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ATR-FTIR Biosensors for Antibody Detection and Analysis. Int J Mol Sci 2022; 23:ijms231911895. [PMID: 36233197 PMCID: PMC9570191 DOI: 10.3390/ijms231911895] [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: 09/04/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level.
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2
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Bi X, Miao K, Wei L. Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange. J Am Chem Soc 2022; 144:8504-8514. [PMID: 35508077 DOI: 10.1021/jacs.2c01991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen-deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm-1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.
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Affiliation(s)
- Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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3
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Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:613-628. [PMID: 33534058 PMCID: PMC8189984 DOI: 10.1007/s00249-021-01502-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/11/2022]
Abstract
FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.
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Das A, Jobelius H, Schleinitz J, Gamboa-Ramirez S, Creste G, Kervern G, Raya J, Le Breton N, Guénet A, Boubegtiten-Fezoua Z, Grimaud L, Orio M, Rogez G, Hellwig P, Choua S, Ferlay S, Desage-El Murr M. A hybrid bioinspired catechol-alloxazine triangular nickel complex stabilizing protons and electrons. Inorg Chem Front 2021. [DOI: 10.1039/d1qi01131f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new class of redox-active ligands merging catechol and alloxazine structures is reported. A trimetallic triangular complex is formed upon complexation to nickel.
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Affiliation(s)
- Agnideep Das
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | - Hannah Jobelius
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
- Université de Strasbourg, Chimie de la Matière Complexe, CNRS UMR7140, 67000 Strasbourg, France
| | - Jules Schleinitz
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Geordie Creste
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | - Gwendal Kervern
- Université de Lorraine, Faculté des Sciences, boulevard des Aiguillettes, CNRS UMR7036, BP 70239, 54506 Vandoeuvre-les-Nancy Cedex, France
| | - Jesus Raya
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | - Nolwenn Le Breton
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | - Aurélie Guénet
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | | | - Laurence Grimaud
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Guillaume Rogez
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR 7504, F-67000 Strasbourg, France
| | - Petra Hellwig
- Université de Strasbourg, Chimie de la Matière Complexe, CNRS UMR7140, 67000 Strasbourg, France
| | - Sylvie Choua
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
| | - Sylvie Ferlay
- Université de Strasbourg, Chimie de la Matière Complexe, CNRS UMR7140, 67000 Strasbourg, France
| | - Marine Desage-El Murr
- Université de Strasbourg, Institut de Chimie, CNRS UMR7177, 67000 Strasbourg, France
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5
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Seica AFS, Iancu CV, Pfeilschifter B, Madej MG, Choe JY, Hellwig P. Asp 22 drives the protonation state of the Staphylococcus epidermidis glucose/H + symporter. J Biol Chem 2020; 295:15253-15261. [PMID: 32859752 DOI: 10.1074/jbc.ra120.014069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/26/2020] [Indexed: 12/24/2022] Open
Abstract
The Staphylococcus epidermidis glucose/H+ symporter (GlcPSe) is a membrane transporter highly specific for glucose and a homolog of the human glucose transporters (GLUT, SLC2 family). Most GLUTs and their bacterial counterparts differ in the transport mechanism, adopting uniport and sugar/H+ symport, respectively. Unlike other bacterial GLUT homologs (for example, XylE), GlcPSe has a loose H+/sugar coupling. Asp22 is part of the proton-binding site of GlcPSe and crucial for the glucose/H+ co-transport mechanism. To determine how pH variations affect the proton site and the transporter, we performed surface-enhanced IR absorption spectroscopy on the immobilized GlcPSe We found that Asp22 has a pKa of 8.5 ± 0.1, a value consistent with that determined previously for glucose transport, confirming the central role of this residue for the transport mechanism of GlcPSe A neutral replacement of the negatively charged Asp22 led to positive charge displacements over the entire pH range, suggesting that the polarity change of the WT reflects the protonation state of Asp22 We expected that the substitution of the residue Ile105 for a serine, located within hydrogen-bonding distance to Asp22, would change the microenvironment, but the pKa of Asp22 corresponded to that of the WT. A167E mutation, selected in analogy to the XylE, introduced an additional protonatable site and perturbed the protonation state of Asp22, with the latter now exhibiting a pKa of 6.4. These studies confirm that Asp22 is the proton-binding residue in GlcPSe and show that charged residues in its vicinity affect the pKa of glucose/H+ symport.
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Affiliation(s)
- Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France
| | - Cristina V Iancu
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA
| | - Benedikt Pfeilschifter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Regensburg, Germany
| | - M Gregor Madej
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Regensburg, Germany
| | - Jun-Yong Choe
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA; Department of Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA.
