1
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Shukri A, Carroll AC, Collins R, Charih F, Wong A, Biggar KK. Systematic in vitro optimization of antimicrobial peptides against Escherichia coli. JAC Antimicrob Resist 2024; 6:dlae096. [PMID: 38966332 PMCID: PMC11220656 DOI: 10.1093/jacamr/dlae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/21/2024] [Indexed: 07/06/2024] Open
Abstract
Objectives Antimicrobial resistance is a growing concern and claims over 1 million lives per year. The discovery of new antimicrobial drugs is expensive and often generates low profitability, with very low success rates. One way to combat this is by the improvement of known antimicrobials, such as antimicrobial peptides (AMPs). The aim of this study was to improve the antimicrobial activities of two known AMPs, UyCT3 and indolicidin, with the use of peptide libraries and growth curves. Methods Peptide permutation libraries were synthesized for two AMPs, indolicidin and UyCT3, which included 520 peptides. These peptides were subsequently tested against MG1655-K12, to which subsequent peptide design was performed, then tested against three clinically Gram-negative relevant drug-resistant isolates. Best-performing candidates were subjected to a haemolysis assay for toxicity validation. Results Single amino acid permutations of UyCT3 and indolicidin were sufficient to inhibit growth of MG1655-K12, and subsequent generations of peptide design were able to inhibit growth of clinical isolates at concentrations as low as 5 µM. Our best-performing AMP, UyCT3I5A, W6Y, K10I, F13I, was not seen to be toxic towards sheep RBCs. Conclusions The efficacy of the AMPs improved with the use of our peptide library technology, whereby an AMP was found that inhibited bacterial growth of clinical Gram-negative isolates 4-fold better than its WT counterpart.
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Affiliation(s)
- Ali Shukri
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Amanda C Carroll
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Ryan Collins
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Francois Charih
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Alex Wong
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
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2
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Keever JM, Banzon PD, Hales MK, Sargent AL, Allen WE. Association between N-Terminal Pyrenes Stabilizes the Collagen Triple Helix. J Org Chem 2023; 88:11885-11894. [PMID: 37531574 DOI: 10.1021/acs.joc.3c01175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Collagen model peptides featuring the fluorophore pyrene at their N-termini have been synthesized, and their thermal denaturation has been examined using circular dichroism (CD) and fluorescence spectroscopies. Flanking the (Pro-Hyp-Gly)7 core of the peptide monomers at positions 1 and/or 23 in the primary sequence, Lys residues were introduced to ensure water solubility. Triple helices derived from such peptides show a broad excimer emission at ∼480 nm, indicative of interaction between the pyrene units. CD experiments show that the fluorophores enhance helix stability primarily through entropic effects. Unfolding temperatures (Tm) increase by up to 7 °C for systems with N-terminal lysine residues and by up to 21 °C for systems in which the first-position Lys is replaced by Ala. Tm values derived from fluorescence measurements (at 50 μM) typically lie within ∼1 °C of those obtained using CD (at 200 μM). Computational modeling in a water continuum using B3LYP-GD3 and M06-2X functionals predicts that face-to-face association of fluorophores can occur while H-bonding within the [(POG)n]3 assembly is retained. Such parallel stacking is consistent with hydrophobically driven stabilization. Labeling collagen peptides with pyrene is a synthetically simple way to promote triple helicity while providing a means to obtain Tm data on relatively dilute samples.
