1
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Fischer N, Tóth A, Jancsó A, Thulstrup P, Diness F. Inducing α-Helicity in Peptides by Silver Coordination to Cysteine. Chemistry 2024; 30:e202304064. [PMID: 38456607 DOI: 10.1002/chem.202304064] [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: 01/18/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α-helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed-phase HPLC separation as well as towards a physiological level of chloride ions, based on far-UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N-terminal nucleation site for inducing α-helicity into longer peptides. This type of silver-mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions.
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Affiliation(s)
- Niklas Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Annamária Tóth
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Attila Jancsó
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Peter Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
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2
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Duque HM, Dos Santos C, Brango-Vanegas J, Díaz-Martín RD, Dias SC, Franco OL. Unwrapping the structural and functional features of antimicrobial peptides from wasp venoms. Pharmacol Res 2024; 200:107069. [PMID: 38218356 DOI: 10.1016/j.phrs.2024.107069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The study of wasp venoms has captured attention due to the presence of a wide variety of active compounds, revealing a diverse array of biological effects. Among these compounds, certain antimicrobial peptides (AMPs) such as mastoparans and chemotactic peptides have emerged as significant players, characterized by their unique amphipathic short linear alpha-helical structure. These peptides exhibit not only antibiotic properties but also a range of other biological activities, which are related to their ability to interact with biological membranes to varying degrees. This review article aims to provide updated insights into the structure/function relationships of AMPs derived from wasp venoms, linking this knowledge to the potential development of innovative treatments against infections.
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Affiliation(s)
- Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160 Brasília, DF, Brazil.
| | - Cristiane Dos Santos
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, PC: (CEP) 79117-010 Campo Grande, MS, Brazil
| | - José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160 Brasília, DF, Brazil; S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, PC: (CEP) 79117-010 Campo Grande, MS, Brazil
| | - Ruben Dario Díaz-Martín
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160 Brasília, DF, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160 Brasília, DF, Brazil; Program in Animal Biology, Universidade de Brasília, Brasília, DF70910-900, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160 Brasília, DF, Brazil; S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, PC: (CEP) 79117-010 Campo Grande, MS, Brazil
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3
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Besenius P, Zengerling L, Kemper B, Hellmich UA. Synthesis and Structural Stability of α-Helical Gold(I)-Metallopeptidesy. Synlett 2021. [DOI: 10.1055/a-1290-8412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe synthesis of hexa- and dodecapeptides functionalized with two Au(I)–phosphine complexes is reported. The high stability of the Au(I)–phosphine bond allowed orthogonal peptide-protecting-group chemistry, even when using hard Lewis acids like boron tribromide. This enabled the preparation of an Fmoc-protected lysine derivative carrying the Au(I) complex in a side chain, which was used in standard Fmoc-based solid-phase peptide synthesis protocols. Alanine and leucine repeats in the metallododecapeptide formed α-helical secondary structures in 2,2,2-trifluoroethanol–H2O and 1,1,1,3,3,3-hexafluoroisopropanol–H2O mixtures with high thermal stability, as shown by temperature-dependent CD spectroscopy studies.
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Affiliation(s)
- Pol Besenius
- Department of Chemistry, Johannes Gutenberg-University Mainz
| | | | - Benedict Kemper
- Department of Chemistry, Johannes Gutenberg-University Mainz
| | - Ute A. Hellmich
- Department of Chemistry, Johannes Gutenberg-University Mainz
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt
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4
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Biomass-Derived Nitrogen-Doped Porous Carbon for Highly Efficient Ambient Electro-Synthesis of NH3. Catalysts 2020. [DOI: 10.3390/catal10030353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this communication, we report a biomass-derived nitrogen-doped porous carbon (named as NC-800) as an electrocatalyst for the ambient conversion of N2 to NH3. The catalyst NC-800 was prepared from naturally renewable and easily available bamboo shoots, with inherently an approximate 8 wt % of N-containing components, such as the N source, in a cost-effective and environmentally benign manner. This exhibited remarkable catalytic activity with a large NH3 yield and a Faradaic efficiency as high as 16.3 μg h−mg-1cat and 27.5%, respectively, at −0.35 V versus a reversible hydrogen electrode (RHE) in 0.1 M HCl solution at ambient conditions. More importantly, the catalyst NC-800 demonstrated excellent electrochemical selectivity and stability.
