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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. Relationships between conformational and vibrational features of tryptophan characteristic Raman markers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124377. [PMID: 38701580 DOI: 10.1016/j.saa.2024.124377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Tryptophan (Trp) residue provides characteristic vibrational markers to the middle wavenumber spectral region of the Raman spectra recorded from peptides and proteins. In this report, we were particularly interested in eight Trp Raman markers, referred to as Wi (i = 1,…,8). All responsible for pronounced Raman lines, these markers originate from indole moiety, a bicyclic conjugated segment involved in the Trp structure. Numerous investigations have previously attempted to relate the variations observed in the spectral features of these markers to the environmental changes of Trp residues. To emphasize the most important points we can mention (i) the variations in the Raman profile of W4 (∼1360 cm-1) and W5 (∼1340 cm-1), frequently observed as a doublet with variable intensity ratio. These two markers were thought to result from a Fermi-resonance effect between certain planar and nonplanar modes; (ii) the changes observed in the wavenumbers and relative intensities of W4, W7 (∼880 cm-1) and W8 (∼760 cm-1) were supposed to be related to the accessibility of Trp to surrounding water molecules; and (iii) the wavenumber fluctuations of W3 (∼1550 cm-1), taken as a Trp side chain orientational marker. However, some ambiguities still exist regarding the interpretation of these markers, needing further clarification. Herein, upon a joint experimental and theoretical analysis based on a multiconformational approach, attention was paid to the relationships between structural and vibrational features of three indole-containing compounds with increasing structural complexity, i.e., skatole (3-methylindole), tryptophan, and tripeptide Gly-Trp-Gly. This study clearly shows that the existing assignments given to certain Trp Raman markers should be reconsidered, especially those based on the Fermi-resonance origin of W4-W5 (∼1360-1340 cm-1) doublet, as well as the purely environmental dependence of W7 and W8 markers.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148. 74 rue Marcel Cachin. 93017 Bobigny Cédex France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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2
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Baruch Leshem A, Sloan-Dennison S, Massarano T, Ben-David S, Graham D, Faulds K, Gottlieb HE, Chill JH, Lampel A. Biomolecular condensates formed by designer minimalistic peptides. Nat Commun 2023; 14:421. [PMID: 36702825 PMCID: PMC9879991 DOI: 10.1038/s41467-023-36060-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications.
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Affiliation(s)
- Avigail Baruch Leshem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sian Sloan-Dennison
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Tlalit Massarano
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shavit Ben-David
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Hugo E Gottlieb
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel. .,Center for Nanoscience and Nanotechnology Tel Aviv University, Tel Aviv, 69978, Israel. .,Sagol Center for Regenerative Biotechnology Tel Aviv University, Tel Aviv, 69978, Israel. .,Center for the Physics and Chemistry of Living Systems Tel Aviv University, Tel Aviv 69978, Israel, Tel Aviv, 69978, Israel.
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3
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Avni A, Joshi A, Walimbe A, Pattanashetty SG, Mukhopadhyay S. Single-droplet surface-enhanced Raman scattering decodes the molecular determinants of liquid-liquid phase separation. Nat Commun 2022; 13:4378. [PMID: 35902591 PMCID: PMC9334365 DOI: 10.1038/s41467-022-32143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease. The authors introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that illuminates a wealth of molecular information within the mesoscopic liquid condensed phase of Fused in Sarcoma in the absence and presence of RNA.
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Affiliation(s)
- Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Swastik G Pattanashetty
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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4
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Zhao G, Zhu H. Cation-π Interactions in Graphene-Containing Systems for Water Treatment and Beyond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905756. [PMID: 32253804 DOI: 10.1002/adma.201905756] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/30/2020] [Indexed: 06/11/2023]
Abstract
Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic characteristics of graphene and greatly affect the device performance based on graphene and its derivatives. Here, the cation-π interactions in graphene containing systems for water treatment applications (e.g., separation membranes, adsorbents) are highlighted. The cross-linking effects caused by cation-π interactions contribute to membrane stability and selectivity and enhanced adsorption. Their roles in dominating the performance of graphene-based structures for other specific applications are also discussed. Relevant theoretical modeling and calculations are summarized to offer an in-depth understanding of the underlying mechanisms which can help in designing more functional materials and structures. Perspectives on the potential directions that deserve effort are also presented.