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France
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6
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De Meutter J, Goormaghtigh E. A convenient protein library for spectroscopic calibrations. Comput Struct Biotechnol J 2020; 18:1864-1876. [PMID: 32728409 PMCID: PMC7369421 DOI: 10.1016/j.csbj.2020.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
While several Raman, CD or FTIR spectral libraries are available for well-characterized proteins of known structure, proteins themselves are usually very difficult to acquire, preventing a convenient calibration of new instruments and new recording methods. The problem is particularly critical in the field of FTIR spectroscopy where numerous new methods are becoming available on the market. The present papers reports the construction of a protein library (cSP92) including commercially available products, that are well characterized experimentally for their purity and solubility in conditions compatible with the recording of FTIR spectra and whose high-resolution structure is available. Overall, 92 proteins were selected. These proteins cover well the CATH space at the level of classes and architectures. In terms of secondary structure content, an analysis of their high-resolution structure by DSSP shows that the mean content in the different secondary structures present in cSP92 is very similar to the mean content found in the PDB. The 92-protein set is analyzed in details for the distribution of helix length, number of strands in β- sheets, length of β-strands and amino acid content, all features that may be important for the interpretation of FTIR spectra.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine CP206/02, Brussels, Belgium
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7
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Xing H, Yaylayan V. Mechanochemically Induced Controlled Glycation of Lysozyme and Its Effect on Enzymatic Activity and Conformational Changes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3249-3255. [PMID: 30811194 DOI: 10.1021/acs.jafc.9b00070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Protein glycation through heating of a mixture of protein and reducing sugars is one of the most commonly used methods of protein modification; however, in most cases, this approach can lead to uncontrolled glycation. The hypothesis that mechanical energy supplied through ball milling can induce glycation of proteins was tested using a well-characterized enzyme lysozyme. The Q-TOF/MS analysis of the milled samples has indicated that the milling of sugar-protein mixtures in stainless steel jars for 30 min and at a frequency of 30 Hz generated mainly monoglycated proteins even with the highly reactive ribose. Increasing the sugar concentration or the milling time did not influence the overall yield or generate more glycoforms. Enzymatic activity measurements, FTIR, and fluorescence spectroscopic studies have indicated that milling of lysozyme alone leads to a significant loss in enzymatic activity and structural integrity in contrast to milling in the presence of sugars.
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Affiliation(s)
- Haoran Xing
- Department of Food Science & Agricultural Chemistry , McGill University , 21111 Lakeshore , Ste Anne de Bellevue , Quebec Canada , H9X 3 V9
| | - Varoujan Yaylayan
- Department of Food Science & Agricultural Chemistry , McGill University , 21111 Lakeshore , Ste Anne de Bellevue , Quebec Canada , H9X 3 V9
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8
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Brielle ES, Arkin IT. Site-Specific Hydrogen Exchange in a Membrane Environment Analyzed by Infrared Spectroscopy. J Phys Chem Lett 2018; 9:4059-4065. [PMID: 29957958 DOI: 10.1021/acs.jpclett.8b01675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrogen exchange is a powerful method to examine macromolecules. In membrane proteins, exchange can distinguish between solvent-accessible and -inaccessible residues due to shielding by the hydrophobic environment of the lipid bilayer. Herein, rather than examining which residues undergo hydrogen exchange, we employ a protocol that enables the full deuteration of all polar hydrogens in a membrane protein. We then measure the impact of hydrogen exchange on the shift of the amide I vibrational mode of individually labeled sites. The results enable us to correlate polarity with vibrational shifts, thereby providing a powerful tool to examine specific locations within a membrane protein in its native membrane environment.
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Affiliation(s)
- Esther S Brielle
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
| | - Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
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9
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Shinzawa H, Mizukado J. Hydrogen/deuterium (H/D) exchange of gelatinized starch studied by two-dimensional (2D) near-infrared (NIR) correlation spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:138-141. [PMID: 29277478 DOI: 10.1016/j.saa.2017.12.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Hydrogen/deuterium (H/D) exchange of gelatinized starch was probed by in-situ near-infrared (NIR) monitoring coupled with two-dimensional (2D) correlation spectroscopy. Gelatinized starch undergoes spontaneous H/D exchange in D2O. During the substitution, the exchange rate essentially becomes different depending on solvent accessibility of various parts of the molecule. Thus, by analyzing the change in the NIR feature observed during the substitution, it becomes possible to sort out local structure and dynamics of the system. 2D correlation analysis of the time-dependent NIR spectra reveals the presence of different local structure of the starch, each having different solvent accessibility. For example, during the H/D exchange, the D2O is first absorbed by starch molecules especially around the surface area between the starch and water, where the water molecules are weakly interacted with the starch molecules. This absorption is quickly followed by the development of HDO species. Further absorption of the D2O results in the penetration of the molecules inside the starch and eventually develops the relatively strong interaction between the HDO and starch molecules because of the presence of dominant starch molecules.
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Affiliation(s)
- Hideyuki Shinzawa
- National Institute of Advanced Industrial Science and Technology (AIST), Japan.
| | - Junji Mizukado
- National Institute of Advanced Industrial Science and Technology (AIST), Japan
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10
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Caporaletti F, Carbonaro M, Maselli P, Nucara A. Hydrogen–Deuterium exchange kinetics in β-lactoglobulin (−)-epicatechin complexes studied by FTIR spectroscopy. Int J Biol Macromol 2017. [DOI: 10.1016/j.ijbiomac.2017.06.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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Keiderling TA. Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides. Chirality 2017; 29:763-773. [DOI: 10.1002/chir.22749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
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12
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Neehaul Y, Kriegel S, Barquera B, Hellwig P. Functional Studies on Membrane Proteins by Means of H/D Exchange in Infrared: Structural Changes in Na + NQR from V. cholerae in the Presence of Lipids. Methods Mol Biol 2017; 1635:247-257. [PMID: 28755373 DOI: 10.1007/978-1-4939-7151-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
H/D exchange kinetics at the level of the amide proton in the mid infrared (1700-1500 cm-1) make it possible to study the conformational flexibility of membrane proteins, independent of size or the presence of detergent or lipids. Slow, medium, and fast exchanging domains are distinguished, which reveal a different accessibility to the solvent. Whereas amide hydrogens undergo rapid exchange with solvent in an open structure, hydrogens experience much slower exchange when involved in H-bonded structures or when sterically inaccessible to the solvent. Here, we describe the protocol that was used to study the effect of phospholipids on the overall structure of the Na+ NQR from V. cholerae, a sodium pumping membrane protein.
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Affiliation(s)
- Yashvin Neehaul
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
- Mauritius Oceanography Institute, Avenue des Anchois, Albion, Mauritius
| | - Sebastien Kriegel
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France.
