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Park HS, Byun BJ, Kang YK. Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations. ACS OMEGA 2022; 7:27755-27768. [PMID: 35967045 PMCID: PMC9366962 DOI: 10.1021/acsomega.2c03942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol-1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII'-bend-like motif at the Gly3-Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII' bend at the Gly2-Gly3 sequence and a βI bend at the Gly3-Phe4 sequence. The calculated ensemble-averaged distance between CGly2 α and CLeu5 α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the "bioactive conformation" like an extended structure when binding to δOR.
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Affiliation(s)
- Hae Sook Park
- Department
of Nursing, Cheju Halla University, 38 Halladaehak-ro, Jeju, Jeju-do 63092, Republic of Korea
| | - Byung Jin Byun
- Drug
Discovery Center, JW Pharmaceutical Co.
Ltd., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic
of Korea
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, 1 Chungdae-ro,
Seowon-gu, Cheongju, Chungbuk 28644, Republic of Korea
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Li Q, Yang X, Zhang L, Wang Y, Kong J, Qi W, Liang Y, Su R, He Z. Thermally Induced Structural Transition of Peptide Nanofibers into Nanoparticles with Enhanced Fluorescence Properties. Chempluschem 2020; 85:1523-1528. [DOI: 10.1002/cplu.202000116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/24/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
| | - Xin Yang
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
| | - Liwei Zhang
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination TechnologyTianjin University Tianjin 300072 P. R. China
| | - Jia Kong
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) Tianjin 300072 P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination TechnologyTianjin University Tianjin 300072 P. R. China
| | - Yaoyu Liang
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) Tianjin 300072 P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination TechnologyTianjin University Tianjin 300072 P. R. China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering School of Chemical Engineering and TechnologyTianjin University Tianjin 300072 P. R. China
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Laaser JE, Skoff DR, Ho JJ, Joo Y, Serrano AL, Steinkruger JD, Gopalan P, Gellman SH, Zanni MT. Two-dimensional sum-frequency generation reveals structure and dynamics of a surface-bound peptide. J Am Chem Soc 2014; 136:956-62. [PMID: 24372101 PMCID: PMC3956615 DOI: 10.1021/ja408682s] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Surface-bound polypeptides and proteins are increasingly used to functionalize inorganic interfaces such as electrodes, but their structural characterization is exceedingly difficult with standard technologies. In this paper, we report the first two-dimensional sum-frequency generation (2D SFG) spectra of a peptide monolayer, which are collected by adding a mid-IR pulse shaper to a standard femtosecond SFG spectrometer. On a gold surface, standard FTIR spectroscopy is inconclusive about the peptide structure because of solvation-induced frequency shifts, but the 2D line shapes, anharmonic shifts, and lifetimes obtained from 2D SFG reveal that the peptide is largely α-helical and upright. Random coil residues are also observed, which do not themselves appear in SFG spectra due to their isotropic structural distribution, but which still absorb infrared light and so can be detected by cross-peaks in 2D SFG spectra. We discuss these results in the context of peptide design. Because of the similar way in which the spectra are collected, these 2D SFG spectra can be directly compared to 2D IR spectra, thereby enabling structural interpretations of surface-bound peptides and biomolecules based on the well-studied structure/2D IR spectra relationships established from soluble proteins.
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Affiliation(s)
- Jennifer E. Laaser
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - David R. Skoff
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Yongho Joo
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Arnaldo L. Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jay D. Steinkruger
- School of Environmental, Physical, and Applied Sciences, University of Central Missouri, Warrensburg, Missouri 64093
| | - Padma Gopalan
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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Distinct behaviour of the homeodomain derived cell penetrating peptide penetratin in interaction with different phospholipids. PLoS One 2010; 5:e15819. [PMID: 21209890 PMCID: PMC3012702 DOI: 10.1371/journal.pone.0015819] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/24/2010] [Indexed: 11/19/2022] Open
Abstract
Background Penetratin is a protein transduction domain derived from the homeoprotein Antennapedia. Thereby it is currently used as a cell penetrating peptide to introduce diverse molecules into eukaryotic cells, and it could also be involved in the cellular export of transcription factors. Moreover, it has been shown that it is able to act as an antimicrobial agent. The mechanisms involved in all these processes are quite controversial. Methodology/Principal Findings In this article, we report spectroscopic, calorimetric and biochemical data on the penetratin interaction with three different phospholipids: phosphatidylcholine (PC) and phosphatidylethanolamine (PE) to mimic respectively the outer and the inner leaflets of the eukaryotic plasma membrane and phosphatidylglycerol (PG) to mimic the bacterial membrane. We demonstrate that with PC, penetratin is able to form vesicle aggregates with no major change in membrane fluidity and presents no well defined secondary structure organization. With PE, penetratin aggregates vesicles, increases membrane rigidity and acquires an α-helical structure. With PG membranes, penetratin does not aggregate vesicles but decreases membrane fluidity and acquires a structure with both α-helical and β–sheet contributions. Conclusions/Significance These data from membrane models suggest that the different penetratin actions in eukaryotic cells (membrane translocation during export and import) and on prokaryotes may result from different peptide and lipid structural arrangements. The data suggest that, for eukaryotic cell penetration, penetratin does not acquire classical secondary structure but requires a different conformation compared to that in solution.
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Rahman LN, Chen L, Nazim S, Bamm VV, Yaish MW, Moffatt BA, Dutcher JR, Harauz G. Interactions of intrinsically disordered Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 with membranes — synergistic effects of lipid composition and temperature on secondary structure. Biochem Cell Biol 2010; 88:791-807. [DOI: 10.1139/o10-026] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dehydrins are intrinsically disordered (unstructured) proteins that are expressed in plants experiencing stressful conditions such as drought or low temperature. Dehydrins are typically found in the cytosol and nucleus, but also associate with chloroplasts, mitochondria, and the plasma membrane. Although their role is not completely understood, it has been suggested that they stabilize proteins or membrane structures during environmental stress, the latter association mediated by formation of amphipathic α-helices by conserved regions called the K-segments. Thellungiella salsuginea is a crucifer that thrives in the Canadian sub-Arctic (Yukon Territory) where it grows on saline-rich soils and experiences periods of both extreme cold and drought. We have cloned and expressed in Escherichia coli two dehydrins from this plant, denoted TsDHN-1 (acidic) and TsDHN-2 (basic). Here, we show using transmission-Fourier transform infrared (FTIR) spectroscopy that ordered secondary structure is induced and stabilized in these proteins by association with large unilamellar vesicles emulating the lipid compositions of plant plasma and organellar membranes. Moreover, this induced folding is enhanced at low temperatures, lending credence to the hypothesis that dehydrins stabilize plant outer and organellar membranes in conditions of cold.
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Affiliation(s)
- Luna N. Rahman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lin Chen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sumaiya Nazim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Vladimir V. Bamm
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mahmoud W. Yaish
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Barbara A. Moffatt
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John R. Dutcher
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - George Harauz
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Physics, University of Guelph, Guelph, ON N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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