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Johnson TS, Bourdine AA, Deber CM. Hydrophobic moment drives penetration of bacterial membranes by transmembrane peptides. J Biol Chem 2023; 299:105266. [PMID: 37734555 PMCID: PMC10585379 DOI: 10.1016/j.jbc.2023.105266] [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: 07/30/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
With antimicrobial resistance (AMR) remaining a persistent and growing threat to human health worldwide, membrane-active peptides are gaining traction as an alternative strategy to overcome the issue. Membrane-embedded multi-drug resistant (MDR) efflux pumps are a prime target for membrane-active peptides, as they are a well-established contributor to clinically relevant AMR infections. Here, we describe a series of transmembrane peptides (TMs) to target the oligomerization motif of the AcrB component of the AcrAB-TolC MDR efflux pump from Escherichia coli. These peptides contain an N-terminal acetyl-A-(Sar)3 (sarcosine; N-methylglycine) tag and a C-terminal lysine tag-a design strategy our lab has utilized to improve the solubility and specificity of targeting for TMs previously. While these peptides have proven useful in preventing AcrB-mediated substrate efflux, the mechanisms by which these peptides associate with and penetrate the bacterial membrane remained unknown. In this study, we have shown peptide hydrophobic moment (μH)-the measure of concentrated hydrophobicity on one face of a lipopathic α-helix-drives bacterial membrane permeabilization and depolarization, likely through lateral-phase separation of negatively-charged POPG lipids and the disruption of lipid packing. Our results show peptide μH is an important consideration when designing membrane-active peptides and may be the determining factor in whether a TM will function in a permeabilizing or non-permeabilizing manner when embedded in the bacterial membrane.
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Affiliation(s)
- Tyler S Johnson
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Aleksandra A Bourdine
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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2
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Elfar SA, Bahgat IM, Shebl MA, Lihoreau M, Tawfik MM. Intraspecific Variability in Proteomic Profiles and Biological Activities of the Honey Bee Hemolymph. INSECTS 2023; 14:365. [PMID: 37103179 PMCID: PMC10142140 DOI: 10.3390/insects14040365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Pollinator declines have raised major concerns for the maintenance of biodiversity and food security, calling for a better understanding of environmental factors that affect their health. Here we used hemolymph analysis to monitor the health status of Western honey bees Apis mellifera. We evaluated the intraspecific proteomic variations and key biological activities of the hemolymph of bees collected from four Egyptian localities characterized by different food diversities and abundances. Overall, the lowest protein concentrations and the weakest biological activities (cytotoxicity, antimicrobial and antioxidant properties) were recorded in the hemolymph of bees artificially fed sucrose solution and no pollen. By contrast, the highest protein concentrations and biological activities were recorded in bees that had the opportunity to feed on various natural resources. While future studies should expand comparisons to honey bee populations exposed to more different diets and localities, our results suggest hemolymph samples can be used as reliable indicators of bee nutrition.
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Affiliation(s)
- Salma A. Elfar
- Zoology Department, Faculty of Science, Port Said University, Port Said 42526, Egypt
| | - Iman M. Bahgat
- Zoology Department, Faculty of Science, Port Said University, Port Said 42526, Egypt
| | - Mohamed A. Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Mathieu Lihoreau
- Research Center on Animal Cognition, Center for Integrative Biology, Centre National de la Recherche Scientifique, University Paul Sabatier, 31062 Toulouse, France
| | - Mohamed M. Tawfik
- Zoology Department, Faculty of Science, Port Said University, Port Said 42526, Egypt
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3
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Britton D, Monkovic J, Jia S, Liu C, Mahmoudinobar F, Meleties M, Renfrew PD, Bonneau R, Montclare JK. Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers. Biomacromolecules 2022; 23:4851-4859. [PMID: 36227640 DOI: 10.1021/acs.biomac.2c01031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to engineer a solvent-exposed surface of self-assembling coiled coils allows one to achieve a higher-order hierarchical assembly such as nano- or microfibers. Currently, these materials are being developed for a range of biomedical applications, including drug delivery systems; however, ways to mechanistically optimize the coiled-coil structure for drug binding are yet to be explored. Our laboratory has previously leveraged the functional properties of the naturally occurring cartilage oligomeric matrix protein coiled coil (C), not only for its favorable motif but also for the presence of a hydrophobic pore to allow for small-molecule binding. This includes the development of Q, a rationally designed pentameric coiled coil derived from C. Here, we present a small library of protein microfibers derived from the parent sequences of C and Q bearing various electrostatic potentials with the aim to investigate the influence of higher-order assembly and encapsulation of candidate small molecule, curcumin. The supramolecular fiber size appears to be well-controlled by sequence-imbued electrostatic surface potential, and protein stability upon curcumin binding is well correlated to relative structure loss, which can be predicted by in silico docking.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Julia Monkovic
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York10016, United States.,Department of Chemistry, New York University, New York, New York10012, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York10010, United States
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4
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Scotti C, Barlow JW. Natural Products Containing the Nitrile Functional Group and Their Biological Activities. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221099973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The importance of nitriles as a key class of chemicals with applications across the sciences is widely appreciated. The natural world is an underappreciated source of chemically diverse nitriles. With this in mind, this review describes novel nitrile-containing molecules isolated from natural sources from 1998 to 2021, as well as a discussion of the biological activity of these compounds. This study gathers 192 molecules from varied origins across the plant, animal, and microbial worlds. Their biological activity is extremely diverse, with many potential medicinal applications.
