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Prusty JS, Kumar A. In silico-driven identification and experimental confirmation of antifungal proteins (AFPs) against Candidaalbicans. Biochimie 2024:S0300-9084(24)00194-9. [PMID: 39134296 DOI: 10.1016/j.biochi.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/30/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Mycoses infect millions of people annually across the world. The most common mycosis agent, Candida albicans is responsible for a great deal of illness and death. C. albicans infection is becoming more widespread and the current antifungals polyenes, triazoles, and echinocandins are less efficient against it. Investigating antifungal peptides (AFPs) as therapeutic is gaining momentum. Therefore, we used MALDI-TOF/MS analysis to identify AFPs and protein-protein docking to analyze their interactions with the C. albicans target protein. Some microorganisms with strong antifungal action against C. albicans were selected for the isolation of AFPs. Using MALDI-TOF/MS, we identified 3 AFPs Chitin binding protein (ACW83017.1; Bacillus licheniformis), the bifunctional protein GlmU (BBQ13478.1; Stenotrophomonas maltophilia), and zinc metalloproteinase aureolysin (BBA25172.1; Staphylococcus aureus). These AFPs showed robust interactions with C. albicans target protein Sap5. We deciphered some important residues in identified APFs and highlighted interaction with Sap5 through hydrogen bonds, protein-protein interactions, and salt bridges using protein-protein docking and MD simulations. The three discovered AFPs-Sap5 complexes exhibit different levels of stability, as seen by the RMSD analysis and interaction patterns. Among protein-protein interactions, the remarkable stability of the BBQ25172.1-2QZX complex highlights the role of salt bridges and hydrogen bonds. Identified AFPs could be further studied for developing successful antifungal candidates and peptide-based new antifungal therapeutic strategies as fresh insights into addressing antifungal resistance also.
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Affiliation(s)
- Jyoti Sankar Prusty
- Department of Biotechnology, National Institute of Technology, Raipur, 492010, CG, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, 492010, CG, India.
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2
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Slezina MP, Odintsova TI. Plant Antimicrobial Peptides: Insights into Structure-Function Relationships for Practical Applications. Curr Issues Mol Biol 2023; 45:3674-3704. [PMID: 37185763 PMCID: PMC10136942 DOI: 10.3390/cimb45040239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Antimicrobial peptides (AMPs) are short polypeptide molecules produced by multicellular organisms that are involved in host defense and microbiome preservation. In recent years, AMPs have attracted attention as novel drug candidates. However, their successful use requires detailed knowledge of the mode of action and identification of the determinants of biological activity. In this review, we focused on structure-function relationships in the thionins, α-hairpinins, hevein-like peptides, and the unique Ib-AMP peptides isolated from Impatiens balsamina. We summarized the available data on the amino acid sequences and 3D structure of peptides, their biosynthesis, and their biological activity. Special attention was paid to the determination of residues that play a key role in the activity and the identification of the minimal active cores. We have shown that even subtle changes in amino acid sequences can affect the biological activity of AMPs, which opens up the possibility of creating molecules with improved properties, better therapeutic efficacy, and cheaper large-scale production.