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5
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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6
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Zamora-Carreras H, Maestro B, Sanz JM, Jiménez MA. Turncoat Polypeptides: We Adapt to Our Environment. Chembiochem 2019; 21:432-441. [PMID: 31456307 DOI: 10.1002/cbic.201900446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 01/25/2023]
Abstract
A common interpretation of Anfinsen's hypothesis states that one amino acid sequence should fold into a single, native, ordered state, or a highly similar set thereof, coinciding with the global minimum in the folding-energy landscape, which, in turn, is responsible for the function of the protein. However, this classical view is challenged by many proteins and peptide sequences, which can adopt exchangeable, significantly dissimilar conformations that even fulfill different biological roles. The similarities and differences of concepts related to these proteins, mainly chameleon sequences, metamorphic proteins, and switch peptides, which are all denoted herein "turncoat" polypeptides, are reviewed. As well as adding a twist to the conventional view of protein folding, the lack of structural definition adds clear versatility to the activity of proteins and can be used as a tool for protein design and further application in biotechnology and biomedicine.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química-Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Beatriz Maestro
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Av. Monforte de Lemos, 3-5. Pabellón, 28029, Madrid, Spain
| | - M Angeles Jiménez
- Instituto de Química-Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
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7
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Morante K, Bellomio A, Viguera AR, González-Mañas JM, Tsumoto K, Caaveiro JMM. The Isolation of New Pore-Forming Toxins from the Sea Anemone Actinia fragacea Provides Insights into the Mechanisms of Actinoporin Evolution. Toxins (Basel) 2019; 11:toxins11070401. [PMID: 31295915 PMCID: PMC6669745 DOI: 10.3390/toxins11070401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/29/2019] [Accepted: 07/05/2019] [Indexed: 01/23/2023] Open
Abstract
Random mutations and selective pressure drive protein adaptation to the changing demands of the environment. As a consequence, nature favors the evolution of protein diversity. A group of proteins subject to exceptional environmental stress and known for their widespread diversity are the pore-forming hemolytic proteins from sea anemones, known as actinoporins. In this study, we identified and isolated new isoforms of actinoporins from the sea anemone Actinia fragacea (fragaceatoxins). We characterized their hemolytic activity, examined their stability and structure, and performed a comparative analysis of their primary sequence. Sequence alignment reveals that most of the variability among actinoporins is associated with non-functional residues. The differences in the thermal behavior among fragaceatoxins suggest that these variability sites contribute to changes in protein stability. In addition, the protein-protein interaction region showed a very high degree of identity (92%) within fragaceatoxins, but only 25% among all actinoporins examined, suggesting some degree of specificity at the species level. Our findings support the mechanism of evolutionary adaptation in actinoporins and reflect common pathways conducive to protein variability.
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Affiliation(s)
- Koldo Morante
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa (Bizkaia), Spain
| | - Augusto Bellomio
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa (Bizkaia), Spain
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) e Instituto de Química Biológica "Dr. Bernabé Bloj," Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000 San Miguel de Tucumán, Argentina
| | - Ana Rosa Viguera
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa (Bizkaia), Spain
| | - Juan Manuel González-Mañas
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
- Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
| | - Jose M M Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
- Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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8
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Azuma Y, Imai H, Kawaguchi Y, Nakase I, Kimura H, Futaki S. Modular Redesign of a Cationic Lytic Peptide To Promote the Endosomal Escape of Biomacromolecules. Angew Chem Int Ed Engl 2018; 57:12771-12774. [DOI: 10.1002/anie.201807534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Yusuke Azuma
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Haruka Imai
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | | | - Ikuhiko Nakase
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Hiroshi Kimura
- Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Shiroh Futaki
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
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9
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Azuma Y, Imai H, Kawaguchi Y, Nakase I, Kimura H, Futaki S. Modular Redesign of a Cationic Lytic Peptide To Promote the Endosomal Escape of Biomacromolecules. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yusuke Azuma
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Haruka Imai
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | | | - Ikuhiko Nakase
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Hiroshi Kimura
- Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
| | - Shiroh Futaki
- Institute for Chemical Research; Kyoto University; Uji Kyoto 611-0011 Japan
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10