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13
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Hellwig P, Kriegel S, Friedrich T. Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:922-7. [PMID: 26702948 DOI: 10.1016/j.bbabio.2015.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Petra Hellwig
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Sébastien Kriegel
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
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14
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FTIR spectral signature of anticancer drugs. Can drug mode of action be identified? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:85-101. [PMID: 26327318 DOI: 10.1016/j.bbapap.2015.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/18/2015] [Accepted: 08/25/2015] [Indexed: 12/26/2022]
Abstract
Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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15
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Korkmaz F, Erdogan DA, Özalp-Yaman Ş. Interaction of a novel platinum drug with bovine serum albumin: FTIR and UV-Vis spectroscopy analysis. NEW J CHEM 2015. [DOI: 10.1039/c5nj00785b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platinum-Blue docks at a hydrophobic cavity at low concentrations with a binding constant comparable to that of cisplatin.
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Affiliation(s)
- Filiz Korkmaz
- Atilim University
- Faculty of Engineering
- Biophysics Laboratory
- Ankara
- Turkey
| | - Deniz Altunoz Erdogan
- Atilim University
- Faculty of Engineering
- Department of Chemical Engineering and Applied Chemistry
- Ankara
- Turkey
| | - Şeniz Özalp-Yaman
- Atilim University
- Faculty of Engineering
- Department of Chemical Engineering and Applied Chemistry
- Ankara
- Turkey
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16
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Dunkelberger EB, Woys AM, Zanni MT. 2D IR cross peaks reveal hydrogen-deuterium exchange with single residue specificity. J Phys Chem B 2013; 117:15297-305. [PMID: 23659731 PMCID: PMC3812256 DOI: 10.1021/jp402942s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A form of chemical exchange, hydrogen-deuterium exchange (HDX), has long been used as a method for studying the secondary and tertiary structure of peptides and proteins using mass spectrometry and NMR spectroscopy. Using two-dimensional infrared (2D IR) spectroscopy, we resolve cross peaks between the amide II band and a (13)C(18)O isotope-labeled amide I band, which we show measures HDX with site-specific resolution. By rapidly scanning 2D IR spectra using mid-IR pulse shaping, we monitor the kinetics of HDX exchange on-the-fly. For the antimicrobial peptide ovispirin bound to membrane bilayers, we find that the amide II peak decays with a biexponential with rate constants of 0.54 ± 0.02 and 0.12 ± 0.01 min(-1), which is a measure of the overall HDX in the peptide. The cross peaks between Ile-10-labeled ovispirin and the amide II mode, which specifically monitor HDX kinetics at Ile-10, decay with a single rate constant of 0.36 ± 0.1 min(-1). Comparing this exchange rate to theoretically determined exchange rates of Ile-10 for ovispirin in a solution random coil configuration, the exchange rate at Ile-10 is at least 100 times slower, consistent with the known α-helix structure of ovispirin in bilayers. Because backbone isotope labels produce only a very small shift of the amide II band, site-specific HDX cannot be measured with FTIR spectroscopy, which is why 2D IR spectroscopy is needed for these measurements.
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Affiliation(s)
| | - Ann Marie Woys
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
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17
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Korkmaz F, Ressl S, Ziegler C, Mäntele W. K+-induced conformational changes in the trimeric betaine transporter BetP monitored by ATR-FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1181-91. [DOI: 10.1016/j.bbamem.2013.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/10/2012] [Accepted: 01/08/2013] [Indexed: 11/28/2022]
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18
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Shai Y. ATR-FTIR studies in pore forming and membrane induced fusion peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23201348 DOI: 10.1016/j.bbamem.2012.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Infrared (IR) spectroscopy has been shown to be very reliable for the characterization, identification and quantification of structural data. Particularly, the Attenuated Total Reflectance (ATR) technique which became one of the best choices to study the structure and organization of membrane proteins and membrane-bound peptides in biologically relevant membranes. An important advantage of IR spectroscopy is its ability to analyze material under a very wide range of conditions including solids, liquids and gases. This method allows elucidation of component secondary structure elements of a peptide or protein in a global manner, and by using site specific isotope labeling allows determination of specific regions. A few advantages in using ATR-FTIR spectroscopy include; a relatively simple technique, allow the determination of peptide orientation in the membrane, allow the determination of secondary structures of very small peptides, and importantly, the method is sensitive to isotopic labeling on the scale of single amino acids. Many studies were reported on the use of ATR-FTIR spectroscopy in order to study the structure and orientation of membrane bound hydrophobic peptides and proteins. The list includes native and de-novo designed peptides, as well as those derived from trans-membrane domains of various receptors (TMDs). The present review will focus on several examples that demonstrate the potential and the simplicity in using the ATR-FTIR approach to determine secondary structures of proteins and peptides when bound, inserted, and oligomerized within membranes. The list includes (i) a channel forming protein/peptide: the Ca(2+) channel phospholamban, (ii) a cell penetrating peptide, (iii) changes in the structure of a transmembrane domain located within ordered and non-ordered domains, and (iv) isotope edited FTIR to directly assign structure to the membrane associated fusion peptide in context of a Key gp41 Structural Motif. Importantly, a unique advantage of infrared spectroscopy is that it allows a simultaneous study of the structure of lipids and proteins in intact biological membranes without an introduction of foreign perturbing probes. Because of the long IR wavelength, light scattering problems are virtually non-existent. This allows the investigation of highly aggregated materials or large membrane fragments. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Yechiel Shai
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel.