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Affiliation(s)
- Guoke Zhao
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, China
| | - Hongwei Zhu
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, China
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5
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Park S, Kim S, Jho Y, Hwang DS. Cation-π Interactions and Their Contribution to Mussel Underwater Adhesion Studied Using a Surface Forces Apparatus: A Mini-Review. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16002-16012. [PMID: 31423790 DOI: 10.1021/acs.langmuir.9b01976] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mussel underwater adhesion is a model phenomenon important for the understanding of broader biological adhesion and the development of biomimetic wet adhesives. The catechol moiety of 3,4-dihydroxyphenyl-l-alanine (DOPA) is known to be actively involved in the mechanism of mussel underwater adhesion; however, other underwater adhesion mechanisms are also crucial. The surface forces apparatus (SFA) has often been used to explore the contributions of other mechanisms to mussel underwater adhesion; e.g., recent SFA-based nanomechanical studies have revealed that cation-π interactions, one of the strongest intermolecular interactions in water, are the pivotal interactions of adhesive proteins involved in underwater mussel adhesion. This mini-review surveys recent research on cation-π interactions and their contributions to strong mussel underwater adhesion, shedding light on some biological processes and facilitating the development of biomedical adhesives.
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Affiliation(s)
- Sohee Park
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
| | - Sangsik Kim
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
- Division of Integrative Biosciences and Biotechnology , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
| | - YongSeok Jho
- Department of Physics and Research Institute of Natural Science , Gyeongsang National University , Jinju 52828 , Republic of Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
- Division of Integrative Biosciences and Biotechnology , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
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6
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Asamoto DK, Kang G, Kim JE. Folding of the β-Barrel Membrane Protein OmpA into Nanodiscs. Biophys J 2019; 118:403-414. [PMID: 31843264 DOI: 10.1016/j.bpj.2019.11.3381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/08/2019] [Accepted: 11/20/2019] [Indexed: 01/19/2023] Open
Abstract
Nanodiscs (NDs) are an excellent alternative to small unilamellar vesicles (SUVs) for studies of membrane protein structure, but it has not yet been shown that membrane proteins are able to spontaneously fold and insert into a solution of freely diffusing NDs. In this article, we present SDS-PAGE differential mobility studies combined with fluorescence, circular dichroism, and ultraviolet resonance Raman spectroscopy to confirm the spontaneous folding of outer membrane protein A (OmpA) into preformed NDs. Folded OmpA in NDs was incubated with Arg-C protease, resulting in the digestion of OmpA to membrane-protected fragments with an apparent molecular mass of ∼26 kDa (major component) and ∼24 kDa (minor component). The OmpA folding yields were greater than 88% in both NDs and SUVs. An OmpA adsorbed intermediate on NDs could be isolated at low temperature and induced to fold via an increase in temperature, analogous to the temperature-jump experiments on SUVs. The circular dichroism spectra of OmpA in NDs and SUVs were similar and indicated β-barrel secondary structure. Further evidence of OmpA folding into NDs was provided by ultraviolet resonance Raman spectroscopy, which revealed the intense 785 cm-1 structural marker for folded OmpA in NDs. The primary difference between folding in NDs and SUVs was the kinetics; the rate of folding was two- to threefold slower in NDs compared to in SUVs, and this decreased rate can tentatively be attributed to the properties of NDs. These data indicate that NDs may be an excellent alternative to SUVs for folding experiments and offer benefits of optical clarity, sample homogeneity, control of ND:protein ratios, and greater stability.
