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Pachetti M, D'Amico F, Pascolo L, Pucciarelli S, Gessini A, Parisse P, Vaccari L, Masciovecchio C. UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction. Biophys J 2021; 120:4575-4589. [PMID: 34474016 PMCID: PMC8553600 DOI: 10.1016/j.bpj.2021.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 06/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.
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Affiliation(s)
- Maria Pachetti
- Elettra - Sincrotrone Trieste, Trieste, Italy; Department of Physics, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.
| | | | - Lorella Pascolo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Pucciarelli
- University of Camerino, School of Biosciences and Veterinary Medicine, Camerino, Italy
| | | | - Pietro Parisse
- Elettra - Sincrotrone Trieste, Trieste, Italy; Istituto Officina dei Materiali - CNR (IOM-CNR), Trieste, Italy
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Vinogradov I, Feng Y, Kumar SKK, Guo C, Udagawa NS, Ge NH. Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy. J Chem Phys 2021; 155:035102. [PMID: 34293882 DOI: 10.1063/5.0054428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.
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Affiliation(s)
- Ilya Vinogradov
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Yuan Feng
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - S K Karthick Kumar
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Chenxu Guo
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nina Saki Udagawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
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3
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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Zhu L, Yan Y, Gu DC, Lu Y, Gan JH, Tao NP, Wang XC, Xu CH. Rapid Quality Discrimination and Amino Nitrogen Quantitative Evaluation of Soy Sauces by Tri-Step IR and E-nose. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1284-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Trefz M, Keller R, Vogt M, Schneider D. The GlpF residue Trp219 is part of an amino-acid cluster crucial for aquaglyceroporin oligomerization and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:887-894. [PMID: 29069569 DOI: 10.1016/j.bbamem.2017.10.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 12/13/2022]
Abstract
The vestibule loop regions of aquaglyceroporins are involved in accumulation of glycerol inside the channel pore. Even though most loop regions do not show high sequence similarity among aquaglyceroporins, loop E is highly conserved in aquaglyceroporins, but not in members of the homologous aquaporins. Specifically, a tryptophan residue is extremely conserved within this loop. We have investigated the role of this residue (Trp219) that deeply protrudes into the protein and potentially interacts with adjacent loops, using the E. coli aqualgyeroporin GlpF as a model. Replacement of Trp219 affects the activity of GlpF and impairs the stability of the tetrameric protein. Furthermore, we have identified an amino acid cluster involving Trp219 that stabilizes the GlpF tetramer. Based on our results we propose that Trp219 is key for formation of a defined vestibule structure, which is crucial for glycerol accumulation as well as for the stability of the active GlpF tetramer.
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Affiliation(s)
- Margareta Trefz
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Rebecca Keller
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Miriam Vogt
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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Watson MD, Monroe J, Raleigh DP. Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand Interactions. J Phys Chem B 2017; 122:5278-5285. [DOI: 10.1021/acs.jpcb.7b05684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Daniel P. Raleigh
- Research Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Zhang W, Markiewicz BN, Doerksen RS, Smith AB, Gai F. C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency? Phys Chem Chem Phys 2016; 18:7027-34. [PMID: 26343769 PMCID: PMC4775302 DOI: 10.1039/c5cp04413h] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recently it has been suggested that the C≡N stretching vibration of a tryptophan analog, 5-cyanotryptophan, could be used as an infrared probe of the local environment, especially the hydration status, of tryptophan residues in proteins. However, the factors that influence the frequency of this vibrational mode are not understood. To determine these factors, herein we carried out linear and nonlinear infrared measurements on the C≡N stretching vibration of the sidechain of 5-cyanotryptophan, 3-methyl-5-cyanoindole, in a series of protic and aprotic solvents. We found that while the C≡N stretching frequencies obtained in these solvents do not correlate well with any individual Kamlet-Taft solvent parameter, i.e., π* (polarizability), β (hydrogen bond accepting ability), and α (hydrogen bond donating ability), they do however, collapse on a straight line when plotted against σ = π* + β - α. This linear relationship provides a firm indication that both specific interactions, i.e., hydrogen-bonding interactions with the C≡N (through α) and indole N-H (through β) groups, and non-specific interactions with the molecule (through π*) work together to determine the C≡N stretching frequency, thus laying a quantitative framework for applying 5-cyanotryptophan to investigate the microscopic environment of proteins in a site-specific manner. Furthermore, two-dimensional and pump-probe infrared measurements revealed that a significant portion (∼31%) of the ground state bleach signal has a decay time constant of ∼12.3 ps, due to an additional vibrational relaxation channel, making it possible to use 5-cyanotryptophan to probe dynamics occurring on a timescale on the order of tens of picoseconds.
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Affiliation(s)
- Wenkai Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. and The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Rosalie S Doerksen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. and The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
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Chao WC, Shen JY, Lu JF, Wang JS, Yang HC, Wee K, Lin LJ, Kuo YC, Yang CH, Weng SH, Huang HC, Chen YH, Chou PT. Probing Water Environment of Trp59 in Ribonuclease T1: Insight of the Structure–Water Network Relationship. J Phys Chem B 2014; 119:2157-67. [DOI: 10.1021/jp503914s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei-Chih Chao
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Jiun-Yi Shen
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | | | | | | | - Kevin Wee
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | | | | | | | | | - Huai-Ching Huang
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - You-Hua Chen
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Pi-Tai Chou
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
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9
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Daus ML, Wagenführ K, Thomzig A, Boerner S, Hermann P, Hermelink A, Beekes M, Lasch P. Infrared microspectroscopy detects protein misfolding cyclic amplification (PMCA)-induced conformational alterations in hamster scrapie progeny seeds. J Biol Chem 2013; 288:35068-80. [PMID: 24163371 DOI: 10.1074/jbc.m113.497131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The self-replicative conformation of misfolded prion proteins (PrP) is considered a major determinant for the seeding activity, infectiousness, and strain characteristics of prions in different host species. Prion-associated seeding activity, which converts cellular prion protein (PrP(C)) into Proteinase K-resistant, infectious PrP particles (PrP(TSE)), can be monitored in vitro by protein misfolding cyclic amplification (PMCA). Thus, PMCA has been established as a valuable analytical tool in prion research. Currently, however, it is under discussion whether prion strain characteristics are preserved during PMCA when parent seeds are amplified in PrP(C) substrate from the identical host species. Here, we report on the comparative structural analysis of parent and progeny (PMCA-derived) PrP seeds by an improved approach of sensitive infrared microspectroscopy. Infrared microspectroscopy revealed that PMCA of native hamster 263K scrapie seeds in hamster PrP(C) substrate caused conformational alterations in progeny seeds that were accompanied by an altered resistance to Proteinase K, higher sedimentation velocities in gradient ultracentrifugations, and a longer incubation time in animal bioassays. When these progeny seeds were propagated in hamsters, misfolded PrP from brain extracts of these animals showed mixed spectroscopic and biochemical properties from both parental and progeny seeds. Thus, strain modifications of 263K prions induced by PMCA seem to have been partially reversed when PMCA products were reinoculated into the original host species.