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Jakob-Grun S, Radeck J, Braun P. Ca(2+)-binding reduces conformational flexibility of RC-LH1 core complex from thermophile Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2012; 111:139-147. [PMID: 22367594 DOI: 10.1007/s11120-012-9727-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/09/2012] [Indexed: 05/31/2023]
Abstract
The light-harvesting complex, LH1, of thermophile purple bacteria Thermochromatium tepidum consists of an array of α- and β-polypeptides which assemble the photoactive bacteriochlorophyll and closely interact with the membrane-lipids. In this study, we investigated the effect of calcium and manganese ions on the protein structure and thermostability of the reaction centre (RC)-LH1/lipid complex. The binding of Ca(2+), but not Mn(2+) is shown to shift the LH1 Q ( y ) absorption maximum from ~889 to 915 nm and to significantly raise the thermostability of the RC-LH1 complex. The ATR-FTIR spectra indicate that interaction of Ca(2+) as monitored by the carboxylates' vibration of aspartate residues, but not Mn(2+) induces changes in the α-helix packing arrangement. The reduced rate of (1)H/(2)H exchange of proteins' amide protons shows that the accessibility to (2)H(2)O is significantly lowered in Ca(2+)-substituted RC-LH1/lipid complexes. In particular, exchange with the associated lipid molecules, is significantly retarded. These results suggest that the thermostability of the RC-LH1 complex is raised by the distinct interaction with calcium cations which reduces the RC-LH1/lipid dynamics, particularly, at the membrane-water interface.
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Affiliation(s)
- Selma Jakob-Grun
- Department Biology I, Botany, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
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Wang SC, Mirarefi P, Faraone A, Lee CT. Light-controlled protein dynamics observed with neutron spin echo measurements. Biochemistry 2011; 50:8150-62. [PMID: 21809812 DOI: 10.1021/bi200206z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoresponsive surfactant has been used as a means to control protein structure and dynamics with light illumination. This cationic azobenzene surfactant, azoTAB, which undergoes a reversible photoisomerization upon exposure to the appropriate wavelength of light, adopts a relatively hydrophobic, trans structure under visible light illumination and a relatively hydrophilic cis structure under UV light illumination. Small-angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy were used to measure the tertiary structure and internal dynamics of lysozyme in the presence of the photosurfactant, respectively. The SANS-based in vitro structures indicate that under visible light the photosurfactant induces partial unfolding that principally occurs away from the active site near the hinge region connecting the α and β domains. Upon UV exposure, however, the protein refolds to a nativelike structure. At the same time, enhanced internal dynamics of lysozyme were detected with the surfactant in the trans form through NSE measurements of the Q-dependent effective diffusion coefficient (D(eff)) of the protein. In contrast, the D(eff) values of lysozyme in the presence of cis azoTAB largely agree with the rigid-body calculation as well as those measured for pure lysozyme, suggesting that the native protein is dormant on the nanosecond time and nanometer length scales. Lysozyme internal motions were modeled by assuming a protein of two (α and β domains) or three (α and β domains and the hinge region) domains connects by either soft linkers or rigid, freely rotating bonds. Protein dynamics were also tracked with Fourier transform infrared spectroscopy through hydrogen-deuterium exchange kinetics, which further demonstrated enhanced protein flexibility induced by the trans form of the surfactant relative to the native protein. Ensemble-averaged intramolecular fluorescent resonance energy transfer measurements similarly demonstrated the enhanced dynamics of lysozyme with the trans form of the photosurfactant. Previous results have shown a significant increase in protein activity in the presence of azoTAB in the trans conformation. Combined, these results provide insight into a unique light-based method of controlling protein structure, dynamics, and function and strongly support the relevance of large domain motions for the activity of proteins.
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Affiliation(s)
- Shao-Chun Wang
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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Hielscher R, Friedrich T, Hellwig P. Far- and Mid-Infrared Spectroscopic Analysis of the Substrate-Induced Structural Dynamics of Respiratory Complex I. Chemphyschem 2010; 12:217-24. [DOI: 10.1002/cphc.201000688] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/22/2010] [Indexed: 11/07/2022]
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Carrillo-Conde B, Schiltz E, Yu J, Chris Minion F, Phillips GJ, Wannemuehler MJ, Narasimhan B. Encapsulation into amphiphilic polyanhydride microparticles stabilizes Yersinia pestis antigens. Acta Biomater 2010; 6:3110-9. [PMID: 20123135 DOI: 10.1016/j.actbio.2010.01.040] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 01/24/2010] [Accepted: 01/27/2010] [Indexed: 11/28/2022]
Abstract
The design of biodegradable polymeric delivery systems based on polyanhydrides that would provide for improved structural integrity of Yersinia pestis antigens was the main goal of this study. Accordingly, the full-length Y. pestis fusion protein (F1-V) or a recombinant Y. pestis fusion protein (F1(B2T1)-V10) was encapsulated and released from microparticles based on 1,6-bis(p-carboxyphenoxy)hexane (CPH) and sebacic acid (SA) copolymers and 1,8-bis(p-carboxyphenoxy)-3,6-dioxaoctane (CPTEG) and CPH copolymers fabricated by cryogenic atomization. An enzyme-linked immunosorbent assay was used to measure changes in the antigenicity of the released proteins. The recombinant F1(B2T1)-V10 was unstable upon release from the hydrophobic CPH:SA microparticles, but maintained its structure and antigenicity in the amphiphilic CPTEG:CPH system. The full-length F1-V was stably released by both CPH:SA and CPTEG:CPH microparticles. In order to determine the effect of the anhydride monomers on the protein structure, changes in the primary, secondary, and tertiary structure, as well as the antigenicity of both Y. pestis antigens, were measured after incubation in the presence of saturated solutions of SA, CPH, and CPTEG anhydride monomers. The results indicated that the amphiphilic environment provided by the CPTEG monomer was important to preserve the structure and antigenicity of both proteins. These studies offer an approach by which a thorough understanding of the mechanisms governing antigenic instability can be elucidated in order to optimize the in vivo performance of biodegradable delivery devices as protein carriers and/or vaccine adjuvants.
