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Environmental factors drive microbial succession and huangjiu flavor formation during raw wheat qu fermentation. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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2
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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3
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Horchani H, Bussières S, Cantin L, Lhor M, Laliberté-Gemme JS, Breton R, Salesse C. Enzymatic activity of Lecithin:retinol acyltransferase: a thermostable and highly active enzyme with a likely mode of interfacial activation. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1128-36. [PMID: 24613493 PMCID: PMC4469483 DOI: 10.1016/j.bbapap.2014.02.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 01/28/2023]
Abstract
Lecithin:retinol acyltransferase (LRAT) plays a major role in the vertebrate visual cycle. Indeed, it is responsible for the esterification of all-trans retinol into all-trans retinyl esters, which can then be stored in microsomes or further metabolized to produce the chromophore of rhodopsin. In the present study, a detailed characterization of the enzymatic properties of truncated LRAT (tLRAT) has been achieved using in vitro assay conditions. A much larger tLRAT activity has been obtained compared to previous reports and to an enzyme with a similar activity. In addition, tLRAT is able to hydrolyze phospholipids bearing different chain lengths with a preference for micellar aggregated substrates. It therefore presents an interfacial activation property, which is typical of classical phospholipases. Furthermore, given that stability is a very important quality of an enzyme, the influence of different parameters on the activity and stability of tLRAT has thus been studied in detail. For example, storage buffer has a strong effect on tLRAT activity and high enzyme stability has been observed at room temperature. The thermostability of tLRAT has also been investigated using circular dichroism and infrared spectroscopy. A decrease in the activity of tLRAT was observed beyond 70°C, accompanied by a modification of its secondary structure, i.e. a decrease of its α-helical content and the appearance of unordered structures and aggregated β-sheets. Nevertheless, residual activity could still be observed after heating tLRAT up to 100°C. The results of this study highly improved our understanding of this enzyme.
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Affiliation(s)
- Habib Horchani
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Sylvain Bussières
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Line Cantin
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Mustapha Lhor
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Laliberté-Gemme
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Rock Breton
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Christian Salesse
- CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHU de Québec, Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada; Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada.
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4
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Zaroog MS, Tayyab S. Halogenol- versus alkanol-induced structural transitions of acid-denatured glucoamylase: Characterization of alcohol-induced states. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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Affiliation(s)
- Guy A Hembury
- Japan Science and Technology Agency and Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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8
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Nakahashi A, Taniguchi T, Miura N, Monde K. Stereochemical studies of sialic acid derivatives by vibrational circular dichroism. Org Lett 2007; 9:4741-4. [PMID: 17935341 DOI: 10.1021/ol702042m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Systematic VCD studies of N-acetylneuraminic acid (Neu5Ac), a recognition-related unique carbohydrate, were performed for the first time. Two pairs of anomeric isomers regarding a quaternary C2 asymmetric carbon of Neu5Ac derivatives were synthesized. VCD spectral patterns around the ester carbonyl region, as well as other Mid-IR regions, would be practical markers to distinguish the C2 stereochemistry.
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Affiliation(s)
- Atsufumi Nakahashi
- Graduate School of Advanced Life Science, Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Kita-ku, Sapporo, Japan
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Taniguchi T, Monde K. Spectrum–Structure Relationship in Carbohydrate Vibrational Circular Dichroism and Its Application to Glycoconjugates. Chem Asian J 2007; 2:1258-66. [PMID: 17768735 DOI: 10.1002/asia.200700180] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Preliminary reports of the nature of the vibrational circular dichroism (VCD) peak at around 1145 cm(-1), which is characteristic of axial glycosidic sugars and is called the glycoside band (J. Am. Chem. Soc. 2004, 126, 9496), have been thoroughly examined. Through systematic carbohydrate measurements, it was found that the sign of the glycoside band reflects not only the anomeric configuration but also the pyranose conformation. Isotope and theoretical studies characterized its vibrational mode as C1-H1 deformation coupled with C1-O1 stretching, which indicates its applicability to more-complicated glycoconjugates. In this study, for the first time, carbohydrate VCD spectra were reliably predicted by means of density functional theory (DFT) calculations. The VCD technique was applied to glycopeptides, and simultaneous analysis of both the carbohydrate and aglycan parts was carried out.