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Affiliation(s)
- DeeAnn K Asamoto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Guipeun Kang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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7
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Yang L, Ma Y, Xu Y, Chang G. Cation-π induced lithium-doped conjugated microporous polymer with remarkable hydrogen storage performance. Chem Commun (Camb) 2019; 55:11227-11230. [PMID: 31469129 DOI: 10.1039/c9cc04174e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cation-π induced lithium-doped conjugated microporous polymer, Li+-PTAT, was constructed. It was proved that the point to face cation-π interactions between Li+ and indole can endow the resulting Li+-PTAT with high Li+ content and without agglomeration, which further leads to its encouraging hydrogen storage capacity.
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Affiliation(s)
- Li Yang
- State Key Laboratory of Environment-friendly Energy Materials & School of Material Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, P. R. China.
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8
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Frański R. Gas-phase stability of sandwich complexes of crown ethers with metal cations - as studied by collision induced dissociation tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1651-1657. [PMID: 29943475 DOI: 10.1002/rcm.8215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/13/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE The gas-phase stabilities of the sandwich complexes formed by 12-crown-4 or 15-crown-5 with metal cations (Na+ , K+ , Rb+ , Tl+ , Ag+ , Ca2+ , Sr2+ , Ba2+ , Pb2+ , Hg2+ , Cd2+ ) are compared with the stability of the sandwich complex formed by benzo-12-crown-4 or benzo-15-crown-5 with the cations. It is interesting to check if the possible cation-π interactions increase the gas-phase stabilities of the sandwich complexes of benzo-crown ethers with metal cations. METHODS The sandwich complexes were generated in the gas phase by electrospray ionization (ESI) and then they were subjected to the collision induced dissociation tandem mass spectrometry experiments (CID-MS/MS). On the basis of the obtained product ion spectra, the respective breakdown plots of the ion abundances ratios against collision energy expressed in the terms of center-of-mass were made. RESULTS The gas-phase stabilities of [(B12C4)2 +Tl]+ , [(B15C5)2 +SrNO3 ]+ , [(B15C5)2 +PbNO3 ]+ and [(B15C5)2 +SrCl]+ were higher than those of [(12C4)2 +Tl]+ , [(15C5)2 +SrNO3 ]+ , [(15C5)2 +PbNO3 ]+ and [(15C5)2 +SrCl]+ , respectively. For the other sandwich complexes the stabilities of the complexes with benzo-crown ethers were not higher than those of the complexes of simple crown ethers. CONCLUSIONS It is reasonable to assume that the cation-π interaction increases the stability of the sandwich complex of B12C4 with Tl+ and the stabilities of sandwich complexes of B15C5 with Sr2+ and Pb2+ .
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9
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Jayanth N, Ogirala N, Yadav A, Puranik M. Structural basis for substrate discrimination by E. colirepair enzyme, AlkB. RSC Adv 2018; 8:1281-1291. [PMID: 35540905 PMCID: PMC9076979 DOI: 10.1039/c7ra11333a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/14/2017] [Indexed: 11/21/2022] Open
Abstract
Positive charge on methylated nucleotides is a prime criterion for substrate recognition byE. coliAlkB.
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Affiliation(s)
- Namrata Jayanth
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
| | - Nirmala Ogirala
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
| | - Anil Yadav
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Mrinalini Puranik
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
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10
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Nagy E, St Germain E, Cosme P, Maity P, Terentis AC, Lepore SD. Ammonium catalyzed cyclitive additions: evidence for a cation-π interaction with alkynes. Chem Commun (Camb) 2016; 52:2311-3. [PMID: 26728333 DOI: 10.1039/c5cc08641h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of carbamate nitrogen to a non-conjugated carbon-carbon triple bond is catalyzed by an ammonium salt leading to a cyclic product. Studies in homogeneous systems suggest that the ammonium agent facilitates nitrogen-carbon bond formation through a cation-π interaction with the alkyne unit that, for the first time, is directly observed by Raman spectroscopy.