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Affiliation(s)
- Marina P Slezina
- Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia
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3
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Cyclo(DAA-DAA) dipeptide as a peptide linker and β-sheet inducer. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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4
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Rajninec M, Jopcik M, Danchenko M, Libantova J. Biochemical and antifungal characteristics of recombinant class I chitinase from Drosera rotundifolia. Int J Biol Macromol 2020; 161:854-863. [DOI: 10.1016/j.ijbiomac.2020.06.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
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5
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Groß A, Hashimoto C, Sticht H, Eichler J. Synthetic Peptides as Protein Mimics. Front Bioeng Biotechnol 2016; 3:211. [PMID: 26835447 PMCID: PMC4717299 DOI: 10.3389/fbioe.2015.00211] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
The design and generation of molecules capable of mimicking the binding and/or functional sites of proteins represents a promising strategy for the exploration and modulation of protein function through controlled interference with the underlying molecular interactions. Synthetic peptides have proven an excellent type of molecule for the mimicry of protein sites because such peptides can be generated as exact copies of protein fragments, as well as in diverse chemical modifications, which includes the incorporation of a large range of non-proteinogenic amino acids as well as the modification of the peptide backbone. Apart from extending the chemical and structural diversity presented by peptides, such modifications also increase the proteolytic stability of the molecules, enhancing their utility for biological applications. This article reviews recent advances by this and other laboratories in the use of synthetic protein mimics to modulate protein function, as well as to provide building blocks for synthetic biology.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Chie Hashimoto
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
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6
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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7
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Kinetic characterization of Aspergillus niger chitinase CfcI using a HPAEC-PAD method for native chitin oligosaccharides. Carbohydr Res 2015; 407:73-8. [DOI: 10.1016/j.carres.2015.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 01/14/2023]
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8
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Molecular simulations of hevein/(GlcNAc)3 complex with weakened OH/O and CH/π hydrogen bonds: implications for their role in complex stabilization. Carbohydr Res 2015; 408:1-7. [PMID: 25816996 DOI: 10.1016/j.carres.2015.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/23/2022]
Abstract
Carbohydrate-protein complexes are often characterized by interactions via aromatic amino acid residues. Several mechanisms have been proposed to explain these stacking-like interactions between pyranose sugars and aromatic moieties. The physical basis of these interactions is being explained as either dispersion CH/π or hydrophobic. In order to elucidate the nature of these interactions, we performed a series of molecular dynamics simulation of hevein domain (HEV32) in complex with (β-D-GlcNAc)3. Selected OH/O and CH/π hydrogen bonds involved in carbohydrate recognition were artificially weakened in 100 ns molecular dynamics simulations. Separate weakening of either OH/O or CH/π hydrogen bonds was not sufficient to destabilize the complex. This indicates that other effects, not solely CH/π dispersion interactions, contribute significantly to the stability of the complex. Significant destabilization of complexes was reached only by simultaneous weakening of OH/O and CH/π hydrogen bonds. This also shows that classical hydrogen bonds and CH/π interactions are working in concert to stabilize this carbohydrate-protein test case.
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Nishimoto K, Tanaka K, Murakami T, Nakashita H, Sakamoto H, Oguri S. Datura stramonium agglutinin: Cloning, molecular characterization and recombinant production in Arabidopsis thaliana. Glycobiology 2014; 25:157-69. [DOI: 10.1093/glycob/cwu098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 633] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
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11
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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12
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Hernández-Gay JJ, Ardá A, Eller S, Mezzato S, Leeflang BR, Unverzagt C, Cañada FJ, Jiménez-Barbero J. Insights into the Dynamics and Molecular Recognition Features of Glycopeptides by Protein Receptors: The 3D Solution Structure of Hevein Bound to the Trisaccharide Core of N-Glycoproteins. Chemistry 2010; 16:10715-26. [DOI: 10.1002/chem.201000939] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Yokoyama S, Iida Y, Kawasaki Y, Minami Y, Watanabe K, Yagi F. The chitin-binding capability of Cy-AMP1 from cycad is essential to antifungal activity. J Pept Sci 2009; 15:492-7. [PMID: 19466694 DOI: 10.1002/psc.1147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antimicrobial peptides are important components of the host innate immune responses by exerting broad-spectrum microbicidal activity against pathogenic microbes. Cy-AMP1 found in the cycad (Cycas revoluta) seeds has chitin-binding ability, and the chitin-binding domain was conserved in knottin-type and hevein-type antimicrobial peptides. The recombinant Cy-AMP1 was expressed in Escherichia coli and purified to study the role of chitin-binding domain. The mutants of Cy-AMP1 lost chitin-binding ability completely, and its antifungal activity was markedly decreased in comparison with native Cy-AMP1. However, the antimicrobial activities of the mutant peptides are nearly identical to that of native one. It was suggested that the chitin-binding domain plays an essential role in antifungal, but not antimicrobial, activity of Cy-AMP1.
