobutyric acid or α-methyl alanine), Deg (α,α-diethyl glycine), Dpg (α,α-dipropyl glycine), Dibg (α,α-di-isobutyl glycine), Dhg (α,α-dihexyl glycine), DΦg (α,α-diphenyl glycine), Dbzg (α,α-dibenzyl glycine), Ac6c (α,α-cyclohexyl glycine), and Dmg (α,α-dihydroxymethyl glycine). It is hypothesized that these amino acids are able to induce well-defined secondary structure in peptidomimetics. To test this hypothesis, new peptidomimetics of Alamethicin were constructed by replacing the native Aib positions of Alamethicin by one or more new α,α-dialkyl glycines. Dhg and Ac6c demonstrated the capacity to induce well-defined α-helical structures. Dhg and Ac6c also promote the thermodynamic stabilization of these peptides in a POPC model membrane and are better alternatives to the Aib in Alamethicin. These noncanonical amino acids also improved secondary structure properties, revealing preorganization in water and maintenance of α helical structure in POPC. We show that it is possible to optimize the helicity and thermodynamic properties of native Alamethicin, and we suggest that these amino acids could be incorporated in other peptides with similar structural effect.
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Affiliation(s)
- Tarsila G Castro
- Departamento de Química, Escola de Ciências, Universidade do Minho , Largo do Paço, Braga 4704-553, Portugal
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19
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Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW, Ren P. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. J Chem Theory Comput 2013; 9:4046-4063. [PMID: 24163642 DOI: 10.1021/ct4003702] [Citation(s) in RCA: 437] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments.
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Affiliation(s)
- Yue Shi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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20
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Toal S, Meral D, Verbaro D, Urbanc B, Schweitzer-Stenner R. pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. J Phys Chem B 2013; 117:3689-706. [PMID: 23448349 DOI: 10.1021/jp310466b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.
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Affiliation(s)
- Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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21
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Stoykova SA, Linden A, Heimgartner H. (S)-N-[(4-{(S)-1-[2-(4-Meth-oxy-benz-amido)-2-methyl-propano-yl]pyrrolidine-2-carboxamido}-3,4,5,6-tetra-hydro-2H-pyran-4-yl)carbon-yl]proline dimethyl sulfoxide monosolvate (4-MeBz-Aib-Pro-Thp-Pro-OH). Acta Crystallogr Sect E Struct Rep Online 2013; 69:o419-20. [PMID: 23476594 PMCID: PMC3588532 DOI: 10.1107/s1600536813004546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 02/15/2013] [Indexed: 11/10/2022]
Abstract
The asymmetric unit of the title compound, C28H38N4O8·C2H6OS, contains one tetra-peptide and one disordered dimethyl sulfoxide (DMSO) mol-ecule. The central five-membered ring (Pro(2)) of the peptide mol-ecule has a disordered envelope conformation [occupancy ratio 0.879 (2):0.121 (2)] with the envelope flap atom, the central C atom of the three ring methylene groups, lying on alternate sides of the mean ring plane. The terminal five-membered ring (Pro(4)) also adopts an envelope conformation with the C atom of the methylene group closest to the carboxylic acid function as the envelope flap, and the six-membered tetra-hydro-pyrane ring shows a chair conformation. The tetra-peptide exists in a helical conformation, stabilized by an intra-molecular hydrogen bond between the amide N-H group of the heterocyclic α-amino acid Thp and the amide O atom of the 4-meth-oxy-benzoyl group. This inter-action has a graph set motif of S(10) and serves to maintain a fairly rigid β-turn structure. In the crystal, the terminal hy-droxy group forms a hydrogen bond with the amide O atom of Thp of a neighbouring mol-ecule, and the amide N-H group at the opposite end of the mol-ecule forms a hydrogen bond with the amide O atom of Thp of another neighbouring mol-ecule. The combination of both inter-molecular inter-actions links the mol-ecules into an extended three-dimensional framework.