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Zamora-Carreras H, Maestro B, Strandberg E, Ulrich AS, Sanz JM, Jiménez MÁ. Roles of Amphipathicity and Hydrophobicity in the Micelle-Driven Structural Switch of a 14-mer Peptide Core from a Choline-Binding Repeat. Chemistry 2018; 24:5825-5839. [PMID: 29369425 DOI: 10.1002/chem.201704802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 01/16/2023]
Abstract
Choline-binding repeats (CBRs) are ubiquitous sequences with a β-hairpin core that are found in the surface proteins of several microorganisms such as S. pneumoniae (pneumococcus). Previous studies on a 14-mer CBR sequence derived from the pneumoccal LytA autolysin (LytA239-252 peptide) have demonstrated a switch behaviour for this peptide, so that it acquires a stable, native-like β-hairpin conformation in aqueous solution but is reversibly transformed into an amphipathic α-helix in the presence of detergent micelles. With the aim of understanding the factors responsible for this unusual β-hairpin to α-helix transition, and to specifically assess the role of peptide hydrophobicity and helical amphipathicity in the process, we designed a series of LytA239-252 variants affecting these two parameters and studied their interaction with dodecylphosphocholine (DPC) micelles by solution NMR, circular dichroism and fluorescence spectroscopies. Our results indicate that stabilising cross-strand interactions become essential for β-hairpin stability in the absence of optimal turn sequences. Moreover, both amphipathicity and hydrophobicity display comparable importance for helix stabilisation of CBR-derived peptides in micelles, indicating that these sequences represent a novel class of micelle/membrane-interacting peptides.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Beatriz Maestro
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Jesús M Sanz
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain.,Biological Research Centre (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
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11
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Lella M, Kamilla S, Jain V, Mahalakshmi R. Molecular Mechanism of Holin Transmembrane Domain I in Pore Formation and Bacterial Cell Death. ACS Chem Biol 2016; 11:910-20. [PMID: 26701742 DOI: 10.1021/acschembio.5b00875] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Bacterial cell lysis during bacteriophage infection is timed by perfect orchestration between components of the holin-endolysin cassette. In bacteria, progressively accumulating holin in the inner membrane, retained in its inactive form by antiholin, is triggered into active hole formation, resulting in the canonical host cell lysis. However, the molecular mechanism of regulation and physical basis of pore formation in the mycobacterial cell membrane by D29 mycobacteriophage holin, particularly in the nonexistence of a known antiholin, is poorly understood. In this study, we report, for the first time, the use of fluorescence resonance transfer measurements to demonstrate that the first transmembrane domain (TM1) of D29 holin undergoes a helix ↔ β-hairpin conformational interconversion. We validate that this structural malleability is mediated by a centrally positioned proline and is responsible for controlled TM1 self-association in membrana, in the presence of a proton gradient across the lipid membrane. We demonstrate that TM1 is sufficient for bacterial growth inhibition. The biological effect of D29 holin structural alteration is presented as a holin self-regulatory mechanism, and its implications are discussed in the context of holin function.
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Affiliation(s)
- Muralikrishna Lella
- Molecular
Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India 462023
| | - Soumya Kamilla
- Microbiology
and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India 462023
| | - Vikas Jain
- Microbiology
and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India 462023
| | - Radhakrishnan Mahalakshmi
- Molecular
Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India 462023
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12
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Morante K, Caaveiro JM, Viguera AR, Tsumoto K, González-Mañas JM. Functional characterization of Val60, a key residue involved in the membrane-oligomerization of fragaceatoxin C, an actinoporin fromActinia fragacea. FEBS Lett 2015; 589:1840-6. [DOI: 10.1016/j.febslet.2015.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/28/2022]
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13
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Zamora-Carreras H, Maestro B, Strandberg E, Ulrich AS, Sanz JM, Jiménez MÁ. Micelle-Triggered β-Hairpin to α-Helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA. Chemistry 2015; 21:8076-89. [PMID: 25917218 PMCID: PMC4471590 DOI: 10.1002/chem.201500447] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/08/2022]
Abstract
Choline-binding modules (CBMs) have a ββ-solenoid structure composed of choline-binding repeats (CBR), which consist of a β-hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline-binding ability, we have analysed the third β-hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native-like β-hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α-helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β-hairpin to α-helix conversion is reversible. Given that the β-hairpin and α-helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this "chameleonic" behaviour is the only described case of a micelle-induced structural transition between two ordered peptide structures.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006-Madrid (Spain)
| | - Beatriz Maestro
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202-Alicante (Spain)
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, 76021 Karlsruhe (Germany)
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, 76021 Karlsruhe (Germany)
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Jesús M Sanz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202-Alicante (Spain)
| | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006-Madrid (Spain).