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Affiliation(s)
- Tohru Taniguchi
- Laboratory of Advanced Chemical Biology, Graduate School of Advanced Life Science, Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Kita-ku, Sapporo 001-0021, Japan
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Taniguchi T, Tone I, Monde K. Observation and characterization of a specific vibrational circular dichroism band in phenyl glycosides. Chirality 2007; 20:446-53. [PMID: 17853396 DOI: 10.1002/chir.20465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Application of vibrational circular dichroism (VCD) spectroscopy to structural analysis of carbohydrates has recently progressed. However, few studies on glycoconjugates VCD have thus far been reported, despite the fact that naturally occurring carbohydrates exist as various glycoconjugates. To further explore the application of the VCD technique, we have measured a series of aromatic glycosides and found that axial aromatic glycosides exhibited a negative band at around 1230 cm(-1) while equatorial ones showed flat features in this region. This is the first structure-spectra relationship on glycoconjugate VCD that distinguishes the stereochemistry of the sugar anomers. Several model compounds were prepared and their vibrational properties calculated by using the density functional theory (DFT) method, which assigned the vibrational mode of this band based on the stretching motion of the glycosidic oxygen and aromatic carbon. This concept that aglycan parts can reflect stereochemical information of sugar moieties may encourage further VCD studies on glycoconjugates to realize practical structural analysis of carbohydrates.
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Affiliation(s)
- Tohru Taniguchi
- Laboratory of Advanced Chemical Biology, Graduate School of Advanced Life Science, Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Kita-ku, Sapporo 001-0021, Japan
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11
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Roberts AG, Atkins WM. Energetics of heterotropic cooperativity between alpha-naphthoflavone and testosterone binding to CYP3A4. Arch Biochem Biophys 2007; 463:89-101. [PMID: 17459328 PMCID: PMC2062487 DOI: 10.1016/j.abb.2007.03.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 03/09/2007] [Accepted: 03/10/2007] [Indexed: 11/17/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of a majority of drugs. Heterotropic cooperativity of drug binding to CYP3A4 was examined with the flavanoid, alpha-naphthoflavone (ANF) and the steroid, testosterone (TST). UV-vis and EPR spectroscopy of CYP3A4 show that ANF binding to CYP3A4 occurs with apparent negative cooperativity and that there are at least two binding sites: (1) a relatively tight spin-state insensitive binding site (CYP.ANF) and (2) a relatively low affinity spin-state sensitive binding site (CYP.ANF.ANF). Since binding to the spin-state insensitive binding site is considerably tighter for ANF than TST, the spin-state insensitive binding site could be occupied by ANF, while titrating TST at the other site(s). The spin-state insensitive binding site of ANF appears to compete with the spin-state insensitive binding site of TST. The formation of the spin-state insensitive CYP.ANF complex is strongly temperature dependent, when compared to the formation of the CYP.TST complex, suggesting that the formation of the CYP3A4.ANF complex leads to long-range conformational changes within the protein. When the CYP.ANF complex is titrated with TST, the formation of CYP.ANF.TST is favored by 3:1 over the formation of CYP.TST.TST, suggesting that there is an allosteric interaction between ANF and TST. A model of heterotropic cooperativity of CYP3A4 is presented, where the spin-state insensitive binding of ANF occurs at the same peripheral binding site of CYP3A4 as TST.