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Affiliation(s)
- Svetlana A Stoykova
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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22
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Schweitzer-Stenner R, Hagarman A, Toal S, Mathieu D, Schwalbe H. Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains. Proteins 2013; 81:955-67. [PMID: 23229832 DOI: 10.1002/prot.24225] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 11/10/2022]
Abstract
We performed a conformational analysis of the central residues of three tripeptides glycyl-L-isoleucyl-glycine (GIG), glycyl-L-tyrosyl-glycine (GYG) and glycyl-L-arginyl-glycine (GRG) in aqueous solution, based on a global analysis of amide I' band profiles and NMR J-coupling constants. The results are compared with recently reported distributions of GVG, GFG and GEG. For GIG and GYG, we found that even though the polyproline II (pPII) fraction is below 0.5, it is still the most populated conformation, whereas GVG and GFG show both a larger β-strand fraction. For GRG, we observed a clear dominance of pPII over β-strand, reminiscent of observations for GEG and GKG. This finding indicates that terminal charges on otherwise hydrophobic residue side chains stabilize pPII over β-strand conformations. For all peptides investigated we found that a variety of compact and turn-like conformations constitute nearly 20 percent of their conformational distributions. Attempts to analyze our data with a simple two-state pPII-->/<--β model therefore do not yield any satisfactory reproduction of experimental results. A comparison of the obtained GxG ensembles with conformational distributions of GxG segments in truncated coil libraries (helices and sheets omitted) revealed a much larger fraction of type II β(i+2) and type III β like conformations for the latter. Thus, a comparison of conformational distributions of unfolded peptide segments in solution and in coil libraries reveal interesting information on how the interplay between intrinsic propensities of amino acid residues and non-local interactions in polypeptide chains determine the conformations of loop segments in proteins.
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23
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Ye S, Wei F, Li H, Tian K, Luo Y. Structure and Orientation of Interfacial Proteins Determined by Sum Frequency Generation Vibrational Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:213-55. [DOI: 10.1016/b978-0-12-416596-0.00007-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Verbaro DJ, Mathieu D, Toal SE, Schwalbe H, Schweitzer-Stenner R. Ionized Trilysine: A Model System for Understanding the Nonrandom Structure of Poly-l-lysine and Lysine-Containing Motifs in Proteins. J Phys Chem B 2012; 116:8084-94. [DOI: 10.1021/jp303794s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel J. Verbaro
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Daniel Mathieu
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Siobhan E. Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Harald Schwalbe
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
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25
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Pellegrino S, Contini A, Clerici F, Gori A, Nava D, Gelmi ML. 1H-Azepine-4-amino-4-carboxylic acid: a new α,α-disubstituted ornithine analogue capable of inducing helix conformations in short Ala-Aib pentapeptides. Chemistry 2012; 18:8705-15. [PMID: 22689465 DOI: 10.1002/chem.201104023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/30/2012] [Indexed: 11/08/2022]
Abstract
A very efficient synthesis of orthogonally protected 1H-azepine-4-amino-4-carboxylic acid, abbreviated as Azn, a conformationally restricted analogue of ornithine, was realized. It was obtained on a gram scale in good overall yield in five steps, three of which did not require isolation of the intermediates, starting from the readily available 1-amino-4-oxo-cyclohexane-4-carboxylic acid. Both enantiomers were used for the preparation of pentapeptide models containing Ala, Aib, and Azn. Conformational studies using both spectroscopic techniques (NMR, CD) and molecular dynamics on model 5-mer peptides showed that the (R)-Azn isomer possesses a marked helicogenic effect.
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Affiliation(s)
- Sara Pellegrino
- DISMAB, Sezione di Chimica Organica A. Marchesini, Facoltà di Farmacia, Università degli Studi Milano, Via Venezian 21, 20133 Milano, Italy.
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26
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Schweitzer-Stenner R. Simulated IR, Isotropic and Anisotropic Raman, and Vibrational Circular Dichroism Amide I Band Profiles of Stacked β-Sheets. J Phys Chem B 2012; 116:4141-53. [DOI: 10.1021/jp2112445] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department
of Chemistry, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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27
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Grubišić S, Brancato G, Pedone A, Barone V. Extension of the AMBER force field to cyclic α,α dialkylated peptides. Phys Chem Chem Phys 2012; 14:15308-20. [DOI: 10.1039/c2cp42713c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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28
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Schweitzer-Stenner R, Soffer JB, Verbaro D. Structure analysis of unfolded peptides I: vibrational circular dichroism spectroscopy. Methods Mol Biol 2012; 895:271-313. [PMID: 22760325 DOI: 10.1007/978-1-61779-927-3_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).