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Affiliation(s)
- Camille Scotti
- Ecole Nationale Supérieure de Chimie de Mulhouse, Université de Haute Alsace, Mulhouse, France
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - James W. Barlow
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
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Chen WL, Ma ST, Chen YW, Chao YC, Chan AC, Tu LH, Liu WM. A Fluorogenic Molecule for Probing Islet Amyloid Using Flavonoid as a Scaffold Design. Biochemistry 2020; 59:1482-1492. [DOI: 10.1021/acs.biochem.0c00076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei-Ling Chen
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Shih-Ting Ma
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Yun-Wen Chen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Yen-Cheng Chao
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Ai-Ci Chan
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Ling-Hsien Tu
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
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Hirano A, Nagatoishi S, Wada M, Tsumoto K, Maluf KN, Arakawa T. Technical Capabilities and Limitations of Optical Spectroscopy and Calorimetry Using Water-Miscible Solvents: The Case of Dimethyl Sulfoxide, Acetonitrile, and 1,4-Dioxane. J Pharm Sci 2019; 109:524-531. [PMID: 31682831 DOI: 10.1016/j.xphs.2019.10.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
In drug development, water-miscible solvents are commonly used to dissolve drug substances. Typical routine procedures in drug development include dilution of the stock drug solution into an aqueous solution containing target macromolecules for drug binding assays. However, water-miscible solvents impose some technical limitations on the assays on account of their light absorption and heat capacity. Here, we examined the effects of the dilution of 3 water-miscible solvents, that is, dimethyl sulfoxide, acetonitrile, and 1,4-dioxane, on the baseline stability and signal/noise ratio in circular dichroism spectroscopy, isothermal titration calorimetry, and differential scanning calorimetry. Dimethyl sulfoxide and 1,4-dioxane affect the signal/noise ratio of circular dichroism spectra at typically used concentrations due to their light absorbance. The water-miscible solvents generate interfering signals in the isothermal titration calorimetry due to their mixing heat. They show negative or positive slope in the differential scanning calorimetry. Such interfering effects of the solvents are reduced by appropriate dilution according to the analytical techniques. Because the water-miscible solvents have solubilization capacity for alkyl chain moieties and aromatic moieties of chemicals, drug substances containing these moieties can be dissolved into the solvents and then subjected to the analyses to examine their interactions with target proteins after appropriate dilution of the drug solutions.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Karl N Maluf
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
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Effects of allantoin and dimethyl sulfoxide on the thermal aggregation of lysozyme. Int J Biol Macromol 2018; 119:180-185. [PMID: 30009897 DOI: 10.1016/j.ijbiomac.2018.07.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/02/2018] [Accepted: 07/11/2018] [Indexed: 11/24/2022]
Abstract
Allantoin is used to suppress protein aggregation without decreasing the melting temperature. However, the solubility of allantoin in water or buffer solutions is too low (approximately 30 mM at ambient temperature) to be used as a protein aggregation suppressor in various situations. Here we show that a high-concentration solution of allantoin in neat dimethyl sulfoxide (DMSO) is useful as a stock solution for the additive that controls protein aggregation. The allantoin concentration from 10 to 100 mM in 10% (v/v) DMSO significantly suppressed the thermal aggregation of hen egg white lysozyme as a model protein, with increasing allantoin concentration. The residual activity of lysozyme in 10% DMSO and 100 mM allantoin after heating at 90 °C for 10 min was increased >3-fold compared to that without allantoin. Thus, it was concluded that allantoin in DMSO is an effective stock solution for practical application in enhancing the recovery of enzymatic activity and suppressing the formation of small aggregate of protein.
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