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Affiliation(s)
- Arthur G. Roberts
- Department of Medicinal Chemistry; Box 357610, University of Washington, Seattle, WA 98195-7610
| | - William M. Atkins
- Department of Medicinal Chemistry; Box 357610, University of Washington, Seattle, WA 98195-7610
- Corresponding Author: Tel: (206) 685-0379; FAX: (206) 685-3252;
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Taniguchi T, Monde K. Chiroptical Analysis of Glycoconjugates by Vibrational Circular Dichroism (VCD). TRENDS GLYCOSCI GLYC 2007. [DOI: 10.4052/tigg.19.147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Shanmugam G, Polavarapu PL. Structures of intact glycoproteins from vibrational circular dichroism. Proteins 2006; 63:768-76. [PMID: 16498615 DOI: 10.1002/prot.20884] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Vibrational circular dichroism (VCD) spectra for the glycoproteins alpha1-acid glycoprotein (AGP) and bovine submaxillary mucin (BSM), have been measured in D2O solutions and for the films prepared from aqueous (H2O) buffer solutions in the 1800 to 900 cm(-1) region. The solution VCD results revealed that AGP has beta-sheet structure, along with a significant amount of alpha-helix as evidenced from a W pattern in the amide I region. The VCD of BSM solution suggested a polyproline II type structure, characterized by the appearance of strong negative couplet in the amide I region. The film VCD results on AGP and BSM suggested that the secondary structures of polypeptide fold in the film state are similar to those in the solution. The absence of any significant film VCD in the low frequency region (1200-900 cm(-1)), suggested that the dominant linkage for carbohydrate residues is likely to be a beta linkage. VCD spectroscopy gains importance in the secondary structural analysis of polypeptide fold in glycoproteins due to the absence of interfering VCD from the carbohydrate residues in the conformationally sensitive amide I region. Also, film VCD studies permit measurements in the low wavenumber region (1200-900 cm(-1)) that reveal the dominant type of linkage for carbohydrate residues. Such clear structural information is unlike that from ECD, where ECD bands of acylated amino sugar residues interfere with those of polypeptide backbone in the conformationally sensitive far-UV region.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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Jafari-Aghdam J, Khajeh K, Ranjbar B, Nemat-Gorgani M. Deglycosylation of glucoamylase from Aspergillus niger: effects on structure, activity and stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1750:61-8. [PMID: 15886078 DOI: 10.1016/j.bbapap.2005.03.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 03/17/2005] [Accepted: 03/22/2005] [Indexed: 11/29/2022]
Abstract
A comparative structure-function study was performed to establish possible roles of carbohydrates in stabilization of glycoproteins, using glucoamylase (GA) as a model system. In addition to kinetic properties, stability toward elevated temperatures, extremes of pH, high salt concentrations together with circular dichroism, intrinsic/extrinsic fluorescence studies, proteolysis and affinity for interaction with hydrophobic ligands were investigated. Related to all the main properties examined, with one exception, glycosylation provided improvement in functional characteristics of the enzyme, especially in relation to its thermostability. Results are explained in terms of provision of stabilizing intermolecular interactions by the sugar molecules. The improvement in protein rigidity together with reduction of surface hydrophobicity appear to be especially important in relation to prevention of aggregation, an important mechanism of irreversible thermoinactivation, occurring at elevated temperatures.
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Affiliation(s)
- Javad Jafari-Aghdam
- Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran
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15
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Urbanová M, Setnicka V, Král V, Volka K. Noncovalent interactions of peptides with porphyrins in aqueous solution: conformational study using vibrational CD spectroscopy. Biopolymers 2002; 60:307-16. [PMID: 11774233 DOI: 10.1002/1097-0282(2001)60:4<307::aid-bip9992>3.0.co;2-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Noncovalent interactions of poly(L-lysine) (PL), oligopeptides L-lysyl-L-alanyl-L-alanine and (L-lysyl-L-alanyl-L-alanine)(2) with meso-tetrakis(4-sulfonatophenyl)porphine (TPPS), and poly(L-glutamic acid) (PLGA) with meso-tetrakis(1-methyl-4-pyridyl)porphine tetra-p-tosylate (TMPyP) in aqueous solutions have been studied using combination of spectroscopic methods: Vibrational circular dichroism (VCD) spectroscopy in the mid-infrared region provides a direct information on conformational changes of the polypeptides and oligopeptides caused by interactions with porphyrins; ultraviolet-visible absorption, fluorescence, and electronic circular dichroism (ECD) reveal the aggregation characterization of the porphyrin part of the complexes. Interactions of TPPS with tripeptide, hexapeptide, and PL containing about ten amino acid residues in the molecular chain are accompanied with the changes of VCD patterns in the amide I' region. In these cases, the conformation of the oligopeptide part of complexes is obviously influenced by interactions with TPPS and partial changes of random coil structure are observed in VCD. When PL was composed of the hundreds of lysine residues, just a weak intensity decrease was detected and the shape of VCD spectrum typical for the random coil structure was preserved. As follows from the uv-vis absorption and fluorescence spectra, porphyrin molecules are attached to peptides by electrostatic interaction as a monomer or dimer and interaction between porphyrin and peptide depends on the polypeptide chain length. For the PLGA-TMPyP system with PLGA containing from tens to hundreds of glutamic acid residues in the chain, the VCD spectra were unchanged when TMPyP was presented in the aqueous solution of PLGA and random coil conformation of PLGA-TMPyP aggregates was preserved.