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Affiliation(s)
- Brenda Carrillo-Conde
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
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Carmona P, Molina M. Interactions of Protein and Nucleic Acid Components of Hepatitis C Virus As Revealed by Fourier Transform Infrared Spectroscopy. Biochemistry 2010; 49:4724-31. [DOI: 10.1021/bi100535k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pedro Carmona
- Instituto de Estructura de la Materia (CSIC), Serrano 121, 28006 Madrid, Spain
| | - Marina Molina
- Departamento de Química Orgánica, Escuela Universitaria de Optica, Arcos de Jalón, s/n, 28037 Madrid, Spain
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Rutkowska-Wlodarczyk I, Kierdaszuk B, Wlodarczyk J. Analysis of proton exchange kinetics with time-dependent exchange rate. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:891-8. [PMID: 20056171 DOI: 10.1016/j.bbapap.2009.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 12/05/2009] [Accepted: 12/28/2009] [Indexed: 10/20/2022]
Abstract
Mass spectrometry is used to probe the kinetics of hydrogen-deuterium exchange in lysozyme in pH 5, 6 and 7.4. An analysis based on a Verhulst growth model is proposed and effectively applied to the kinetics of the hydrogen exchange. The data are described by a power-like function which is based on a time-dependence of the exchange rate. Experimental data ranging over many time scales is considered and accurate fits of a power-like function are obtained. Results of fittings show correlation between faster hydrogen-deuterium exchange and increase of pH. Furthermore a model is presented that discriminates between easily exchangeable hydrogens (located in close proximity to the protein surface) and those protected from the exchange (located in the protein interior). A possible interpretation of the model and its biological significance are discussed.
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Goormaghtigh E, Gasper R, Bénard A, Goldsztein A, Raussens V. Protein secondary structure content in solution, films and tissues: redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1332-43. [PMID: 19540367 DOI: 10.1016/j.bbapap.2009.06.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Revised: 05/25/2009] [Accepted: 06/03/2009] [Indexed: 11/27/2022]
Abstract
The paper presents a simple and robust method to determine protein secondary structure from circular dichroism, transmission and attenuated total reflection (ATR) Fourier transform infrared spectra. It is found that the different spectroscopic methods bring valuable but roughly identical information on the secondary structure of proteins. ATR and transmission FTIR spectra display distinct differences, yet the secondary structure can be predicted from their spectra with roughly the same success. It is also found that one wavenumber or wavelength includes the large majority of the information correlated with secondary structure content and no more than 3 significant independent wavenumbers/wavelengths could be found for any of the spectroscopic data. This finding indicates that more complex linear combinations of the absorbance or ellipticities will not further improve secondary structure predictions. Furthermore, the information content in CD, transmission and ATR FTIR spectra is largely redundant. If combining CD and FTIR results in some improvement of structure prediction quality, the improvement is too modest to prompt spectroscopists to collect different spectroscopic data for structure prediction purposes. On the other hand, the data collected show that the quality of the FTIR spectrometers is such that biosensors or imaging methods sampling from 10(-9) to 10(-15) g yield spectra of sufficient quality to analyze protein secondary structure. These new techniques open the way to a new area of research, both in protein conformational response to ligand and imaging at sub-cellular scales.
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Affiliation(s)
- Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine CP206/02; Université Libre de Bruxelles, Bld du Triomphe 2, CP206/2, B1050 Brussels, Belgium.
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Infrared spectroscopic study of the structural and functional properties of the Na+/H+ antiporter MjNhaP1 from Methanococcus jannaschii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:730-7. [DOI: 10.1016/j.bbabio.2009.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 04/02/2009] [Accepted: 04/02/2009] [Indexed: 11/23/2022]
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Dzafić E, Klein O, Screpanti E, Hunte C, Mäntele W. Flexibility and dynamics of NhaA Na+/H+-antiporter of Escherichia coli studied by Fourier transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 72:102-109. [PMID: 18930435 DOI: 10.1016/j.saa.2008.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/15/2008] [Accepted: 08/20/2008] [Indexed: 05/26/2023]
Abstract
NhaA (41,355Da) is a Na(+)/H(+) antiporter of Escherichia coli which plays a central role in regulation of intracellular pH, cellular Na(+) content, and cell volume [E. Padan, S. Schuldiner, J. Exp. Biol. 196 (1994) 443]. Its activity is strongly regulated by pH and increases over 3 orders of magnitude between pH 7 and 8 [A. Rothman, Y. Gerchman, E. Padan, S. Schuldiner, Biochemistry 36 (1997) 14572]. Protein dynamics and flexibility in the activated and inactivated state, respectively, was analysed by probing accessibility in (1)H/(2)H exchange experiments for the wild type and the mutant G338S which is constitutively active independent of pH [A. Rimon, Y. Gerchman, Z. Kariv, E. Padan, J. Biol. Chem. 273 (1998) 26470]. This was studied by ATR-FTIR difference spectroscopy using a home built microvolume (<5 microl) perfusion chamber [E. Agić, O. Klein, W. Mäntele, Proceedings of the 10th European Conference on the Spectroscopy of Biological Molecules, vol. 93, 2003, ISBN 9634826148; S. Gourion-Arsiquaud, S. Chevance, P. Bouyer, L. Garnier, J.-L. Montillet, A. Bondon, C. Berthomieu, Biochemistry 44 (2005) 8652]. The solution or suspension of the target protein is contained in a chamber with sample volumes of below 5 microl. It is in contact with the ATR crystal and separated from the flowing effector molecules by a dialysis membrane. The flow-ATR unit is characterised by high stability, fast response, and high sensitivity for the IR spectroscopic detection of binding-induced conformational changes and reactions. On the basis of (1)H-(2)H exchange of NhaA followed in the amide I and amide II region of the IR spectrum, it is concluded that the accessible fraction of the polypeptide chain of NhaA increases by more than 10% in the active state. For the mutant, no changes in accessibility were observed for different pH values. The increase of Na(+) concentration increases the extent of exchange. The stability of the wild type protein in the active and inactive form was analysed by measuring the temperature profiles of the IR spectra. A decrease of the structural stability of the protein with activation was observed. Together with the results from (1)H/(2)H exchange, the inactive state represents a more compact form whereas activation induces a more open conformation of the protein.