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Affiliation(s)
- Martin L Daus
- From FG 14-AG 5: Unconventional Pathogens and Their Inactivation, Applied Infection Control and Hospital Hygiene, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany and
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10
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Fabian H, Gast K, Laue M, Jetzschmann KJ, Naumann D, Ziegler A, Uchanska-Ziegler B. IR spectroscopic analyses of amyloid fibril formation of β2-microglobulin using a simplified procedure for its in vitro generation at neutral pH. Biophys Chem 2013; 179:35-46. [PMID: 23727989 DOI: 10.1016/j.bpc.2013.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 11/16/2022]
Abstract
β2-microglobulin (β2m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant β2m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the β-strands in the fully formed amyloid structure of β2m. This study highlights the power of an approach to investigate the formation of β2m fibrils by a combination of biophysical techniques including IR spectroscopy.
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Affiliation(s)
- Heinz Fabian
- Robert Koch-Institut, ZBS 6, Nordufer 20, D-13353 Berlin, Germany.
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11
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Feng YW, Ooishi A, Honda S. Aggregation factor analysis for protein formulation by a systematic approach using FTIR, SEC and design of experiments techniques. J Pharm Biomed Anal 2011; 57:143-52. [PMID: 21920692 DOI: 10.1016/j.jpba.2011.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 08/24/2011] [Accepted: 08/25/2011] [Indexed: 11/19/2022]
Abstract
A simple systematic approach using Fourier transform infrared (FTIR) spectroscopy, size exclusion chromatography (SEC) and design of experiments (DOE) techniques was applied to the analysis of aggregation factors for protein formulations in stress and accelerated testings. FTIR and SEC were used to evaluate protein conformational and storage stabilities, respectively. DOE was used to determine the suitable formulation and to analyze both the main effect of single factors and the interaction effect of combined factors on aggregation. Our results indicated that (i) analysis at a low protein concentration is not always applicable to high concentration formulations; (ii) an investigation of interaction effects of combined factors as well as main effects of single factors is effective for improving conformational stability of proteins; (iii) with the exception of pH, the results of stress testing with regard to aggregation factors would be available for suitable formulation instead of performing time-consuming accelerated testing; (iv) a suitable pH condition should not be determined in stress testing but in accelerated testing, because of inconsistent effects of pH on conformational and storage stabilities. In summary, we propose a three-step strategy, using FTIR, SEC and DOE techniques, to effectively analyze the aggregation factors and perform a rapid screening for suitable conditions of protein formulation.
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Affiliation(s)
- Yan Wen Feng
- National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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12
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Luo JJ, Wu FG, Yu JS, Wang R, Yu ZW. Denaturation Behaviors of Two-State and Non-Two-State Proteins Examined by an Interruption–Incubation Protocol. J Phys Chem B 2011; 115:8901-9. [DOI: 10.1021/jp200296v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-Jie Luo
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Fu-Gen Wu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Ji-Sheng Yu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Rui Wang
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wu Yu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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13
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Fabian H, Loll B, Huser H, Naumann D, Uchanska-Ziegler B, Ziegler A. Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy. FEBS J 2011; 278:1713-27. [DOI: 10.1111/j.1742-4658.2011.08097.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Sul S, Feng Y, Le U, Tobias DJ, Ge NH. Interactions of tyrosine in Leu-enkephalin at a membrane-water interface: an ultrafast two-dimensional infrared study combined with density functional calculations and molecular dynamics simulations. J Phys Chem B 2010; 114:1180-90. [PMID: 20017523 DOI: 10.1021/jp9105844] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The interactions of neuropeptides and membranes play an important role in peptide hormone function. Our current understanding of peptide-membrane interactions remains limited due to the paucity of experimental techniques capable of probing such interactions. In this work, we study the nature of opioid peptide-membrane interactions using ultrafast two-dimensional infrared (2D IR) spectroscopy. The high temporal resolution of 2D IR is particularly suited for studying highly flexible opioid peptides. We investigate the location of the tyrosine (Tyr) side chain of leucine-enkephalin (Lenk) in lipid bilayer membranes by measuring spectral diffusion of the phenolic ring vibrational mode in three different systems: Lenk in lipid bilayer membranes (bicelles), Lenk in deuterated water, and p-cresol in deuterated water. Frequency-frequency correlation functions obtained from waiting-time-dependent 2D IR spectra reveal an ultrafast decaying component with an approximately 1 ps time constant that is common for all three systems. On the basis of density functional theory calculations and molecular dynamics simulations, this spectral diffusion component is attributed to hydrogen-bond dynamics of the phenolic hydroxyl group interacting with bulk water. Unlike p-cresol in water, both Lenk systems exhibit static spectral inhomogeneity, which can be attributed to conformational distributions of Lenk that do not interconvert within 4 ps. Our results suggest that the Tyr side chain of Lenk in bicelles is located at the water-abundant region at the membrane-water interface and not embedded into the hydrophobic core.
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Affiliation(s)
- Soohwan Sul
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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15
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Hamdani S, Tajmir-Riahi H, Carpentier R. Methylamine interaction with proteins of photosystem II: A comparison with biogenic polyamines. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:201-6. [DOI: 10.1016/j.jphotobiol.2009.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 06/16/2009] [Accepted: 06/17/2009] [Indexed: 11/15/2022]
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16
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Takekiyo T, Wu L, Yoshimura Y, Shimizu A, Keiderling TA. Relationship between Hydrophobic Interactions and Secondary Structure Stability for Trpzip β-Hairpin Peptides. Biochemistry 2009; 48:1543-52. [DOI: 10.1021/bi8019838] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takahiro Takekiyo
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Yukihiro Yoshimura
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Akio Shimizu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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Wang LX, Meersman F, Wu Y. A principal component analysis and two-dimensional correlation infrared spectroscopy study on the thermal unfolding of ribonuclease A under reducing conditions. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.11.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Fabian H, Gast K, Laue M, Misselwitz R, Uchanska-Ziegler B, Ziegler A, Naumann D. Early stages of misfolding and association of beta2-microglobulin: insights from infrared spectroscopy and dynamic light scattering. Biochemistry 2008; 47:6895-906. [PMID: 18540682 DOI: 10.1021/bi800279y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational changes associated with the assembly of recombinant beta 2-microglobulin in vitro under acidic conditions were investigated using infrared spectroscopy and static and dynamic light scattering. In parallel, the morphology of the different aggregated species obtained under defined conditions was characterized by electron microscopy. The initial salt-induced aggregate form of beta 2-microglobulin, composed of small oligomers (dimers to tetramers), revealed the presence of beta-strands organized in an intramolecular-like fashion. Further particle growth was accompanied by the formation of intermolecular beta-sheet structure and led to short curved forms. An increase in temperature by only 25 degrees C was able to disaggregate these assemblies, followed by the formation of longer filamentous structures. In contrast, a rise in temperature up to 100 degrees C was associated with a reorganization of the short curved forms at the level of secondary structure and the state of assembly, leading to a species with a characteristic infrared spectrum different from those of all the other aggregates observed before, suggesting a unique overall structure. The infrared spectral features of this species were nearly identical to those of beta 2-microglobulin assemblies formed at low ionic strength with agitation, indicating the presence of fibrils, which was confirmed by electron microscopy. The observed spectroscopic changes suggest that the heat-triggered conversion of the short curved assemblies into fibrils involves a reorganization of the beta-strands from an antiparallel arrangement to a parallel arrangement, with the latter being characteristic of amyloid fibrils of beta 2-microglobulin.