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Affiliation(s)
- Seiya Yokoyama
- Department of Applied Biological Chemistry, The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
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14
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Laughrey ZR, Kiehna SE, Riemen AJ, Waters ML. Carbohydrate-pi interactions: what are they worth? J Am Chem Soc 2008; 130:14625-33. [PMID: 18844354 DOI: 10.1021/ja803960x] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.
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Affiliation(s)
- Zachary R Laughrey
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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15
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Sharma R, McNamara JP, Raju RK, Vincent MA, Hillier IH, Morgado CA. The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections. Phys Chem Chem Phys 2008; 10:2767-74. [PMID: 18464992 DOI: 10.1039/b719764k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate-aromatic and amino acid-aromatic interactions. The interaction energy for three simple sugars in different conformations with benzene, all give interaction energies close to 5 kcal mol(-1). Our original parameterization of PM3 (PM3-D) seriously overestimates this value, and has prompted a reparametrization which includes a modified core-core interaction term. With two additional parameters, the carbohydrate complexes, as well as the S22 data set, are well reproduced. The new PM3 scheme (PM3-D*) is found to describe the peptide bond-aromatic ring interactions accurately and, together with the DFT-D method, it is used to investigate the interaction of six amino acids with pyrene. Whilst the peptide backbone can adopt both stacked and T-shaped structures in the complexes with similar interaction energies, there is a preference for the unsaturated ring to adopt a stacked structure. Thus, peptides in which the latter interactions are maximised are likely to be the most effective for the functionalisation of carbon nanotubes.
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Affiliation(s)
- Raman Sharma
- School of Chemistry, University of Manchester, Manchester, UK
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16
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On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR. PURE APPL CHEM 2008. [DOI: 10.1351/pac200880081827] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This revision describes an up-to-date review of our efforts to investigate the interaction of carbohydrates with aromatic moieties at different levels of complexity. Protein-sugar interactions have been studied using NMR experiments on a variety of hevein/chitooligosaccharide systems. In addition, NMR and computational methods have also been used to evaluate the interaction of simple aromatic entities with simple monosaccharides. In between, the stacking features of aromatic-containing glycomolecules have also been described by using an analogous experimental-theoretical approach.
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17
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Melton-Witt JA, Bentsen LM, Tweten RK. Identification of functional domains of Clostridium septicum alpha toxin. Biochemistry 2007; 45:14347-54. [PMID: 17128973 PMCID: PMC2561313 DOI: 10.1021/bi061334p] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alpha toxin (AT) is the major virulence factor of Clostridium septicum that is a proteolytically activated pore-forming toxin that belongs to the aerolysin-like family of toxins. AT is predicted to be a three-domain molecule on the basis of its functional and sequence similarity with aerolysin, for which the crystal structure has been determined. In this study, we have substituted the entire primary structure of AT with alanine or cysteine to identify those amino acids that comprise functional domains involved in receptor binding, oligomerization, and pore formation. These studies revealed that receptor binding is restricted to domain 1 of the AT structure, whereas domains 1 and 3 are involved in oligomerization. These studies also revealed the presence of a putative functional region of AT proximal to the receptor-binding domain but distal from the pore-forming domain that is proposed to regulate the insertion of the transmembrane beta-hairpin of the prepore oligomer.
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Affiliation(s)
| | | | - Rodney K. Tweten
- To whom correspondence should be addressed: Department of Microbiology and Immunology, 940 Stanton L. Young Blvd., The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190. Tel.:405-271-2133; Fax: 405-271-3117; E-mail:
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18
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Kiehna SE, Laughrey ZR, Waters ML. Evaluation of a carbohydrate–π interaction in a peptide model system. Chem Commun (Camb) 2007:4026-8. [PMID: 17912404 DOI: 10.1039/b711431a] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A carbohydrate-pi interaction contributes -0.8 kcal mol(-1) to the stabilization of a beta-hairpin peptide.