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Affiliation(s)
- Edith Nagy
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
| | - Elijah St Germain
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
| | - Patrick Cosme
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
| | - Pradip Maity
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
| | - Andrew C Terentis
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
| | - Salvatore D Lepore
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
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11
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Peverari CR, David-Parra DN, Barsan MM, Teixeira MF. Mechanistic study of the formation of multiblock π-conjugated metallopolymer. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Milán-Garcés EA, Thaore P, Udgaonkar JB, Puranik M. Formation of a CH−π Contact in the Core of Native Barstar during Folding. J Phys Chem B 2015; 119:2928-32. [DOI: 10.1021/jp512036p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erix A. Milán-Garcés
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Pallavi Thaore
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Mrinalini Puranik
- Indian Institute
of Science Education and Research, Pune 411008, India
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13
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Characterising protein, salt and water interactions with combined vibrational spectroscopic techniques. Food Chem 2013; 138:679-86. [DOI: 10.1016/j.foodchem.2012.10.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 11/21/2022]
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14
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 719] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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15
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Schlamadinger DE, Leigh BS, Kim JE. UV resonance Raman study of TrpZip2 and related peptides: π-π interactions of tryptophan. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2012; 43:1459-1464. [PMID: 25525290 PMCID: PMC4267580 DOI: 10.1002/jrs.4061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high-resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β-hairpin peptide that is stabilized by edge-to-face and face-to-face tryptophan π-π interactions. The vibrational markers of isolated edge-to-face π-π interactions are investigated in the related β-hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the Bb absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross-sections of Bb-coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π-π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces.
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Affiliation(s)
- Diana E. Schlamadinger
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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16
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Sanchez KM, Kang G, Wu B, Kim JE. Tryptophan-lipid interactions in membrane protein folding probed by ultraviolet resonance Raman and fluorescence spectroscopy. Biophys J 2011; 100:2121-30. [PMID: 21539779 DOI: 10.1016/j.bpj.2011.03.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/02/2011] [Accepted: 03/14/2011] [Indexed: 01/24/2023] Open
Abstract
Aromatic amino acids of membrane proteins are enriched at the lipid-water interface. The role of tryptophan on the folding and stability of an integral membrane protein is investigated with ultraviolet resonance Raman and fluorescence spectroscopy. We investigate a model system, the β-barrel outer membrane protein A (OmpA), and focus on interfacial tryptophan residues oriented toward the lipid bilayer (trp-7, trp-170, or trp-15) or the interior of the β-barrel pore (trp-102). OmpA mutants with a single tryptophan residue at a nonnative position 170 (Trp-170) or a native position 7 (Trp-7) exhibit the greatest stability, with Gibbs free energies of unfolding in the absence of denaturant of 9.4 and 6.7 kcal/mol, respectively. These mutants are more stable than the tryptophan-free OmpA mutant, which exhibits a free energy of unfolding of 2.6 kcal/mol. Ultraviolet resonance Raman spectra of Trp-170 and Trp-7 reveal evolution of a hydrogen bond in a nonpolar environment during the folding reaction, evidenced by systematic shifts in hydrophobicity and hydrogen bond markers. These observations suggest that the hydrogen bond acceptor is the lipid acyl carbonyl group, and this interaction contributes significantly to membrane protein stabilization. Other spectral changes are observed for a tryptophan residue at position 15, and these modifications are attributed to development of a tryptophan-lipid cation-π interaction that is more stabilizing than an intraprotein hydrogen bond by ∼2 kcal/mol. As expected, there is no evidence for lipid-protein interactions for the tryptophan residue oriented toward the interior of the β-barrel pore. These results highlight the significance of lipid-protein interactions, and indicate that the bilayer provides more than a hydrophobic environment for membrane protein folding. Instead, a paradigm of lipid-assisted membrane protein folding and stabilization must be adopted.
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Affiliation(s)
- Katheryn M Sanchez
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
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17
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Macrae MX, Schlamadinger D, Kim JE, Mayer M, Yang J. Using charge to control the functional properties of self-assembled nanopores in membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2016-2020. [PMID: 21626687 DOI: 10.1002/smll.201100394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Michael X Macrae
- University of California-San Diego, Department of Chemistry and Biochemistry, La Jolla, CA 92093-0358, USA
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