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Affiliation(s)
- Heinz Fabian
- Robert Koch-Institut, P 25 and ZBS4, Nordufer 20, D-13353 Berlin, Germany.
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Conformational analysis of Na,K-ATPase in drug-protein complexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 91:167-74. [PMID: 18374596 DOI: 10.1016/j.jphotobiol.2008.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/22/2022]
Abstract
This review reports the effects of several drugs such as AZT (anti-AIDS), cis-Pt (antitumor), aspirin (anti-inflammatory) and vitamin C (antioxidant) on the stability and conformation of Na,K-ATPase in vitro. Drug-enzyme binding was found to be via H-bonding to the polypeptide CO and C-N groups with two binding constants K(1(AZT))=5.30 (+/-2.1)x10(5)M(-1) and K(2(AZT))=9.80 (+/-2.9)x10(3)M(-1) for AZT and one binding constant K(cis)(-Pt)=1.93 (+/-1.2)x10(4)M(-1) for cis-Pt, K(aspirin)=6.45 (+/-2.5)x10(3)M(-1) and K(ascorbate)=1.04 (+/-0.5)x10(4)M(-1) for aspirin and ascorbic acid. The enzyme secondary structure was altered with major increase of alpha-helix from 19.9% (free protein) to 22-26% and reduction of beta-sheet from 25.6% (free protein) to 17-23% upon drug complexation indicating a partial stabilization of protein conformation. The order of induced stability is AZT>cis-Pt>ascorbate>aspirin.
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20
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Hu X, Kaplan D, Cebe P. Dynamic Protein−Water Relationships during β-Sheet Formation. Macromolecules 2008. [DOI: 10.1021/ma071551d] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao Hu
- Department of Physics and Astronomy and Departments of Biomedical Engineering and Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - David Kaplan
- Department of Physics and Astronomy and Departments of Biomedical Engineering and Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Peggy Cebe
- Department of Physics and Astronomy and Departments of Biomedical Engineering and Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
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21
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Fabian H, Huser H, Narzi D, Misselwitz R, Loll B, Ziegler A, Böckmann RA, Uchanska-Ziegler B, Naumann D. HLA-B27 Subtypes Differentially Associated with Disease Exhibit Conformational Differences in Solution. J Mol Biol 2008; 376:798-810. [DOI: 10.1016/j.jmb.2007.12.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/23/2007] [Accepted: 12/05/2007] [Indexed: 10/22/2022]
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22
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Neault JF, Diamantoglou S, Beauregard M, Nafisi S, Tajmir-Riahi HA. Protein unfolding in drug-RNase complexes. J Biomol Struct Dyn 2007; 25:387-94. [PMID: 18092833 DOI: 10.1080/07391102.2008.10507187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of P-O5' bonds in RNA on the 3' side of pyrimidine to form cyclic 2', 5'-phosphates. It has several high affinity binding sites that make it possible target for many organic and inorganic molecules. Ligand binding to RNase A can alter protein secondary structure and its catalytic activity. In this review, the effects of several drugs such as AZT (anti-AIDS), cis-Pt (antitumor), aspirin (anti-inflammatory), and vitamin C (antioxidant) on the stability and conformation of RNase A in vitro are compared. The results of UV-visible, FTIR, and CD spectroscopic analysis of RNase complexes with aspirin, AZT, cis-Pt, and vitamin C at physiological conditions are discussed here. Spectroscopic results showed one major binding for each drug-RNase adduct with KAZT=5.29 (+/-1.6)x10(4) M(-1), Kaspirin=3.57 (+/-1.4)x10(4) M(-1), Kcis-Pt=5.66 (+/-1.9)x10(3) M(-1), and Kascorbate=3.50 (+/-1.5)x10(3) M(-1). Major protein unfolding occurred with reduction of alpha-helix from 29% (free protein) to 20% and increase of beta-sheet from 39% (free protein) to 45% in the aspirin-, ascorbate-, and cis-Pt-RNase complexes, while minor increase of alpha-helix was observed for AZT-RNase adduct.
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Affiliation(s)
- J F Neault
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Canada G9A 5H7
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23
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Yuan B, Murayama K, Yan H. Study of thermal dynamics of defatted bovine serum albumin in D2O solution by Fourier transform infrared spectra and evolving factor analysis. APPLIED SPECTROSCOPY 2007; 61:921-7. [PMID: 17910787 DOI: 10.1366/000370207781745919] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Fourier transform infrared (FT-IR) spectra have been measured for defatted bovine serum albumin (BSA) in D(2)O with a concentration of 2.0 wt % over a temperature range of 26-90 degrees C and the corresponding difference spectra have been calculated by subtracting the contribution of D(2)O at the same temperature. Evolving factor analysis (EFA) by selecting two factors and three factors has been employed to analyze the temperature-dependent difference IR spectra in the 1700-1600 cm(-1) spectral region of the defatted BSA in D(2)O solution. Three-factor EFA has been employed to determine the distinction of the three protein species involved in the process of temperature elevation: native, transitional, and denatured protein. The temperature profiles obtained from three-factor EFA indicate that heat-induced conformational change in the secondary structures of defatted BSA in D(2)O undergoes two two-state transitions, a drastic transition and a slight transition, which occur in the temperature ranges of 68-82 degrees C and 56-76 degrees C, respectively.
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Affiliation(s)
- Bo Yuan
- State Key Laboratory of Modern Optical Instrumentation, CNERC for Optical Instrument, Zhejiang University, Hangzhou 310027, China.
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24
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Barth A. Infrared spectroscopy of proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1073-101. [PMID: 17692815 DOI: 10.1016/j.bbabio.2007.06.004] [Citation(s) in RCA: 2795] [Impact Index Per Article: 164.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 12/12/2022]
Abstract
This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.
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Affiliation(s)
- Andreas Barth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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25
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Beauchemin R, Harnois J, Rouillon R, Tajmir-Riahi H, Carpentier R. Interaction of polyamines with proteins of photosystem II: Cation binding and photosynthetic oxygen evolution. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Czaja R, Perbandt M, Betzel C, Hahn U. Purine activity of RNase T1RV is further improved by substitution of Trp59 by tyrosine. Biochem Biophys Res Commun 2005; 336:882-9. [PMID: 16157302 DOI: 10.1016/j.bbrc.2005.08.188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Accepted: 08/24/2005] [Indexed: 11/23/2022]
Abstract
Ribonuclease T1 is an enzyme that cleaves single-stranded RNA with high specificity after guanylyl residues. Although this enzyme is a very good characterized protein with respect to structure and enzymatic function, we were only recently successful in generating RNase T1-RV, a variant where the specificity was changed from guanine to purine. As this change of substrate specificity was made at the cost of activity, the aim was now to further improve the overall activity of the enzyme. Therefore, we have substituted the tryptophan in position 59 by tyrosine. This substitution led to an increase of enzymatic activity in comparison to variant RV to 425%. As the extent of this enhancement is unique so far we have crystallized and analyzed the structure of this variant in order to get more insights into the reasons for this. Here, we present the crystal structure of this so-called RNase T1-R2 at 2.1A resolution. The structure was determined by molecular replacement using the coordinates of the RV variant (PDB entry: 1Q9E). The data were refined to an R-factor of 18.7% and R(free) of 24%, respectively. The asymmetric unit contains three molecules and the crystal packing is very similar to that of variant RV.