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Affiliation(s)
- Sarah E Kiehna
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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19
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Chávez MI, Andreu C, Vidal P, Aboitiz N, Freire F, Groves P, Asensio JL, Asensio G, Muraki M, Cañada FJ, Jiménez-Barbero J. On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues. Chemistry 2006; 11:7060-74. [PMID: 16220560 DOI: 10.1002/chem.200500367] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar complexes have been obtained. The thermodynamic analysis of the interactions that occur upon complex formation have also been carried out. Regarding binding affinity, the obtained data have permitted the deduction that the larger the aromatic group, the higher the association constant and the binding enthalpy. In all cases, entropy opposes binding. In contrast, deactivation of the aromatic rings by attaching fluorine atoms decreases the binding affinity, with a concomitant decrease in enthalpy. The role of the chemical nature of the aromatic ring for establishing sugar contacts has been thus evaluated.
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Affiliation(s)
- M Isabel Chávez
- Department of Protein Structure and Function, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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20
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Jiménez-Barbero J, Javier Cañada F, Asensio JL, Aboitiz N, Vidal P, Canales A, Groves P, Gabius HJ, Siebert HC. Hevein Domains: An Attractive Model to Study Carbohydrate–Protein Interactions at Atomic Resolution. Adv Carbohydr Chem Biochem 2006; 60:303-54. [PMID: 16750446 DOI: 10.1016/s0065-2318(06)60007-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Aboitiz N, Vila-Perelló M, Groves P, Asensio JL, Andreu D, Cañada FJ, Jiménez-Barbero J. NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides. Chembiochem 2005; 5:1245-55. [PMID: 15368576 DOI: 10.1002/cbic.200400025] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
HEV32, a 32-residue, truncated hevein lacking eleven C-terminal amino acids, was synthesized by solid-phase methodology and correctly folded with three cysteine bridge pairs. The affinities of HEV32 for small chitin fragments--in the forms of N,N',N"-triacetylchitotriose ((GlcNAc)3) (millimolar) and N,N',N",N"',N"",N""'-hexaacetylchitohexaose ((GlcNAc)6) (micromolar)--as measured by NMR and fluorescence methods, are comparable with those of native hevein. The HEV32 ligand-binding process is enthalpy driven, while entropy opposes binding. The NMR structure of ligand-bound HEV32 in aqueous solution was determined to be highly similar to the NMR structure of ligand-bound hevein. Solvated molecular-dynamics simulations were performed in order to monitor the changes in side-chain conformation of the binding site of HEV32 and hevein upon interaction with ligands. The calculations suggest that the Trp21 side-chain orientation of HEV32 in the free form differs from that in the bound state; this agrees with fluorescence and thermodynamic data. HEV32 provides a simple molecular model for studying protein-carbohydrate interactions and for understanding the physiological relevance of small native hevein domains lacking C-terminal residues.
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Affiliation(s)
- Nuria Aboitiz
- Department of Protein Structure and Function, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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22
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Ng TB. Antifungal proteins and peptides of leguminous and non-leguminous origins. Peptides 2004; 25:1215-22. [PMID: 15245883 DOI: 10.1016/j.peptides.2004.03.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2003] [Revised: 03/18/2004] [Accepted: 03/19/2004] [Indexed: 11/28/2022]
Abstract
Antifungal proteins and peptides, as their names imply, serve a protective function against fungal invasion. They are produced by a multitude of organisms including leguminous flowering plants, non-leguminous flowering plants, gymnosperms, fungi, bacteria, insects and mammals. The intent of the present review is to focus on the structural and functional characteristics of leguminous, as well as non-leguminous, antifungal proteins and peptides. A spectacular diversity of amino acid sequences has been reported. Some of the antifungal proteins and peptides are classified, based on their structures and/or functions, into groups including chitinases, glucanases, thaumatin-like proteins, thionins, and cyclophilin-like proteins. Some of the well-known proteins such as lectins, ribosome inactivating proteins, ribonucleases, deoxyribonucleases, peroxidases, and protease inhibitors exhibit antifungal activity. Different antifungal proteins may demonstrate different fungal specificities. The mechanisms of antifungal action of only some antifungal proteins including thaumatin-like proteins and chitinases have been elucidated.