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Affiliation(s)
- E Dzafić
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany.
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A hypoallergenic variant of Der p 1 as a candidate for mite allergy vaccines. J Allergy Clin Immunol 2009; 123:1150-6. [PMID: 19152967 DOI: 10.1016/j.jaci.2008.11.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 01/29/2023]
Abstract
BACKGROUND Recombinant hypoallergens that display reduced allergenicity but retain T-cell reactivity represent promising candidates to improve the safety and efficacy of allergen-specific vaccines or immunotherapy. OBJECTIVE The current study reports the immunologic characterization of a hypoallergenic variant of the major mite allergen Der p 1. METHODS The recombinant proform of Der p 1 (ProDer p 1) was expressed in Escherichia coli (ProDer p 1 coli), purified and characterized at the level of its secondary structure, and IgE and T-cell reactivities. Moreover, the prophylactic potential of ProDer p 1 coli vaccinations was evaluated in a murine Der p 1 sensitization model. RESULTS After purification and refolding, ProDer p 1 coli remained aggregated with a higher beta-sheet content and altered Der p 1 conformational epitopes compared with the correctly folded monomeric ProDer p 1 produced in Chinese hamster ovary cells. Both ProDer p 1 forms were able to retain the Der p 1-specific T-cell reactivity but direct ELISA, competitive inhibition, and rat basophil leukemia assays clearly showed that ProDer p 1 coli displays a very weak IgE reactivity. Mice vaccinations with aggregated ProDer p 1 adjuvanted with alum induced a T(H)1-biased immune response that prevented the subsequent allergic response after Der p 1 sensitization and airway challenge with aerosolized mite extracts. Furthermore, ProDer p 1 coli treatment inhibited the development of airway eosinophilia and airway hyperresponsiveness to inhaled methacholine. CONCLUSION Aggregated forms of Der p 1 could represent hypoallergens suitable for the prevention of mite allergy.
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Goff KL, Quaroni L, Wilson KE. Measurement of metabolite formation in single living cells of Chlamydomonas reinhardtii using synchrotron Fourier-Transform Infrared spectromicroscopy. Analyst 2009; 134:2216-9. [DOI: 10.1039/b915810c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. These studies were performed to determine the order of events during the exchange process, the extent of H/D exchange, and associated kinetics of exchange for a comparative analysis of these ligands. Furthermore, the secondary structure composition of amphiregulin (AR) and heparin-binding-epidermal growth factor (HB-EGF) was determined. All ligands were found to have similar contributions of 3(10)-helix and random coil with varying contributions of beta-sheets and beta-turns. The extent of exchange was 40%, 65%, 55%, 65%, and 98% for EGF, transforming growth factor-alpha (TGF-alpha), AR, HB-EGF, and epiregulin (ER), respectively. The rate constants were determined and classified as fast, intermediate, and slow: for EGF the 0.20 min(-1) (Tyr), 0.09 min(-1) (Arg, beta-turns), and 1.88 x 10(-3) min(-1) (beta-sheets and 3(10)-helix); and for TGF-alpha 0.91 min(-1) (Tyr), 0.27 min(-1) (Arg, beta-turns), and 1.41 x 10(-4) min(-1) (beta-sheets). The time constants for AR 0.47 min(-1) (Tyr), 0.04 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (buried 3(10)-helix, beta-turns, and beta-sheets); for HB-EGF 0.89 min(-1) (Tyr), 0.14 min(-1) (Arg and 3(10)-helix), and 1.00 x 10(-3) min(-1) (buried 3(10)-helix, beta-sheets, and beta-turns); and for epiregulin 0.16 min(-1) (Tyr), 0.03 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (3(10)-helix and beta-sheets). These results provide essential information toward understanding secondary structure, H/D exchange kinetics, and solvation of these epidermal growth factor receptor ligands in their unbound state.