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Affiliation(s)
- R Czaja
- Department of Chemistry, Division of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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27
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Tremmel S, Beyermann M, Oschkinat H, Bienert M, Naumann D, Fabian H. 13C-Labeled Tyrosine Residues as Local IR Probes for Monitoring Conformational Changes in Peptides and Proteins. Angew Chem Int Ed Engl 2005; 44:4631-5. [PMID: 15977271 DOI: 10.1002/anie.200500547] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sandra Tremmel
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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28
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Tremmel S, Beyermann M, Oschkinat H, Bienert M, Naumann D, Fabian H. 13C-markierte Tyrosinreste als lokale IR-Sonden zur Analyse konformativer Änderungen in Peptiden und Proteinen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Xie MX, Xu XY, Wang YD. Interaction between hesperetin and human serum albumin revealed by spectroscopic methods. Biochim Biophys Acta Gen Subj 2005; 1724:215-24. [PMID: 15923087 DOI: 10.1016/j.bbagen.2005.04.009] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2005] [Revised: 04/05/2005] [Accepted: 04/07/2005] [Indexed: 11/15/2022]
Abstract
Hesperetin (5,7,3'-trihydroxyl-4'-methoxyl-flavanone) is an important bioactive compound in Chinese traditional medicine and has multiple biological and pharmacological activities. The interaction of hesperetin with human serum albumin (HSA) has been investigated by UV absorption, fluorescence and Fourier transformed infrared spectrometry. Fluorescence results showed that one molecule of protein combined with one molecule of drug at the molar ratio of drug to HSA ranging from 0.3 to 7 and the binding affinity (K(A)) was 8.11x10(4) M(-1). The primary binding site was most likely located on subdomain IIA. The binding ability of the drug to protein decreased from pH 6.4 to 8.4 in the drug to protein molar ratio of 1. Combining the curve-fitting results of infrared amide I band in D2O and H2O phosphate buffers, the alterations of protein secondary structure after drug complexation were estimated. With increasing the drug concentration, the percentage of protein alpha-helix structure decreased gradually. The reduction of protein alpha-helix structure reached about 7-9% after the protein interacted with hesperetin in D2O and H2O buffer solution at pH 7.4 when the drug to protein molar ratio was 10. This indicated a partial unfolding of HSA in the presence of the drug. From the results of UV absorption, fluorescence and Fourier transformed infrared spectrometry, the binding mode was discussed. The main mechanism of protein fluorescence quenching was a static quenching process and the hydroxyl groups of the drug in its neutral part played an important role in the binding process.
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Affiliation(s)
- Meng-Xia Xie
- Analytical & Testing Center of Beijing Normal University, Beijing 100875, People's Republic of China.
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30
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Sukumaran S, Hauser K, Rauscher A, Mäntele W. Thermal stability of outer membrane protein porin fromParacoccus denitrificans: FT-IR as a spectroscopic tool to study lipid-protein interaction. FEBS Lett 2005; 579:2546-50. [PMID: 15862288 DOI: 10.1016/j.febslet.2005.03.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 03/15/2005] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
Lipid protein interactions play a key role in the stability and function of various membrane proteins. Earlier we have reported the extreme thermal stability of porin from Paracoccus denitrificans reconstituted into liposomes. Here, we used Fourier transform infrared spectroscopy for a label free analysis of the global secondary structural changes and local changes in the tyrosine microenvironment. Our results show that a mixed lipid system (non-uniform bilayer) optimizes the thermal stability of porin as compared to the porin in pure lipids (uniform bilayer) or detergent micelles. This is in line with the fact that the bacterial outer membrane is a dynamic system made up of lipids of varying chain lengths, head groups and the barrel wall height contacting the membrane is uneven.
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Affiliation(s)
- Suja Sukumaran
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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31
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Ouameur AA, Marty R, Tajmir-Riahi HA. Human serum albumin complexes with chlorophyll and chlorophyllin. Biopolymers 2005; 77:129-36. [PMID: 15630698 DOI: 10.1002/bip.20173] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Porphyrins and their metal derivatives are strong protein binders. Some of these compounds have been used for radiation sensitization therapy of cancer and are targeted to interact with cellular DNA and protein. The presence of several high-affinity binding sites on human serum albumin (HSA) makes it possible target for many organic and inorganic molecules. Chlorophyll a and chlorophyllin (a food-grade derivative of chlorophyll), the ubiquitous green plant pigment widely consumed by humans, are potent inhibitors of experimental carcinogenesis and interact with protein and DNA in many ways. This study was designed to examine the interaction of HSA with chlorophyll (Chl) and chlorophyllin (Chln) in aqueous solution at physiological conditions. Fourier transform infrared, UV-visible, and CD spectroscopic methods were used to determine the pigment binding mode, the binding constant, and the effects of porphyrin complexation on protein secondary structure. Spectroscopic results showed that chlorophyll and chlorophyllin are located along the polypeptide chains with no specific interaction. Stronger protein association was observed for Chl than for Chln, with overall binding constants of K(Chl) = 2.9 x 10(4)M(-1) and K(Chln) = 7.0 x 10(3)M(-1). The protein conformation was altered (infrared data) with reduction of alpha-helix from 55% (free HSA) to 41-40% and increase of beta-structure from 22% (free HSA) to 29-35% in the pigment-protein complexes. Using the CDSSTR program (CD data) also showed major reduction of alpha-helix from 66% (free HSA) to 58 and 55% upon complexation with Chl and Chln, respectively.
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Affiliation(s)
- A Ahmed Ouameur
- Department of Chemistry-Biology, University of Québec at Trois-Riviéres, C.P. 500, TR (Québec), Canada G9A 5H7
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32
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Keiderling TA, Xu Q. Unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra. ADVANCES IN PROTEIN CHEMISTRY 2004; 62:111-61. [PMID: 12418103 DOI: 10.1016/s0065-3233(02)62007-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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33
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Ouameur AA, Mangier E, Diamantoglou S, Rouillon R, Carpentier R, Tajmir-Riahi HA. Effects of organic and inorganic polyamine cations on the structure of human serum albumin. Biopolymers 2004; 73:503-9. [PMID: 14991668 DOI: 10.1002/bip.10557] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many organic and inorganic molecules. Organic polyamines are widely distributed in living cells and their biological roles have been associated with their physical and chemical interactions with proteins, nucleic acids, and lipids. This study is designed to examine the effects of spermine, spermidine, putrescine, and cobalt [Co(III)]-hexamine cations on the solution structure of HSA using Fourier transform IR, UV-visible, and circular dichroism (CD) spectroscopic methods. The spectroscopic results show that polyamine cations are located along the polypeptide chains with no specific interaction. The order of perturbations is associated with the number of positive charges of the polyamine cation: spermine > Co(III)-hexamine > spermidine > putrescine. The overall binding constants are 1.7 x 10(4), 1.1 x 10(4), 5.4 x 10(3), and 3.9 x 10(3)M(-1), respectively. The protein conformation is altered (IR and CD data) with reductions of alpha helices from 60 to 55% for free HSA to 50-40% and with increases of beta structures from 22 to 15% for free HSA to 33-23% in the presence of polyamine cations.