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29
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Gebreslasie HG, Jacobsen Ø, Görbitz CH. N-(tert-butoxycarbonyl)-O-allyl-L-seryl-α-aminoisobutyryl-L-valine methyl ester: a protected tripeptide with an allylated serine residue. Acta Crystallogr C 2011; 67:o359-63. [PMID: 21881187 DOI: 10.1107/s0108270111029647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/22/2011] [Indexed: 11/10/2022] Open
Abstract
The title compound [systematic name (6S,12S)-methyl 6-(allyloxymethyl)-12-isopropyl-2,2,9,9-tetramethyl-4,7,10-trioxo-3-oxa-5,8,11-triazatridecan-13-oate], C(21)H(37)N(3)O(7), containing the little studied O-allyl-L-serine residue [Ser(All)], crystallizes in the monoclinic space group C2 with one molecule in the asymmetric unit. The compound is an analogue of the Ser140-Val142 segment of the water channel aquaporin-4 (AQP4). It forms a distorted type-II β-turn with a P(II)-3(10L)-P(II) backbone conformation (P(II) is polyproline II). The overall backbone conformation is markedly different from that of the CO(Pro139)-Val142 stretch of rat AQP4, but is quite similar to the corresponding segment of human AQP4, despite significant differences at the level of the individual residues. The side chain of the Ser(All) residue adopts a gauche conformation relative to the backbone CO-C(α) and C(α)-N bonds. The H atoms of the two CH(2) groups in the Ser(All) side chain are almost eclipsed. The crystal packing of the title compound is divided into one-molecule-thick layers, each layer having a hydrophilic core and distinct hydrophobic interfaces on either side.
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Castelletto V, Hamley IW, Cenker Ç, Olsson U, Adamcik J, Mezzenga R, Miravet JF, Escuder B, Rodríguez-Llansola F. Influence of End-Capping on the Self-Assembly of Model Amyloid Peptide Fragments. J Phys Chem B 2011; 115:2107-16. [DOI: 10.1021/jp111168s] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ian W. Hamley
- Department of Chemistry, University of Reading, Reading RG6 6AD, U.K
| | - Çelen Cenker
- Physical Chemistry 1, Lund University, Lund S-221 00, Sweden
| | - Ulf Olsson
- Physical Chemistry 1, Lund University, Lund S-221 00, Sweden
| | - Jozef Adamcik
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zürich, Switzerland
| | - Raffaele Mezzenga
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zürich, Switzerland
| | - Juan F. Miravet
- Departament de Química Inorgànica i OrgànicaUniversitat Jaume I, 12071 Castelló, Spain
| | - Beatriu Escuder
- Departament de Química Inorgànica i OrgànicaUniversitat Jaume I, 12071 Castelló, Spain
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Mawad N, Ghorbani-Salman Pour F, Linden A, Heimgartner H. Synthesis and Crystal Structure of 3,3,6,6-Tetramethylmorpholine-2,5-dione, and Its 5-Monothioxo and 2,5-Dithioxo Derivatives. Helv Chim Acta 2010. [DOI: 10.1002/hlca.201000318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Oh KI, Kim W, Joo C, Yoo DG, Han H, Hwang GS, Cho M. Azido Gauche Effect on the Backbone Conformation of β-Azidoalanine Peptides. J Phys Chem B 2010; 114:13021-9. [DOI: 10.1021/jp107359m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Woosung Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Cheonik Joo
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Dong-Geun Yoo
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Geum-Sook Hwang
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
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Wang D, Friedmann M, Gattin Z, Jaun B, van Gunsteren W. The Propensity of α-Aminoisobutyric Acid (=2-Methylalanine; Aib) to Induce Helical Secondary Structure in an α-Heptapeptide: A Computational Study. Helv Chim Acta 2010. [DOI: 10.1002/hlca.200900420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sheet T, Banerjee R. Sulfate ion interaction with 'anion recognition' short peptide motif at the N-terminus of an isolated helix: A conformational landscape. J Struct Biol 2010; 171:345-52. [PMID: 20570734 DOI: 10.1016/j.jsb.2010.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
Anion-binding motifs in proteins are typically conserved in sequence and conformation. Crystal structural studies have shown that such motifs often occur in loop regions preceding a helix and interaction with the anions can induce their well defined conformational changes. In order to understand the properties of such motifs in isolation, we have synthesized an 18-residue chimeric polypeptide whose C-terminal part is a designed helix and its N-terminal consists of a C(alpha)NN anion binding structural motif containing residues Leu-Gly-Lys-Gln (residues 107-110 of protein DNA-glycosylase). We present evidence for the interaction of a sulfate (SO(4)(2-)) ion with the L-G-K-Q segment using complementary spectroscopic techniques. Moreover, upon interaction with SO(4)(2-) ion the N-terminal L-G-K-Q segment undergoes a non-helical to helical transition similar to what is observed in protein crystal structure. This work clearly demonstrates the "local" nature of anion binding and the accompanying conformational change that helps in understanding the influence of sequence/structural context of anion binding in proteins.