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14
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Smith SJ, Du K, Radford RJ, Tezcan FA. Functional, metal-based crosslinkers for α-helix induction in short peptides. Chem Sci 2013; 4:3740-3747. [PMID: 24156013 PMCID: PMC3800689 DOI: 10.1039/c3sc50858g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many protein-protein interactions that play a central role in cellular processes involve α-helical domains. Consequently, there has been great interest in developing strategies for stabilizing short peptides in α-helical conformations toward the inhibition and interrogation of protein-protein interactions. Here, we show that tridentate Hybrid Coordination Motifs (HCMs), which consist of a natural (histidine, His) and an unnatural (8-hydroxyquinoline, Quin) metal binding functionality, can bind divalent metal ions with high affinity and thereby induce/stabilize an α-helical configuration in short peptide sequences. The Quin functionality is readily introduced onto peptide platforms both during or after solid-state peptide synthesis, demonstrating the preparative versatility of HCMs. A systematic study involving a series of HCM-bearing peptides has revealed the critical importance of the length of the linkage between the Quin moiety and the peptide backbone as well as the metal coordination geometry in determining the extent of α-helix induction. Through ZnII coordination or modification with ReI(Quin)(CO)3, the HCM-bearing peptides can be rendered luminescent in the visible region, thus showing that HCMs can be exploited to simultaneously introduce structure and functionality into short peptides.
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Affiliation(s)
- Sarah J Smith
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093-0356
| | - Kang Du
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093-0356
| | - Robert J Radford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093-0356
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093-0356
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15
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Madhongsa K, Pasan S, Phophetleb O, Nasompag S, Thammasirirak S, Daduang S, Taweechaisupapong S, Lomize AL, Patramanon R. Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization. PLoS Negl Trop Dis 2013; 7:e2267. [PMID: 23785532 PMCID: PMC3681726 DOI: 10.1371/journal.pntd.0002267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/01/2013] [Indexed: 01/05/2023] Open
Abstract
Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ); however, the risk of a relapse is possible. Peptide antibiotics are an alternative to classical antibiotics as they exhibit rapid action and are less likely to result in the development of resistance. The aim of this study was to determine the bactericidal activity against B. pseudomallei and examine the membrane disrupting abilities of the potent antimicrobial peptides: bactenecin, RTA3, BMAP-18 and CA-MA. All peptides exhibited >97% bactericidal activity at 20 µM, with bactenecin having slightly higher activity. Long term time-kill assays revealed a complete inhibition of cell growth at 50 µM bactenecin and CA-MA. All peptides inhibited biofilm formation comparable to CAZ, but exhibited faster kinetics (within 1 h). Bactenecin exhibited stronger binding to LPS and induced perturbation of the inner membrane of live cells. Interaction of bactenecin with model membranes resulted in changes in membrane fluidity and permeability, leading to leakage of dye across the membrane at levels two-fold greater than that of other peptides. Modeling of peptide binding on the membrane showed stable and deep insertion of bactenecin into the membrane (up to 9 Å). We propose that bactenecin is able to form dimers or large β-sheet structures in a concentration dependent manner and subsequently rapidly permeabilize the membrane, leading to cytosolic leakage and cell death in a shorter period of time compared to CAZ. Bactenecin might be considered as a potent antimicrobial agent for use against B. pseudomallei. Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ), however, the risk of a relapse is possible. In this study we demonstrate that bactenecin, CA-MA, RTA3 and BMAP-18 are able to inhibit the growth and biofilm formation of B. pseudomallei. The strong bactericidal activity of bactenecin is attributed to its greater ability to permeabilize the membrane. Computational modeling of these peptide-membrane interactions provide support for a model in which bactenecin is able to penetrate the membrane most effectively due to its cyclical structure. The peptide, bactenecin has the potential to act as a highly effective alternative to CAZ, or as a combination therapy with CAZ in the treatment of melioidosis. Furthermore, understanding the mechanism of bactenecin may help us better design more effective peptides therapeutics of choice for melioidosis.