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Affiliation(s)
- A Ahmed Ouameur
- GREIB, Département de Chemie-Biologie, Université du Québec á Trois-Riviéres, C. P. 500, Québec G9A 5H7, Canada
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34
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Gaussier H, Lefèvre T, Subirade M. Binding of pediocin PA-1 with anionic lipid induces model membrane destabilization. Appl Environ Microbiol 2003; 69:6777-84. [PMID: 14602640 PMCID: PMC262285 DOI: 10.1128/aem.69.11.6777-6784.2003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Accepted: 08/19/2003] [Indexed: 11/20/2022] Open
Abstract
To obtain molecular insights into the action mode of antimicrobial activity of pediocin PA-1, the interactions between this bacteriocin and dimyristoylphosphatidylcholine (DMPC) or dimyristoylphosphatidylglycerol (DMPG) model membranes have been investigated in D(2)O at pD 6 by Fourier transform infrared spectroscopy. The interactions were monitored with respect to alteration of the secondary structure of pediocin, as registered by the amide I' band, and phospholipid conformation, as revealed by the methylene nu(s)(CH(2)) and carbonyl nu(C;O) stretching vibrations. The results show that no interaction between pediocin and DMPC occurs. By contrast, pediocin undergoes a structural reorganization in the presence of DMPG. Upon heating, pediocin self-aggregates, which is not observed for this pD in aqueous solution. The gel-to-crystalline phase transition of DMPG shifts to higher temperatures with a concomitant dehydration of the interfacial region. Our results indicate that pediocin is an extrinsic peptide and that its action mechanism may lie in a destabilization of the cell membrane.
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Affiliation(s)
- Hélène Gaussier
- Centre de recherche en Sciences et Technologie du Lait (STELA), and Institut sur les nutraceutiques et aliments fonctionnels (INAF), Département des sciences des aliments et de nutrition, Université Laval, Pavillon Paul-Comtois, Sainte-Foy, Québec, Canada
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35
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Gallego-Nicasio J, López-Rodríguez G, Martínez R, Tarancón MJ, Fraile MV, Carmona P. Structural changes of low density lipoproteins with Cu2+and glucose induced oxidation. Biopolymers 2003; 72:514-20. [PMID: 14587073 DOI: 10.1002/bip.10486] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The compositional and structural changes of lipids and apolipoproteins during in vitro oxidation of low density lipoprotein (LDL) are investigated in this study by IR spectroscopy. For comparison, LDL samples containing either copper or glucose at physiological or pathological concentrations are considered in order to know the separate affects of these chemical factors on LDL oxidation. The results show that the initial steps of lipid oxidation proceed through hydrogen atom loss from methylene groups, as well as loss of cholesteryl ester molecules, and later a recovering of carbonyl compounds resulting from aldehyde formation that generally occurs in autooxidation processes. Lipid oxidation is induced by copper ions, and glucose enhances metal ion induced LDL oxidation as determined by conjugated diene formation. As to the protein conformational changes, IR spectroscopy reveals for the first time that LDL oxidation involves formation of beta-sheet structures, these being more abundant in LDL samples with pathological concentrations of glucose or copper. Consequently, the LDL structural changes may contribute to the recognition of oxidized LDL particles by scavenger receptors.
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Affiliation(s)
- J Gallego-Nicasio
- Departamento de Ciencias Básicas, Facultad de Ciencias Experimentales y Técnicas, Universidad S. Pablo-CEU, 28668 Boadilla del Monte, Madrid, Spain
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36
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Liu Y, Xie MX, Kang J, Zheng D. Studies on the interaction of total saponins of panax notoginseng and human serum albumin by Fourier transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:2747-2758. [PMID: 14499835 DOI: 10.1016/s1386-1425(03)00055-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Total saponins of panax notoginseng (TPNS), isolated from the roots of panax notoginseng (Burk) F.H. Chen, have been considered as the main active components of San-Chi and have various therapeutical actions. Their interactions with human serum albumin have been investigated by Fourier transformed infrared spectrometry and fluorescence methods. The results showed that TPNS combined with HSA through C=O and C-N groups of polypeptide chain. The drug-protein combination caused the significant loss of alpha-helix structure and the microenvironment changes of the tyrosine residues in protein at higher drug concentration. Combining the curve-fitting results of amide I and amide III bands, the alterations of protein secondary structure after drug complexation were quantitatively determined. The alpha-helix structure has a decrease of approximately 6%, from 55 to 49% and the beta-sheet increased approximately 3%, from 23 to 26% at high drug concentration. However, no major alterations were observed for the beta-turn and random coil structures up on drug-protein binding.
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Affiliation(s)
- Yuan Liu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, People's Republic of China
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37
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Zscherp C, Aygün H, Engels JW, Mäntele W. Effect of proline to alanine mutation on the thermal stability of the all-β-sheet protein tendamistat. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2003; 1651:139-45. [PMID: 14499598 DOI: 10.1016/s1570-9639(03)00263-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The temperature dependent denaturation of wild-type tendamistat and of the proline-free triple mutant P7A/P9A/P50A was investigated using Fourier-transform infrared (FTIR) spectroscopy. Whereas the temperature-induced unfolding is reversible in the wild type, aggregation was observed for the proline-free tendamistat when studied under the same conditions. The midpoint unfolding temperature T(m) was found as 82.3+/-0.5 degrees C in (2)H2O. The thermal stability of the proline-free mutant is reduced by 15 degrees C as compared to the wild type. Changes in the strength of hydrogen bonding of tyrosine O-H groups upon unfolding and aggregation are reflected in small shifts of the C-C stretching mode of the aromatic ring near 1515 cm(-1). Evaluation of data from different infrared (IR) bands sensitive to changes in secondary structure as well as to changes in tertiary structure strongly supports a two-state model for the unfolding process of wild-type tendamistat.
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Affiliation(s)
- Christian Zscherp
- Institut für Biophysik der Johann Wolfgang Goethe-Universität, 60590 Frankfurt am Main, Germany.
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38
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Gaussier H, Lavoie M, Subirade M. Conformational changes of pediocin in an aqueous medium monitored by fourier transform infrared spectroscopy: a biological implication. Int J Biol Macromol 2003; 32:1-9. [PMID: 12719125 DOI: 10.1016/s0141-8130(03)00018-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy was used to investigate the secondary structure of pediocin PA-1 in different aqueous media in relation to its antimicrobial activity. The experiments were performed at pD (pH meter corrected for deuterium isotope effect) 6, 7, and 8 and during a heating-cooling cycle of 20-80 degrees C. At pD 6, (i.e. pediocin's most active form), the FTIR results show that pediocin adopts an unordered structure with a small contribution of beta-turn. After a heating-cooling cycle, thermally-induced changes in pediocin are reversed and its activity is maintained. Increasing the pD to 7 and 8 leads to a more ordered secondary structure. For these two pD values, an increase in temperature induces an irreversible aggregation of protein as revealed by the amide I' band. The analysis of the Tyr region provides more insight into the aggregation process. In fact, it appears to be a two-step process, involving first the C (carboxy)-terminus of pediocin and then the N (amino)-terminus. This study reveals two major points: (1) the preservation of pediocin flexibility is essential for maintaining its activity; and (2) the aggregation of its C-terminus is sufficient to induce a loss of activity, suggesting that this region plays an important role in the activity of pediocin.