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Affiliation(s)
- Jared M Keever
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Patrick D Banzon
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Megan K Hales
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Andrew L Sargent
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - William E Allen
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
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3
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Jacob MH, D’Souza RN, Lazar AI, Nau WM. Diffusion-Enhanced Förster Resonance Energy Transfer in Flexible Peptides: From the Haas-Steinberg Partial Differential Equation to a Closed Analytical Expression. Polymers (Basel) 2023; 15:polym15030705. [PMID: 36772006 PMCID: PMC9919848 DOI: 10.3390/polym15030705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In the huge field of polymer structure and dynamics, including intrinsically disordered peptides, protein folding, and enzyme activity, many questions remain that cannot be answered by methodology based on artificial intelligence, X-ray, or NMR spectroscopy but maybe by fluorescence spectroscopy. The theory of Förster resonance energy transfer (FRET) describes how an optically excited fluorophore transfers its excitation energy through space to an acceptor moiety-with a rate that depends on the distance between donor and acceptor. When the donor and acceptor moiety are conjugated to different sites of a flexible peptide chain or any other linear polymer, the pair could in principle report on chain structure and dynamics, on the site-to-site distance distribution, and on the diffusion coefficient of mutual site-to-site motion of the peptide chain. However, the dependence of FRET on distance distribution and diffusion is not defined by a closed analytical expression but by a partial differential equation (PDE), by the Haas-Steinberg equation (HSE), which can only be solved by time-consuming numerical methods. As a second complication, time-resolved FRET measurements have thus far been deemed necessary. As a third complication, the evaluation requires a computationally demanding but indispensable global analysis of an extended experimental data set. These requirements have made the method accessible to only a few experts. Here, we show how the Haas-Steinberg equation leads to a closed analytical expression (CAE), the Haas-Steinberg-Jacob equation (HSJE), which relates a diffusion-diagnosing parameter, the effective donor-acceptor distance, to the augmented diffusion coefficient, J, composed of the diffusion coefficient, D, and the photophysical parameters that characterize the used FRET method. The effective donor-acceptor distance is easily retrieved either through time-resolved or steady-state fluorescence measurements. Any global fit can now be performed in seconds and minimizes the sum-of-square difference between the experimental values of the effective distance and the values obtained from the HSJE. In summary, the HSJE can give a decisive advantage in applying the speed and sensitivity of FRET spectroscopy to standing questions of polymer structure and dynamics.
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4
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Vujovic F, Hunter N, Farahani RM. Notch ankyrin domain: evolutionary rise of a thermodynamic sensor. Cell Commun Signal 2022; 20:66. [PMID: 35585601 PMCID: PMC9118731 DOI: 10.1186/s12964-022-00886-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/21/2022] [Indexed: 12/19/2022] Open
Abstract
Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notchon to Notchoff state, characterised by dissociation of Notch intracellular domain (NICD) from DNA-bound RBPJ. Here we provide evidence that transitioning to the Notchoff state is regulated by heat flux, a phenomenon that aligns resolution of fate dichotomies to mitochondrial activity. A combination of phylogenetic analysis and computational biochemistry was utilised to disclose structural adaptations of Notch1 ankyrin domain that enabled function as a sensor of heat flux. We then employed DNA-based micro-thermography to measure heat flux during brain development, followed by analysis in vitro of the temperature-dependent behaviour of Notch1 in mouse neural progenitor cells. The structural capacity of NICD to operate as a thermodynamic sensor in metazoans stems from characteristic enrichment of charged acidic amino acids in β-hairpins of the ankyrin domain that amplify destabilising inter-residue electrostatic interactions and render the domain thermolabile. The instability emerges upon mitochondrial activity which raises the perinuclear and nuclear temperatures to 50 °C and 39 °C, respectively, leading to destabilization of Notch1 transcriptional complex and transitioning to the Notchoff state. Notch1 functions a metazoan thermodynamic sensor that is switched on by intercellular contacts, inputs heat flux as a proxy for mitochondrial activity in the Notchon state via the ankyrin domain and is eventually switched off in a temperature-dependent manner. Video abstract
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Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia. .,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia.