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Affiliation(s)
- T B Ng
- Department of Biochemistry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories.
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Veronese P, Ruiz MT, Coca MA, Hernandez-Lopez A, Lee H, Ibeas JI, Damsz B, Pardo JM, Hasegawa PM, Bressan RA, Narasimhan ML. In defense against pathogens. Both plant sentinels and foot soldiers need to know the enemy. PLANT PHYSIOLOGY 2003; 131:1580-90. [PMID: 12692317 PMCID: PMC1540302 DOI: 10.1104/pp.102.013417] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Paola Veronese
- Center for Plant Environmental Stress Physiology, 1165 Horticulture Building, Purdue University, West Lafayette, Indiana 47907-1165, USA
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Muraki M, Harata K. X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine. J Mol Recognit 2003; 16:72-82. [PMID: 12720276 DOI: 10.1002/jmr.611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In spite of the belonging to the same c-type lysozyme family, hen egg-white lysozyme (HEWL) was much less susceptible to the dual-affinity labeling with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine (Galbeta1,4GlcNAc-Epo) than human lysozyme (HL). The three-dimensional structures of the HEWL labeled with single Galbeta1,4GlcNAc-Epo and the Glu102-mutant HL labeled with double Galbeta1,4GlcNAc-Epo were determined by X-ray crystallography at resolutions of 1.85 and 2.0 A, respectively. The overall conformation and the interaction mode of the carbohydrate ligand part in the singly labeled HEWL and the doubly labeled Glu102-mutant HL were basically identical to those of the correspondingly labeled wild-type HL with minor alterations in some stereochemical parameters. A detailed comparison of the structures revealed the key protein-carbohydrate and carbohydrate-carbohydrate interactions essential for the dual labeling. It was suggested that the difference in the efficiency of the dual labeling was caused by the structural difference between Gln104 in HL and Asn103 in HEWL. The relevance to our previous study and the carbohydrate-carbohydrate interaction on cell-surface membranes were discussed.
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Affiliation(s)
- Michiro Muraki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
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Van den Bergh KPB, Proost P, Van Damme J, Coosemans J, Van Damme EJM, Peumans WJ. Five disulfide bridges stabilize a hevein-type antimicrobial peptide from the bark of spindle tree (Euonymus europaeus L.). FEBS Lett 2002; 530:181-5. [PMID: 12387889 DOI: 10.1016/s0014-5793(02)03474-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A small 45 amino acid residue antifungal polypeptide was isolated from the bark of spindle tree (Euonymus europaeus L.). Though the primary structure of this so-called E. europaeus chitin-binding protein or Ee-CBP is highly similar to the hevein domain, it distinguishes itself from most previously identified hevein-type antimicrobial peptides (AMP) by the presence of two extra cysteine residues that form an extra disulfide bond. Due to these five disulfide bonds Ee-CBP is a remarkably stable protein. Agar diffusion and microtiterplate assays demonstrated that Ee-CBP is a potent antimicrobial protein. IC(50)-values as low as 1 microg/ml were observed for the fungus Botrytis cinerea. Comparative assays further demonstrated that Ee-CBP is a stronger inhibitor of fungal growth than Ac-AMP2 from Amaranthus caudatus seeds, which is considered one of the most potent antifungal hevein-type plant proteins.