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Affiliation(s)
- Hélène Gaussier
- Chaire de recherche du Canada sur les protéine et les ailments fonctionnels, Université Laval, département des aliments et de nutrition, Pavillon Paul Comtois, Sainte-Foy, Québec, G1K 7P4, Canada
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39
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Kidric M, Fabian H, Brzin J, Popovic T, Pain RH. Folding, stability, and secondary structure of a new dimeric cysteine proteinase inhibitor. Biochem Biophys Res Commun 2002; 297:962-7. [PMID: 12359248 DOI: 10.1016/s0006-291x(02)02328-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Clitocypin, a new type of cysteine proteinase inhibitor from the mushroom Clitocybe nebularis, is a 34-kDa homodimer lacking disulphide bonds, reported to have unusual stability properties. Sequence similarity is limited solely to certain proteins from mushrooms. Infrared spectroscopy shows that clitocypin is a high beta-structure protein which was lost at high temperatures. The far UV circular dichroism spectrum is not that of classical beta-structure, but similar to those of a group of small beta-strand proteins, with a peak at 189nm and a trough at 202nm. An aromatic peak at 232nm and infrared bands at 1633 and 1515cm(-1) associated with the peptide backbone and the tyrosine microenvironment, respectively, were used to characterize the thermal unfolding. The reversible transition has a midpoint at 67 degrees C, with DeltaG=34kJ/mol and DeltaH=300kJ/mol, and is, unusually, independent of protein concentration. The kinetics of thermal unfolding and refolding are slow, with activation energies of 167 and 44kJ/mol, respectively. A model for folding and assembly is discussed.
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Affiliation(s)
- Marjetka Kidric
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
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40
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Neault JF, Malonga H, Diamantoglou S, Carpentier R, Stepp RL, Tajmir-Riahi HA. Secondary structural analysis of the Na(+),K(+)-ATPase and its Na(+) (E(1)) and K(+) (E(2)) complexes by FTIR spectroscopy. J Biomol Struct Dyn 2002; 20:173-8. [PMID: 12354069 DOI: 10.1080/07391102.2002.10506833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The Na(+),K(+)-ATPase is an integral membrane protein which transports sodium and potassium cations against an electrochemical gradient. The transport of Na(+) and K(+) ions is presumably connected to an oscillation of the enzyme between the two conformational states, the E(1) (Na(+)) and the E(2) (K(+)) conformations. The E(1) and E(2) states have different affinities for ligand interaction. However, the determination of the secondary structure of this enzyme in its sodium and potassium forms has been the subject of much controversy. This study was designed to provide a quantitative analysis of the secondary structure of the Na(+),K(+)-ATPase in its sodium (E(1)) and potassium (E(2)) states in both H(2)O and D(2)O solutions at physiological pH, using Fourier transform infrared (FTIR) with its self-deconvolution and second derivative resolution enhancement methods, as well as curve-fitting procedures. Spectroscopic analysis showed that the secondary structure of the sodium salt of the Na(+),K(+)-ATPase in H(2)O solution contains alpha-helix 19.8+/-1%, beta-sheet 25.6+/-1%, turn 9.1+/-1%, and beta-anti 7.5+/-1%, whereas in D(2)O solution, the enzyme shows alpha-helix 16.8+/-1%, beta-sheet 24.5+/-1.5%, turn 10.9+/-1%, beta-anti 9.8+/-1%, and random coil 38.0+/-2%. Similarly, the potassium salt in H(2)O solution contains alpha-helix 16.6+/-1%, beta-sheet 26.4+/-1.5%, turn 8.9+/-1%, and beta-anti 8.1+/-1%, while in D(2)O solution it shows alpha-helix 16.2+/-1%, beta-sheet 24.5+/-1.5%, turn 10.3+/-1%, beta-anti 9.0+/-1%, and random coil 40+/-2%. Thus the main differences for the sodium and potassium forms of the Na(+),K(+)-ATPase are alpha-helix 3.2% in H(2)O and 0.6% in D(2)O, beta-sheet (pleated and anti) 1.5% in H(2)O and random structure 2% (D(2)O), while for other minor components (turn structure), the differences are less than 1%.
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Affiliation(s)
- J F Neault
- Groupe de Recherche en Energie et Information Biomoléculaires, Université du Québec Trois-Rivières, Canada
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41
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Moritz R, Fabian H, Hahn U, Diem M, Naumann D. Impact of four (13)C-proline isotope labels on the infrared spectra of ribonuclease T1. J Am Chem Soc 2002; 124:6259-64. [PMID: 12033852 DOI: 10.1021/ja011749s] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonuclease T1 was biosynthesized, with all four prolines (13)C-labeled in the peptide C[double bond]O bond, using a proline auxotrophic yeast strain of Saccharomyces cerevisiae. The (13)C- and (12)C-proline isotopomers of ribonuclease T1 were investigated by infrared spectroscopy in the thermally unfolded and natively folded state at 80 and 20 degrees C, respectively. In the thermally unfolded state, both proteins established almost indistinguishable spectral features in the secondary structure sensitive amide I region. In contrast, the spectra measured at 20 degrees C revealed substantial qualitative and quantitative differences, though parallel analysis by circular dichroism suggested identical native folds for both isotopomers. Major spectral differences in the infrared spectra were detected at 1626 and 1679 cm(-1), which are diagnostic marker bands for antiparallel beta-sheets in ribonuclease T1 and at 1645 cm(-1), a region that is characteristic for the infrared absorption of irregular structures. Starting with the known three-dimensional structure of ribonuclease T1, the observed effects of the isotope labeling are discussed on the basis of transition dipole coupling between the (12)C[double bond]O and (13)C[double bond]O groups. The experimental results were confirmed by transition dipole coupling calculations of the amide I manifold of the labeled and unlabeled variant.
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Affiliation(s)
- Ralf Moritz
- Robert Koch-Institut, P34, Nordufer 20, 13353 Berlin, Germany.
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42
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Gaudreau S, Neault JF, Tajmir-Riahi HA. Interaction of AZT with human serum albumin studied by capillary electrophoresis, FTIR and CD spectroscopic methods. J Biomol Struct Dyn 2002; 19:1007-14. [PMID: 12023803 DOI: 10.1080/07391102.2002.10506804] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The thymidine analog 3'-azido-3'-deoxythymidine (AZT) is still one of the effective drugs against human immunodeficiency (HIV) infection. AZT has been used as inhibitor of HIV-1 reverse transcriptase, the virus encoded enzyme which catalyzes transcription of viral RNA to DNA. The drug interaction with protein has been included in its mechanism of action. Human serum albumin (HSA) is a carrier of many drugs in vivo and thus AZT-HSA complexation can serve as a model for drug-protein interaction. This study was designed to examine the interaction of AZT with human serum albumin at physiological conditions using constant protein concentration (0.2% or 2%) and different drug contents (5 to 1000 microM). Capillary electrophoresis, FTIR and CD spectroscopic methods were used to determine the drug binding mode, the drug binding constant and the effects of drug-HSA complexation on the protein and AZT conformations in aqueous solution. Capillary electrophoresis and spectroscopic results showed two major bindings for the AZT-HSA complexes with K(1)=1.9 x 10(6) M(-1)and K(2)= 2.1 x 10(4) M(-1). Minor alterations of the protein secondary structure from that of the alpha-helix to beta-sheet were observed upon drug complexation, whereas the drug sugar pucker remained in the C2'-endo/anti conformation upon protein interaction.