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5
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Electrostatically induced pKa shifts in oligopeptides: the upshot of neighboring side chains. Amino Acids 2022; 54:277-287. [DOI: 10.1007/s00726-021-03116-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/29/2021] [Indexed: 11/01/2022]
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6
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Thoma JL, Duhamel J. Characterization of the Local Volume Probed by the Side-Chain Ends of Poly(oligo(ethylene glycol) 1-Pyrenemethyl ether methacrylate) Bottle Brushes in Solution Using Pyrene Excimer Fluorescence. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janine L. Thoma
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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7
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Konermann L, Aliyari E, Lee JH. Mobile Protons Limit the Stability of Salt Bridges in the Gas Phase: Implications for the Structures of Electrosprayed Protein Ions. J Phys Chem B 2021; 125:3803-3814. [PMID: 33848419 DOI: 10.1021/acs.jpcb.1c00944] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrosprayed protein ions can retain native-like conformations. The intramolecular contacts that stabilize these compact gas-phase structures remain poorly understood. Recent work has uncovered abundant salt bridges in electrosprayed proteins. Salt bridges are zwitterionic BH+/A- contacts. The low dielectric constant in the vacuum strengthens electrostatic interactions, suggesting that salt bridges could be a key contributor to the retention of compact protein structures. A problem with this assertion is that H+ are mobile, such that H+ transfer can convert salt bridges into neutral B0/HA0 contacts. This possible salt bridge annihilation puts into question the role of zwitterionic motifs in the gas phase, and it calls for a detailed analysis of BH+/A- versus B0/HA0 interactions. Here, we investigate this issue using molecular dynamics (MD) simulations and electrospray experiments. MD data for short model peptides revealed that salt bridges with static H+ have dissociation energies around 700 kJ mol-1. The corresponding B0/HA0 contacts are 1 order of magnitude weaker. When considering the effects of mobile H+, BH+/A- bond energies were found to be between these two extremes, confirming that H+ migration can significantly weaken salt bridges. Next, we examined the protein ubiquitin under collision-induced unfolding (CIU) conditions. CIU simulations were conducted using three different MD models: (i) Positive-only runs with static H+ did not allow for salt bridge formation and produced highly expanded CIU structures. (ii) Zwitterionic runs with static H+ resulted in abundant salt bridges, culminating in much more compact CIU structures. (iii) Mobile H+ simulations allowed for the dynamic formation/annihilation of salt bridges, generating CIU structures intermediate between scenarios (i) and (ii). Our results uncover that mobile H+ limit the stabilizing effects of salt bridges in the gas phase. Failure to consider the effects of mobile H+ in MD simulations will result in unrealistic outcomes under CIU conditions.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Justin H Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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8
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Casier R, Duhamel J. The Effect of Amino Acid Size on the Internal Dynamics and Conformational Freedom of Polypeptides. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
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9
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Hennig A, Nau WM. Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays. Front Chem 2020; 8:806. [PMID: 33134264 PMCID: PMC7511663 DOI: 10.3389/fchem.2020.00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.