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Affiliation(s)
- Karolien P B Van den Bergh
- Laboratory of Phytopathology and Plant Protection, Katholieke Universiteit Leuven, Willem de Croylaan 42, Belgium
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Takahashi O, Yasunaga K, Gondoh Y, Kohno Y, Saito K, Nishio M. The Conformation of 2-Phenylpropionaldehyde and Alkyl 1-Phenylethyl Ketones as Evidenced by Ab Initio Calculations. Relevance of the CH/π and CH/O Interactions in Stereochemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1777] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Itoh Y, Kawase T, Nikaidou N, Fukada H, Mitsutomi M, Watanabe T, Itoh Y. Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function. Biosci Biotechnol Biochem 2002; 66:1084-92. [PMID: 12092819 DOI: 10.1271/bbb.66.1084] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chitinase C (ChiC) is the first bacterial family 19 chitinase discovered in Streptomyces griseus HUT6037. While it shares significant similarity with the plant family 19 chitinases in the catalytic domain, its N-terminal chitin-binding domain (ChBD(ChiC)) differs from those of the plant enzymes. ChBD(ChiC) and the catalytic domain (CatD(ChiC)), as well as intact ChiC, were separately produced in E. coli and purified to homogeneity. Binding experiments and isothermal titration calorimetry assays demonstrated that ChBD(ChiC) binds to insoluble chitin, soluble chitin, cellulose, and N-acetylchitohexaose (roughly in that order). A deletion of ChBD(ChiC) resulted in moderate (about 50%) reduction of the hydrolyzing activity toward insoluble chitin substrates, but most (about 90%) of the antifungal activity against Trichoderma reesei was abolished by this deletion. Thus, this domain appears to contribute more importantly to antifungal properties than to catalytic activities. ChBD(ChiC) itself did not have antifungal activity or a synergistic effect on the antifungal activity of CatD(ChiC) in trans.
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Affiliation(s)
- Yoshikane Itoh
- Department of Biosystem Science, Graduate School of Science and Technology, Niigata University, Japan
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Muraki M, Ishimura M, Harata K. Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1569:10-20. [PMID: 11853952 DOI: 10.1016/s0304-4165(01)00231-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The interactions of wheat-germ agglutinin (WGA) with the GlcNAc beta 1,6Gal sequence, a characteristic component of branched poly-N-acetyllactosaminoglycans, were investigated using isothermal titration calorimetry and X-ray crystallography. GlcNAc beta 1,6Gal exhibited an affinity greater than GlcNAc beta 1,4GlcNAc to all WGA isolectins, whereas Gal beta 1,6GlcNAc showed much less affinity than GlcNAc beta 1,4GlcNAc. X-ray structural analyses of the glutaraldehyde-crosslinked WGA isolectin 3 crystals in complex with GlcNAc beta 1,6Gal, GlcNAc beta 1,4GlcNAc and GlcNAc beta 1,6Gal beta 1,4Glc were performed at 2.4, 2.2 and 2.2 A resolution, respectively. In spite of different glycosidic linkages, GlcNAc beta 1,6Gal and GlcNAc beta 1,4GlcNAc exhibited basically similar binding modes to each other, in contact with side chains of two aromatic residues, Tyr64 and His66. However, the conformations of the ligands in the two primary binding sites were not always identical. GlcNAc beta 1,6Gal showed more extensive variation in the parameters defining the glycosidic linkage structure compared to GlcNAc beta 1,4GlcNAc, demonstrating large conformational flexibility of the former ligand in the interaction with WGA. The difference in the ligand binding conformation was accompanied by alterations of the side chain conformation of the amino acid residues involved in the interactions. The hydrogen bond between Ser62 and the non-reducing end GlcNAc was always observed regardless of the ligand type, indicating the key role of this interaction. In addition to the hydrogen bonding and van der Waals interactions, CH--pi interactions involving Tyr64, His66 and Tyr73 are suggested to play an essential role in determining the ligand binding conformation in all complexes. One of the GlcNAc beta 1,6Gal ligands had no crystal packing contact with another WGA molecule, therefore the conformation might be more relevant to the interaction mode in solution.
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Affiliation(s)
- Michiro Muraki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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Takahashi O, Kohno Y, Iwasaki S, Saito K, Iwaoka M, Tomoda S, Umezawa Y, Tsuboyama S, Nishio M. Hydrogen-Bond-Like Nature of the CH/π Interaction as Evidenced by Crystallographic Database Analyses and Ab Initio Molecular Orbital Calculations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.2421] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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