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Affiliation(s)
- S Gaudreau
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7
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43
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Purcell M, Neault JF, Malonga H, Arakawa H, Tajmir-Riahi HA. Interaction of human serum albumin with oxovanadium ions studied by FT-IR spectroscopy and gel and capillary electrophoresis. CAN J CHEM 2001. [DOI: 10.1139/v01-162] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Some oxovanadium compounds have shown potential to inhibit RNase activity, while at the same time not inhibiting DNase activity. Some vanadyl complexes also inhibit protein synthesis in rabbit reticulocytes, but induce activation of proteintyrosine kinase. To gain an insight into the interaction of oxovanadium ions with proteins, the present study was designed to examine the bindings of VOSO4 and NaVO3 salts with human serum albumin (HSA) in aqueous solution at physiological pH with metal ion concentrations of 0.0001 to 1 mM and HSA (fatty acid free) concentration of 2% w/v. Gel and capillary electrophoresis (CE) and Fourier transform infrared (FT-IR) spectroscopic methods were used to determine the metal ion binding mode, association constant, and the secondary structure of the protein in the presence of the oxovanadium compounds. Gel electrophoresis results showed that a maximum of 20 vanadyl cations (VO2+) are bound per HSA molecule with strong (K1 = 7.0 × 107 M1) and weak (K2 = 6.5 × 105 M1) bindings. Similarly, capillary electrophoresis showed two major bindings for vanadyl cation with K1 = 1.2 × 108 M1 and K2 = 8.5 × 105 M1, whereas vanadate (VO3) has only a weak binding affinity (K = 6.0 × 103 M1) with HSA molecule. The VO3 binds mainly to the lysine ε-amino NH+3 groups, while VO2+ binds possibly to the histidine nitrogen atom and the N-terminal of the α-amine residue. Infrared spectroscopic analysis showed metal ion binding results in major protein secondary structural changes from that of the α-helix (55.0 to 4344%) to the β-sheet (22.0 to 2326%), β-antiparallel (12.0 to 1316%), and turn (11.0 to 1718%), at high metal ion concentration. The observed spectral changes indicate a partial unfolding of the protein structure, in the presence of oxovanadium ions.Key words: oxovanadium, protein, binding mode, binding constant, secondary structure, electrophoresis, FT-IR spectroscopy.
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Neault JF, Benkiran A, Malonga H, Tajmir-Riahi HA. The effects of anions on the solution structure of Na,K-ATPase. J Biomol Struct Dyn 2001; 19:95-102. [PMID: 11565855 DOI: 10.1080/07391102.2001.10506723] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Anions interact with protein to induce structural changes at ligand binding sites. The effects of anion complexation include structural stabilization and promote cation-protein interaction. This study was designed to examine the interaction of aspirin and ascorbate anions with the Na+, K+-dependent adenosine triphosphatase (Na,K-ATPase) in H2O and D2O solutions at physiological pH, using anion concentrations of 0.1 microM to 1 mM with final protein concentration of 0.5 to 1 mg/ml. Absorption spectra and Fourier transform infrared (FTIR) difference spectroscopy with its self-deconvolution, second derivative resolution enhancement and curve-fitting procedures were applied to characterize the anion binding mode, binding constant, and the protein secondary structure in the anion-ATPase complexes. Spectroscopic evidence showed that the anion interaction is mainly through the polypeptide C=O and C-N groups with minor perturbation of the lipid moiety. Evidence for this came from major spectral changes (intensity variations) of the protein amide I and amide II vibrations at 1651 and 1550 cm(-1). respectively. The anion-ATPase binding constants were K=6.45 x 10(3) M(-1) for aspirin and K=1.04 x 10(4) M(-1) for ascorbate complexes. The anion interaction resulted in major protein secondary structural changes from that of the alpha-helix 19.8%; beta-pleated sheet 25.6%; turn 9.1%; beta-antiparallel 7.5% and random 38% in the free Na,K-ATPase to that of the alpha-helix 24-26%; beta-pleated 17-18%; turn 8%; beta-antiparallel 5-3% and random 45.0% in the anion-ATPase complexes.
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Affiliation(s)
- J F Neault
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Canada
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Purcell M, Neault JF, Malonga H, Arakawa H, Carpentier R, Tajmir-Riahi HA. Interactions of atrazine and 2,4-D with human serum albumin studied by gel and capillary electrophoresis, and FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1548:129-38. [PMID: 11451446 DOI: 10.1016/s0167-4838(01)00229-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The herbicides 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine (atrazine) and 2,4-dichlorophenoxyacetic acid (2,4-D) are widely used in agricultural practice to fight dicotyledon weeds mainly in maize, cereals, and lucerne. As a result, these compounds are found not only in the plants, soil, and water, but also in the cultivated ground in the following years as well as in agricultural products such as fruits, milk, butter, and sugar beet. The toxicological effects of herbicides occur in vivo, when transported to the target organ through the bloodstream. It has been suggested that human serum albumin (HSA) serves as a carrier protein to transport 2,4-D to molecular targets. This study was designed to examine the interaction of atrazine and 2,4-D with HSA in aqueous solution at physiological pH with herbicide concentrations of 0.0001-1 mM, and final protein concentration of 1% w/v. Gel and capillary electrophoresis, UV-visible and Fourier transform infrared spectroscopic methods were used to determine the drug binding mode, the drug binding constant, and the protein secondary structure in aqueous solution. Structural analysis showed that different types of herbicide-HSA complexes are formed with stoichiometric ratios (drug/protein) of 3:1 and 11:1 for atrazine and 4.5:1 and 10:1 for 2,4-D complexes. Atrazine showed a weak binding affinity (K=3.50 x 10(4) M(-1)), whereas two bindings (K(1)=2.50 x 10(4) M(-1) and K(2)=8.0 x 10(3) M(-1)) were observed for 2,4-D complexes. The herbicide binding results in major protein secondary structural changes from that of the alpha-helix 55% to 45--39% and beta-sheet 22% to 24--32%, beta-anti 12% to 10--22% and turn 11% to 12--15%, in the drug-HSA complexes. The observed spectral changes indicate a partial unfolding of the protein structure, in the presence of herbicides in aqueous solution.
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Affiliation(s)
- M Purcell
- Department of Chemistry--Biology, University of Quebec at Trois-Rivières, C.P. 500, Trois-Rivières, QC, Canada G9A 5H7
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Barth A. The infrared absorption of amino acid side chains. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 74:141-73. [PMID: 11226511 DOI: 10.1016/s0079-6107(00)00021-3] [Citation(s) in RCA: 879] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Amino acid side chains play fundamental roles in stabilising protein structures and in catalysing enzymatic reactions. These fields are increasingly investigated by infrared spectroscopy at the molecular level. To help the interpretation of the spectra, a review of the infrared absorption of amino acid side chains in H(2)O and 2H(2)O is given. The spectral region of 2600-900cm(-1) is covered.
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Affiliation(s)
- A Barth
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Theodor Stern-Kai 7, Haus 74, D-60590 Frankfurt am Main, Germany.