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Andersson J, Hauser K, Karjalainen EL, Barth A. Protonation and hydrogen bonding of Ca2+ site residues in the E2P phosphoenzyme intermediate of sarcoplasmic reticulum Ca2+-ATPase studied by a combination of infrared spectroscopy and electrostatic calculations. Biophys J 2007; 94:600-11. [PMID: 17890386 PMCID: PMC2157260 DOI: 10.1529/biophysj.107.114033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protonation of the Ca(2+) ligands of the SR Ca(2+)-ATPase (SERCA1a) was studied by a combination of rapid scan FTIR spectroscopy and electrostatic calculations. With FTIR spectroscopy, we investigated the pH dependence of C=O bands of the Ca(2+)-free phosphoenzyme (E2P) and obtained direct experimental evidence for the protonation of carboxyl groups upon Ca(2+) release. At least three of the infrared signals from protonated carboxyl groups of E2P are pH dependent with pK(a) values near 8.3: a band at 1758 cm(-1) characteristic of nonhydrogen-bonded carbonyl groups, a shoulder at 1720 cm(-1), and part of a band at 1710 cm(-1), both characteristic of hydrogen-bonded carbonyl groups. The bands are thus assigned to H(+) binding residues, some of which are involved in H(+) countertransport. At pH 9, bands at 1743 and 1710 cm(-1) remain which we do not attribute to Ca(2+)/H(+) exchange. We also obtained evidence for a pH-dependent conformational change in beta-sheet or turn structures of the ATPase. With MCCE on the E2P analog E2(TG+MgF(4)(2-)), we assigned infrared bands to specific residues and analyzed whether or not the carbonyl groups of the acidic Ca(2+) ligands are hydrogen bonded. The carbonyl groups of Glu(771), Asp(800), and Glu(908) were found to be hydrogen bonded and will thus contribute to the lower wave number bands. The carbonyl group of some side-chain conformations of Asp(800) is left without a hydrogen-bonding partner; they will therefore contribute to the higher wave number band.
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Affiliation(s)
- Julia Andersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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Kheterpal I, Cook KD, Wetzel R. Hydrogen/deuterium exchange mass spectrometry analysis of protein aggregates. Methods Enzymol 2006; 413:140-66. [PMID: 17046395 DOI: 10.1016/s0076-6879(06)13008-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The elucidation of the structure of amyloid fibrils and related aggregates is an important step toward understanding the pathogenesis of diseases like Alzheimer's disease, which feature protein misfolding and/or aggregation. However, the large size, heterogeneous morphology, and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Using amyloid fibrils and protofibrils of the Alzheimer's plaque peptide amyloid beta as examples, we describe here the use of hydrogen/deuterium exchange methods in conjunction with electrospray ionization mass spectrometry to determine regions of the peptide involved in beta-sheet network when it is incorporated into protein aggregates. The advantages of this method are low sample utilization and high speed. The basic methodology exploits the fact that protons either involved in H-bonded secondary structures or buried in a protein's core structure exchange more slowly with deuterium than do solvent-exposed and non-H-bonded protons. Details of all aspects of this methodology, including sample preparation, data acquisition, and data analysis, are described. These data provide insights into the structures of monomers, protofibrils, and fibrils and to the structural relations among these states.
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Affiliation(s)
- Indu Kheterpal
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
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Krasteva M, Barth A. Structures of the Ca2+-ATPase complexes with ATP, AMPPCP and AMPPNP. An FTIR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1767:114-23. [PMID: 17157262 DOI: 10.1016/j.bbabio.2006.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 11/02/2006] [Accepted: 11/07/2006] [Indexed: 11/17/2022]
Abstract
We studied binding of ATP and of the ATP analogs adenosine 5'-(beta,gamma-methylene)triphosphate (AMPCP) and beta,gamma-imidoadenosine 5'-triphosphate (AMPPNP) to the Ca(2+)-ATPase of the sarcoplasmic reticulum membrane (SERCA1a) with time-resolved infrared spectroscopy. In our experiments, ATP reacted with ATPase which had AMPPCP or AMPPNP bound. These experiments monitored exchange of ATP analog by ATP and phosphorylation to the first phosphoenzyme intermediate Ca(2)E1P. These reactions were triggered by the release of ATP from caged ATP. Only small differences in infrared absorption were observed between the ATP complex and the complexes with AMPPCP and AMPPNP indicating that overall the interactions between nucleotide and ATPase are similar and that all complexes adopt a closed conformation. The spectral differences between ATP and AMPPCP complex were more pronounced at high Ca(2+) concentration (10 mM). They are likely due to a different position of the gamma-phosphate which affects the beta-sheet in the P domain.
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Affiliation(s)
- Maria Krasteva
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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Rodríguez-Casado A, Molina M, Carmona P. Spectroscopic study of conformational changes accompanying self-assembly of HCV core protein. Proteins 2006; 66:110-7. [PMID: 17078073 DOI: 10.1002/prot.21192] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electron microscopy and infrared and Raman spectroscopy have been used here to study the morphology, size distribution, secondary and tertiary structures of protein particles assembled from a truncated hepatitis C virus (HCV) core protein covering the first 120 aa. Particles of pure protein, having similar morphology and size distribution of those of nucleocapsids found in sera from HCV-infected patients, have been visualized for the first time. The secondary structure of these protein particles involve beta-sheet enrichment in relation to its protein monomer. Tertiary/quaternary structure has also been studied using the dynamics of H/D exchange. With this aim infrared spectra were measured as a function of H/D exchange time and subsequently analyzed by principal component analysis and two-dimensional correlation spectroscopy. Temporal dynamics of exchange for these protein particles were as follows: arginine residues exchanged first, followed by turn and unordered structures, followed by beta-sheets which may act as linkers of protein monomers.
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Arkin IT. Isotope-edited IR spectroscopy for the study of membrane proteins. Curr Opin Chem Biol 2006; 10:394-401. [PMID: 16935550 PMCID: PMC7185810 DOI: 10.1016/j.cbpa.2006.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has long been a powerful tool for structural analysis of membrane proteins. However, because of difficulties in resolving contributions from individual residues, most of the derived measurements tend to yield average properties for the system under study. Isotope editing, through its ability to resolve individual vibrations, establishes FTIR as a method that is capable of yielding accurate structural data on individual sites in a protein.
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Affiliation(s)
- Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmund J Safra Campus, Givat-Ram, Jerusalem, Israel.