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Affiliation(s)
- Kanjana Madhongsa
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Supaluk Pasan
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Onanong Phophetleb
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sawinee Nasompag
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sompong Thammasirirak
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sakda Daduang
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Suwimol Taweechaisupapong
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Andrei L. Lomize
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rina Patramanon
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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16
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Perez-Aguilar JM, Saven JG. Computational design of membrane proteins. Structure 2012; 20:5-14. [PMID: 22244752 DOI: 10.1016/j.str.2011.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/21/2011] [Accepted: 12/21/2011] [Indexed: 11/26/2022]
Abstract
Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues, and this review discusses recent studies that tailor membrane proteins to display specific structures or functions and examines how redesigned membrane proteins are being used to facilitate structural and functional studies.
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17
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Computational studies of membrane proteins: models and predictions for biological understanding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:927-41. [PMID: 22051023 DOI: 10.1016/j.bbamem.2011.09.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 01/26/2023]
Abstract
We discuss recent progresses in computational studies of membrane proteins based on physical models with parameters derived from bioinformatics analysis. We describe computational identification of membrane proteins and prediction of their topology from sequence, discovery of sequence and spatial motifs, and implications of these discoveries. The detection of evolutionary signal for understanding the substitution pattern of residues in the TM segments and for sequence alignment is also discussed. We further discuss empirical potential functions for energetics of inserting residues in the TM domain, for interactions between TM helices or strands, and their applications in predicting lipid-facing surfaces of the TM domain. Recent progresses in structure predictions of membrane proteins are also reviewed, with further discussions on calculation of ensemble properties such as melting temperature based on simplified state space model. Additional topics include prediction of oligomerization state of membrane proteins, identification of the interfaces for protein-protein interactions, and design of membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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18
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Harris F, Dennison SR, Singh J, Phoenix DA. On the selectivity and efficacy of defense peptides with respect to cancer cells. Med Res Rev 2011; 33:190-234. [PMID: 21922503 DOI: 10.1002/med.20252] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we review potential determinants of the anticancer efficacy of innate immune peptides (ACPs) for cancer cells. These determinants include membrane-based factors, such as receptors, phosphatidylserine, sialic acid residues, and sulfated glycans, and peptide-based factors, such as residue composition, sequence length, net charge, hydrophobic arc size, hydrophobicity, and amphiphilicity. Each of these factors may contribute to the anticancer action of ACPs, but no single factor(s) makes an overriding contribution to their overall selectivity and toxicity. Differences between the anticancer actions of ACPs seem to relate to different levels of interplay between these peptide and membrane-based factors.
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Affiliation(s)
- Frederick Harris
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, Lancashire, United Kingdom
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19
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Samish I, MacDermaid CM, Perez-Aguilar JM, Saven JG. Theoretical and Computational Protein Design. Annu Rev Phys Chem 2011; 62:129-49. [DOI: 10.1146/annurev-physchem-032210-103509] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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20
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Saven JG. Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins. Curr Opin Chem Biol 2011; 15:452-7. [PMID: 21493122 DOI: 10.1016/j.cbpa.2011.03.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 11/18/2022]
Abstract
Computational and theoretical methods are advancing protein design as a means to create and investigate proteins. Such efforts further our capacity to control, design and understand biomolecular structure, sequence and function. Herein, the focus is on some recent applications that involve using theoretical and computational methods to guide the design of protein sequence ensembles, new enzymes, proteins with novel cofactors, and membrane proteins.
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Affiliation(s)
- Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
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21
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Abstract
Interactions of copper and membranes with α-synuclein have been implicated in pathogenic mechanisms of Parkinson's disease, yet work examining both concurrently is scarce. We have examined the effect of copper(ii) on protein/vesicle binding and found that both the copper(ii) affinity and α-helical content are enhanced for the membrane-bound protein.