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Torrent J, Rubens P, Ribó M, Heremans K, Vilanova M. Pressure versus temperature unfolding of ribonuclease A: an FTIR spectroscopic characterization of 10 variants at the carboxy-terminal site. Protein Sci 2001; 10:725-34. [PMID: 11274463 PMCID: PMC2373970 DOI: 10.1110/ps.43001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
FTIR spectroscopy was used to characterize and compare the temperature- and pressure-induced unfolding of ribonuclease A and a set of its variants engineered in a hydrophobic region of the C-terminal part of the molecule postulated as a CFIS. The results show for all the ribonucleases investigated, a cooperative, two-state, reversible unfolding transition using both pressure and temperature. The relative stabilities, among the different sites and different variants at the same site, monitored either through the changes in the position of the maximum of the amide I' band and the tyrosine band, or the maximum of the band assigned to the beta-sheet structure, corroborate the results of a previous study using fourth-derivative UV absorbance spectroscopy. In addition, variants at position 108 are the most critical for ribonuclease structure and stability. The V108G variant seems to present a greater conformational flexibility than the other variants. The pressure- and temperature-denaturated states of all the ribonucleases characterized retained some secondary structure. However, their spectral maxima were centered at different wavenumbers, which suggests that pressure- and temperature-denaturated states do not have the same structural characteristics. Nevertheless, there was close correlation between the pressure and temperature midpoint transition values for the whole series of protein variants, which indicated a common tendency of stability toward pressure and heat.
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Affiliation(s)
- J Torrent
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain
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48
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Lasch P, Petras T, Ullrich O, Backmann J, Naumann D, Grune T. Hydrogen peroxide-induced structural alterations of RNAse A. J Biol Chem 2001; 276:9492-502. [PMID: 11115501 DOI: 10.1074/jbc.m008528200] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins exposed to oxidative stress are degraded via proteolytic pathways. In the present study, we undertook a series of in vitro experiments to establish a correlation between the structural changes induced by mild oxidation of the model protein RNase A and the proteolytic rate found upon exposure of the modified protein toward the isolated 20 S proteasome. Fourier transform infrared spectroscopy was used as a structure-sensitive probe. We report here strong experimental evidence for oxidation-induced conformational rearrangements of the model protein RNase A and, at the same time, for covalent modifications of amino acid side chains. Oxidation-related conformational changes, induced by H(2)O(2) exposure of the protein may be monitored in the amide I region, which is sensitive to changes in protein secondary structure. A comparison of the time- and H(2)O(2) concentration-dependent changes in the amide I region demonstrates a high degree of similarity to spectral alterations typical for temperature-induced unfolding of RNase A. In addition, spectral parameters of amino acid side chain marker bands (Tyr, Asp) revealed evidence for covalent modifications. Proteasome digestion measurements on oxidized RNase A revealed a specific time and H(2)O(2) concentration dependence; at low initial concentration of the oxidant, the RNase A turnover rate increases with incubation time and concentration. Based on these experimental findings, a correlation between structural alterations detected upon RNase A oxidation and proteolytic rates of RNase A is established, and possible mechanisms of the proteasome recognition process of oxidatively damaged proteins are discussed.
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Affiliation(s)
- P Lasch
- Robert Koch Institute, P 34 Biophysical Structure Analysis, D-13353 Berlin, Nordufer 20, Germany
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49
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Purcell M, Neault JF, Tajmir-Riahi HA. Interaction of taxol with human serum albumin. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1478:61-8. [PMID: 10719175 DOI: 10.1016/s0167-4838(99)00251-4] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Taxol (paclitaxel) is an anticancer drug, which interacts with microtuble proteins, in a manner that catalyzes their formation from tubulin and stabilizes the resulting structures (Nogales et al., Nature 375 (1995) 424-427). This study was designed to examine the interaction of taxol with human serum albumin (HSA) in aqueous solution at physiological pH with drug concentrations of 0.0001-0.1 mM, and HSA (fatty acid free) concentration of 2% w/v. Gel electrophoresis, absorption spectra and Fourier transform infrared (FTIR) spectroscopy with self-deconvolution and second-derivative resolution enhancement were used to determine the drug binding mode, binding constant and the protein secondary structure in the presence of taxol in aqueous solution. Spectroscopic evidence showed that taxol-protein interaction results into two types of drug-HSA complexes with overall binding constant of K=1.43 x 10(4) M(-1). The molar ratios of complexes were of taxol/HSA 30/1 (30 mM taxol) and 90/1 (90 mM taxol) with the complex ratios of 1.9 and 3.4 drug molecules per HSA molecule, respectively. The taxol binding results in major protein secondary structural changes from that of the alpha-helix 55 to 45% and beta-sheet 22 to 26%, beta-anti 12 to 15% and turn 11 to 16%, in the taxol-HSA complexes. The observed spectral changes indicate a partial unfolding of the protein structure, in the presence of taxol in aqueous solution.
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Affiliation(s)
- M Purcell
- Department of Chemistry-Biology, University of Quebec, C.P. 500, Trois-Rivières, Que., Canada
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50
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von Germar F, Barth A, Mäntele W. Structural changes of the sarcoplasmic reticulum Ca(2+)-ATPase upon nucleotide binding studied by fourier transform infrared spectroscopy. Biophys J 2000; 78:1531-40. [PMID: 10692337 PMCID: PMC1300750 DOI: 10.1016/s0006-3495(00)76705-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Changes in the vibrational spectrum of the sarcoplasmic reticulum Ca(2+)-ATPase upon nucleotide binding were recorded in H(2)O and (2)H(2)O at -7 degrees C and pH 7.0. The reaction cycle was triggered by the photochemical release of nucleotides (ATP, ADP, and AMP-PNP) from a biologically inactive precursor (caged ATP, P(3)-1-(2-nitrophenyl) adenosine 5'-triphosphate, and related caged compounds). Infrared absorbance changes due to ATP release and two steps of the Ca(2+)-ATPase reaction cycle, ATP binding and phosphorylation, were followed in real time. Under the conditions used in our experiments, the rate of ATP binding was limited by the rate of ATP release (k(app) congruent with 3 s(-1) in H(2)O and k(app) congruent with 7 s(-1) in (2)H(2)O). Bands in the amide I and II regions of the infrared spectrum show that the conformation of the Ca(2+)-ATPase changes upon nucleotide binding. The observation of bands in the amide I region can be assigned to perturbations of alpha-helical and beta-sheet structures. According to similar band profiles in the nucleotide binding spectra, ATP, AMP-PNP, and ADP induce similar conformational changes. However, subtle differences between ATP and AMP-PNP are observed; these are most likely due to the protonation state of the gamma-phosphate group. Differences between the ATP and ADP binding spectra indicate the significance of the gamma-phosphate group in the interactions between the Ca(2+)-ATPase and the nucleotide. Nucleotide binding affects Asp or Glu residues, and bands characteristic of their protonated side chains are observed at 1716 cm(-1) (H(2)O) and 1706 cm(-1) ((2)H(2)O) and seem to depend on the charge of the phosphate groups. Bands at 1516 cm(-1) (H(2)O) and 1514 cm(-1) ((2)H(2)O) are tentatively assigned to a protonated Tyr residue affected by nucleotide binding. Possible changes in Arg, Trp, and Lys absorption and in the nucleoside are discussed. The spectra are compared with those of nucleotide binding to arginine kinase, creatine kinase, and H-ras P21.
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Affiliation(s)
- F von Germar
- Institut für Biophysik, Johann Wolfgang Goethe Universität Frankfurt, D-60590 Frankfurt am Main, Germany
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