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Affiliation(s)
- Andreas Hennig
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,Institute of Chemistry of New Materials, School of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
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10
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Aliyari E, Konermann L. Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry. Anal Chem 2020; 92:10807-10814. [DOI: 10.1021/acs.analchem.0c02290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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11
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Casier R, Duhamel J. Effect of Like Charges on the Conformation and Internal Dynamics of Polypeptides Probed by Pyrene Excimer Fluorescence. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo N2L3G1, Ontario, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo N2L3G1, Ontario, Canada
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12
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Augmenting Peptide Flexibility by Inserting Gamma-Aminobutyric Acid (GABA) in Their Sequence. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10054-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Wu J, Huang Y, Yin H, Chen T. The role of solvent quality and chain stiffness on the end-to-end contact kinetics of semiflexible polymers. J Chem Phys 2018; 149:234903. [PMID: 30579311 DOI: 10.1063/1.5054829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Motivated by loop closure during protein folding and DNA packing, we systemically studied the effects of the solvent quality and chain stiffness on the thermodynamics and kinetics of the end-to-end contact formation for semiflexible polymer chains with reactive ends by Langevin dynamics simulations. In thermodynamics, a rich variety of products of the end-to-end contact have been discovered, such as loop, hairpin, toroid, and rodlike bundle, the populations of which are dependent on the solvent quality and chain stiffness. In kinetics, the overall pathways to form the end-to-end contact have been identified. The change of solvent quality and chain stiffness can tune the roughness of energy landscape and modulate the kinetic partitioning of the end-to-end contact formation pathways, leading to differing kinetic behaviors. In good or poor solvents, the first end-to-end contact rate k c decreases with increasing the strength of bending stiffness k θ monotonically. In very poor solvents, however, the dependence of the logarithm of the first end-to-end contact rate ln k c on k θ exhibits erratic behavior, which stems from more rugged energy landscape due to the polymer chain getting trapped into the intermediate state composed of the rodlike bundles with two ends in separation. For semiflexible chains, with increasing chain length N, the rate k c increases initially and then decreases: in good solvents, the rate k c exhibits a power-law relationship to chain length N with an exponent of ∼-1.50 in the region of long chains, which is in good agreement with the value derived from the experiment in the asymptotic limit of large N; and in poor solvents, the rate k c exhibits a significantly stronger chain length dependence than those observed in good solvents in the region of long chains due to frustration to form the end-to-end contact along a specific path, especially the scaling exponent between the rate k c and chain length N is ∼-3.62 for the case of polymer chains with k θ = 4 at the solvent quality ε ij = 1, in accord with the value obtained from the experiments.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Yiran Huang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Hongmei Yin
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
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14
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Jacob MH, Ghosh I, D'Souza RN, Nau WM. Two Orders of Magnitude Variation of Diffusion-Enhanced Förster Resonance Energy Transfer in Polypeptide Chains. Polymers (Basel) 2018; 10:E1079. [PMID: 30961004 PMCID: PMC6403563 DOI: 10.3390/polym10101079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
A flexible peptide chain displays structural and dynamic properties that correspond to its folding and biological activity. These properties are mirrored in intrachain site-to-site distances and diffusion coefficients of mutual site-to-site motion. Both distance distribution and diffusion determine the extent of Förster resonance energy transfer (FRET) between two sites labeled with a FRET donor and acceptor. The relatively large Förster radii of traditional FRET methods (R₀ > 20 Å) lead to a fairly low contribution of diffusion. We introduced short-distance FRET (sdFRET) where Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, acts as acceptor paired with donors, such as naphtylalanine (NAla), tryptophan, 5-l-fluorotryptophan, or tyrosine. The Förster radii are always close to 10 Å, which makes sdFRET highly sensitive to diffusional motion. We recently found indications that the FRET enhancement caused by diffusion depends symmetrically on the product of the radiative fluorescence lifetime of the donor and the diffusion coefficient. In this study, we varied this product by two orders of magnitude, using both donors of different lifetime, NAla and FTrp, as well as a varying viscogen concentration, to corroborate this statement. We demonstrate the consequences of this relationship in evaluating the impact of viscogenic coadditives on peptide dimensions.
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Affiliation(s)
- Maik H Jacob
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany.
| | - Indrajit Ghosh
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany.
| | - Roy N D'Souza
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany.
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany.
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15
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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16
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Jacob MH, D'Souza RN, Schwarzlose T, Wang X, Huang F, Haas E, Nau WM. Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding. J Phys Chem B 2018; 122:4445-4456. [PMID: 29617564 DOI: 10.1021/acs.jpcb.8b00879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.
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Affiliation(s)
- Maik H Jacob
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Roy N D'Souza
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Thomas Schwarzlose
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Xiaojuan Wang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Fang Huang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Elisha Haas
- Department of Life Science , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Werner M Nau
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany.,Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
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17
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Affiliation(s)
- Shiva Farhangi
- Institute for Polymer Research,
Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research,
Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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