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Affiliation(s)
- Heather R. Lucas
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer C. Lee
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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22
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Carlton DD, Schug KA. A review on the interrogation of peptide–metal interactions using electrospray ionization-mass spectrometry. Anal Chim Acta 2011; 686:19-39. [DOI: 10.1016/j.aca.2010.11.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 11/27/2022]
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23
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Bryan PN, Orban J. Proteins that switch folds. Curr Opin Struct Biol 2010; 20:482-8. [PMID: 20591649 DOI: 10.1016/j.sbi.2010.06.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 06/02/2010] [Indexed: 11/26/2022]
Abstract
An increasing number of proteins demonstrate the ability to switch between very different fold topologies, expanding their functional utility through new binding interactions. Recent examples of fold switching from naturally occurring and designed systems have a number of common features: (i) The structural transitions require states with diminished stability; (ii) Switching involves flexible regions in one conformer or the other; (iii) A new binding surface is revealed in the alternate fold that can lead to both stabilization of the alternative state and expansion of biological function. Fold switching not only provides insight into how new folds evolve, but also indicates that an amino acid sequence has more information content than previously thought. A polypeptide chain can encode a stable fold while simultaneously hiding latent propensities for alternative states with novel functions.
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Affiliation(s)
- Philip N Bryan
- Institute for Bioscience and Biotechnology Research, Department of Bioengineering, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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24
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Saven JG. Computational protein design: Advances in the design and redesign of biomolecular nanostructures. Curr Opin Colloid Interface Sci 2010; 15:13-17. [PMID: 21544231 DOI: 10.1016/j.cocis.2009.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational protein design facilitates the continued development of methods for the design of biomolecular structure, sequence and function. Recent applications include the design of novel protein sequences and structures, proteins incorporating nonbiological components, protein assemblies, soluble variants of membrane proteins, and proteins that modulate membrane function.
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Affiliation(s)
- Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, United States
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25
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Kuciauskas D, Caputo GA. Self-assembly of peptide-porphyrin complexes leads to pH-dependent excitonic coupling. J Phys Chem B 2010; 113:14439-47. [PMID: 19845410 DOI: 10.1021/jp905468y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Using absorbance, fluorescence, resonance light scattering, and circular dichroism spectroscopy, we studied the self-assembly of the anionic meso-tetra(4-sulfonatophenyl)porphine (TPPS(4)(2-/4-)) and a cationic 22-residue polypeptide. We found that three TPPS(4)(2-/4-) molecules bind to the peptide, which contains nine lysine residues in the primary sequence. In acidic solutions, when the peptide is in the random-coil conformation, TPPS(4)(2-) bound to the peptide forms excitonically coupled J-aggregates. In pH 7.6 solutions, when the peptide secondary structure is partially alpha-helical, the porphyrin-to-peptide binding constants are approximately the same as in acidic solutions (approximately 3 x 10(6) M(-1)), but excitonic interactions between the porphyrins are insignificant. The binding of TPPS(4)(2-/4-) to lysine-containing peptides is cooperative and can be described by the Hill model. Our results show that porphyrin binding can be used to change the secondary structure of peptide-based biomaterials. In addition, binding to peptides could be used to optimize porphyrin intermolecular electronic interactions (exciton coupling), which is relevant for the design of light-harvesting antennas for artificial photosynthesis.
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Affiliation(s)
- Darius Kuciauskas
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, USA.
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26
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Azuma Y, Imanishi M, Yoshimura T, Kawabata T, Futaki S. Cobalt(II)-responsive DNA binding of a GCN4-bZIP protein containing cysteine residues functionalized with iminodiacetic acid. Angew Chem Int Ed Engl 2009; 48:6853-6. [PMID: 19655361 DOI: 10.1002/anie.200902888] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yusuke Azuma
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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27
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Azuma Y, Imanishi M, Yoshimura T, Kawabata T, Futaki S. Cobalt(II)-Responsive DNA Binding of a GCN4-bZIP Protein Containing Cysteine Residues Functionalized with Iminodiacetic Acid. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902888] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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