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36
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Azarkan M, Dibiani R, Goormaghtigh E, Raussens V, Baeyens-Volant D. The papaya Kunitz-type trypsin inhibitor is a highly stable beta-sheet glycoprotein. BIOCHIMICA ET BIOPHYSICA ACTA 2006; 1764:1063-72. [PMID: 16731056 DOI: 10.1016/j.bbapap.2006.02.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/27/2006] [Accepted: 02/03/2006] [Indexed: 11/16/2022]
Abstract
The papaya Kunitz-type trypsin inhibitor, a 24-kDa glycoprotein, was purified to homogeneity. The purified inhibitor stoichiometrically inhibits bovine trypsin in a 1:1 molar ratio. Circular dichroism and infrared spectroscopy analyses demonstrated that the inhibitor contains extensive beta-sheet structures. The inhibitor was found to retain its full inhibitory activity over a broad pH range (1.5-11.0) and temperature (up to 80 degrees C), besides being stable at very high concentrations of strong chemical denaturants (e.g., 5.5 M guanidine hydrochloride). The inhibitor retained its compact structure over the pH range analyzed as shown by 8-anilino-1-naphtalenesulfonic acid binding characteristics, excluding the formation of some relaxed or molten state. Exposure to 2.5 mM dithiothreitol for 120 min caused a 33% loss of the inhibitory activity, while a loss of 75% was obtained in the presence of 20 mM of dithiothreitol during the same time period. A complete loss of the inhibitory activity was observed after incubation with 50 mM dithiothreitol for 5 min. Incubation of the inhibitor with general proteases belonging to different families revealed its extraordinary resistance to proteolysis in comparison with the soybean trypsin inhibitor, the archetypal member of the Kunitz-type inhibitors family. The inhibitor also exhibited a remarkable resistance to proteolytic degradation against pepsin for at least a 24-h incubation period. Instead, the soybean inhibitor was completely degraded after 2 h incubation with this aspartic protease. All these data demonstrated the high stability of the papaya trypsin inhibitor.
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Affiliation(s)
- Mohamed Azarkan
- University of Brussels, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808, route de Lennik, Bz-1070 Brussels, Belgium
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37
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Goormaghtigh E, Ruysschaert JM, Raussens V. Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys J 2006; 90:2946-57. [PMID: 16428280 PMCID: PMC1414549 DOI: 10.1529/biophysj.105.072017] [Citation(s) in RCA: 275] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 12/22/2005] [Indexed: 11/18/2022] Open
Abstract
Fourier-transform infrared spectroscopy is a method of choice for the experimental determination of protein secondary structure. Numerous approaches have been developed during the past 15 years. A critical parameter that has not been taken into account systematically is the selection of the wavenumbers used for building the mathematical models used for structure prediction. The high quality of the current Fourier-transform infrared spectrometers makes the absorbance at every single wavenumber a valid and almost noiseless type of information. We address here the question of the amount of independent information present in the infrared spectra of proteins for the prediction of the different secondary structure contents. It appears that, at most, the absorbance at three distinct frequencies of the spectra contain all the nonredundant information that can be related to one secondary structure content. The ascending stepwise method proposed here identifies the relevance of each wavenumber of the infrared spectrum for the prediction of a given secondary structure and yields a particularly simple method for computing the secondary structure content. Using the 50-protein database built beforehand to contain as little fold redundancy as possible, the standard error of prediction in cross-validation is 5.5% for the alpha-helix, 6.6% for the beta-sheet, and 3.4% for the beta-turn.
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Affiliation(s)
- Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Université Libre de Bruxelles, Brussels, Belgium.
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38
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Vanderkooi JM, Dashnau JL, Zelent B. Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:214-33. [PMID: 15927875 DOI: 10.1016/j.bbapap.2005.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 02/15/2005] [Accepted: 03/09/2005] [Indexed: 11/22/2022]
Abstract
Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.
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Affiliation(s)
- Jane M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, 19104-6059, USA.
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39
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Ortiz M, Sanoguet Z, Hu H, Chazin WJ, McMurray CT, McMurray C, Salisbury JL, Pastrana-Rios B. Dynamics of Hydrogen−Deuterium Exchange in Chlamydomonas Centrin. Biochemistry 2005; 44:2409-18. [PMID: 15709753 DOI: 10.1021/bi0484419] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlamydomonas reinhardtii centrin is a 169-amino acid residue calcium binding protein belonging to the EF-hand protein superfamily. Centrin is associated with the microtubule organizing center (MTOC) in all eukaryotes, and in Chlamydomonas, centrin is a component of the flagellar basal body apparatus. Recombinant full-length centrin, calmodulin, and terminal domain fragments [Ccen-N (residues 1-94) and Ccen-C (residues 99-169)] were used to examine hydrogen-deuterium (H --> D) exchange dynamics using combined attenuated total reflectance (ATR) Fourier transform-infrared (FT-IR) spectroscopy, curve fit, and two-dimensional correlation analysis. Analysis of the Ccen-N and Ccen-C fragments allowed separation of domain specific solvent exchange events and together with analysis of the full-length proteins provides novel insight into domain accessibility to the aqueous environment and the internal dynamics of the protein.
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Affiliation(s)
- Mildred Ortiz
- Department of Chemistry and Center for Protein Structure Function and Dynamics, University of Puerto Rico, Mayagüez Campus, P.O. Box 9019, Mayagüez, Puerto Rico 00681-9019
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40
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Busenlehner LS, Armstrong RN. Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 2005; 433:34-46. [PMID: 15581564 DOI: 10.1016/j.abb.2004.09.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 09/02/2004] [Indexed: 11/25/2022]
Abstract
Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.
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Affiliation(s)
- Laura S Busenlehner
- Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0416, USA.
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