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Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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Heimgartner H, Löpfe M, Linden A. N-Methyl-N-phenyl-5-oxa-1-azaspiro[2.5]oct-1-en-2-amine — Synthesis and Reactions of a Synthon for an Unknown α-Amino Acid. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Nagaraj S, Peddha MS, Manjappara UV. Fragment analogs as better mimics of obestatin. ACTA ACUST UNITED AC 2009; 158:143-8. [DOI: 10.1016/j.regpep.2009.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 08/07/2009] [Accepted: 08/16/2009] [Indexed: 10/20/2022]
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Banerjee R, Chattopadhyay S, Basu G. Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. Proteins 2009; 76:184-200. [PMID: 19137603 DOI: 10.1002/prot.22337] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.
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Affiliation(s)
- Raja Banerjee
- Department of Biotechnology, West Bengal University of Technology, Kolkata 700064, India.
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Yongye AB, Li Y, Giulianotti MA, Yu Y, Houghten RA, Martínez-Mayorga K. Modeling of peptides containing D-amino acids: implications on cyclization. J Comput Aided Mol Des 2009; 23:677-89. [PMID: 19593648 DOI: 10.1007/s10822-009-9295-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022]
Abstract
Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclizes in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated alpha(L) rotamers even when simulations were performed at a higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L: -amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods.
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Affiliation(s)
- Austin B Yongye
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, FL 34987, USA
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Best RB, Hummer G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B 2009; 113:9004-15. [PMID: 19514729 PMCID: PMC3115786 DOI: 10.1021/jp901540t] [Citation(s) in RCA: 649] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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Barbaras D, Gademann K. Stable β Turns of Tripeptides in Water through Cation-π Interactions. Chembiochem 2008; 9:2398-401. [DOI: 10.1002/cbic.200800344] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
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Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
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Gentilucci L, Squassabia F, Demarco R, Artali R, Cardillo G, Tolomelli A, Spampinato S, Bedini A. Investigation of the interaction between the atypical agonist c[YpwFG] and MOR. FEBS J 2008; 275:2315-37. [DOI: 10.1111/j.1742-4658.2008.06386.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pizzanelli S, Forte C, Monti S, Schweitzer-Stenner R. Interaction of a tripeptide with cesium perfluorooctanoate micelles. J Phys Chem B 2008; 112:1251-61. [PMID: 18173254 DOI: 10.1021/jp073947x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water was studied in the isotropic phase by means of 1H NMR and by molecular dynamics (MD) simulations. Information on the location of the peptide was experimentally obtained from selective variations in Ala-Phe-Ala chemical shifts and from differential line broadening in the presence of the paramagnetic ion Mn2+. The peptide-micelle association constant was estimated analyzing the chemical shift variations of the most sensitive Ala-Phe-Ala resonances with the peptide concentration. MD simulations of Ala-Phe-Ala in the micellar environment confirmed the experimental observations, identifying the hydrogen bonding interactions of the different peptide moieties with the micelle, yielding a binding constant close to the experimental one. NOESY experiments suggest that the peptide in the micellar environment does not adopt a preferred conformation but is mainly unstructured. Details on the conformational behavior of the peptide in the micellar solution observed through MD were consistent with a different conformational equilibrium in the proximity of the micelle. Information on Ala-Phe-Ala dynamics was obtained from 1H T1 data and compared to MD simulation results on the overall tumbling motion.
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Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico-Fisici (IPCF-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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