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Affiliation(s)
- M Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Technická 5, 166 28 Prague 6, Czech Republic.
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Golczak M, Kicinska A, Bandorowicz-Pikula J, Buchet R, Szewczyk A, Pikula S. Acidic pH‐induced folding of annexin VI is a prerequisite for its insertion into lipid bilayers and formation of ion channels by the protein molecules. FASEB J 2001. [DOI: 10.1096/fsb2fj000523fje] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marcin Golczak
- Department of Cellular Biochemistry Nencki Institute of Experimental Biology 3 Pasteur St. 02-093 Warsaw Poland
| | - Anna Kicinska
- Department of Cellular Biochemistry Nencki Institute of Experimental Biology 3 Pasteur St. 02-093 Warsaw Poland
| | - Joanna Bandorowicz-Pikula
- Department of Cellular Biochemistry Nencki Institute of Experimental Biology 3 Pasteur St. 02-093 Warsaw Poland
| | - Rene Buchet
- Laboratoire Physico-Chimie Biologique Université Claude Bernard-Lyon I, UFR de Chimie-Biochimie CNRS UMR 5013 Villeurbanne France
| | - Adam Szewczyk
- Department of Cellular Biochemistry Nencki Institute of Experimental Biology 3 Pasteur St. 02-093 Warsaw Poland
| | - Slawomir Pikula
- Department of Cellular Biochemistry Nencki Institute of Experimental Biology 3 Pasteur St. 02-093 Warsaw Poland
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Urbanova M, Setnicka V, Volka K. Measurements of concentration dependence and enantiomeric purity of terpene solutions as a test of a new commercial VCD spectrometer. Chirality 2000; 12:199-203. [PMID: 10790190 DOI: 10.1002/(sici)1520-636x(2000)12:4<199::aid-chir6>3.0.co;2-l] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Vibrational circular dichroism (VCD) spectra of (+)-alpha-pinene solutions in carbon tetrachloride have been measured in the range of volume fractions 5-100% (v/v) in the mid-infrared region. The concentration dependence measured was statistically analyzed with the aim of obtaining a reliable correlation between the VCD band areas and the concentrations of individual enantiomers. The quality of the spectra was estimated by means of noise spectra which were defined as half the difference of the two following blocks of scans. In addition to this, the enantiomeric purity was studied. This study was carried out for both (+)- and (-)-alpha-pinene enantiomers in the range of the percent enantiomeric excess in the interval 10-100%. The relationship between VCD intensity and enantiomeric purity was determined by least-square regression and statistically evaluated. All measurements performed in this study were intended as a basic tool for testing of a new commercial VCD setup from Bruker. Copyright 2000 Wiley-Liss, Inc.
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Affiliation(s)
- M Urbanova
- Department of Physics and Measurement, Institute of Chemical Technology at Prague, Czech Republic
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Yoder G, Pancoska P, Keiderling TA. Characterization of alanine-rich peptides, Ac-(AAKAA)n-GY-NH2 (n = 1-4), using vibrational circular dichroism and Fourier transform infrared. Conformational determination and thermal unfolding. Biochemistry 1997; 36:15123-33. [PMID: 9398240 DOI: 10.1021/bi971460g] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Vibrational circular dichroism (VCD) and Fourier transform IR (FTIR) were measured for a series of short alanine-based peptides having the general formula Ac-(AAKAA)n-GY-NH2 (n = 1-4) from 5 to 50 degrees C in D2O and at room temperature in both TFE and H2O. In both of these latter solvents, the dominant structural form at the lowest temperature for the longest oligomers is alpha-helical. The same is true for the n = 4 peptide in D2O, but under these more dilute aqueous conditions, the shorter (n = 3) peptides have mixed helix-coil structures and the n = 1 and 2 peptides are random coils. The VCD data do not support the 310-helix as a dominant contributor to the conformation of these oligomers in any of these solvents. These vibrational spectral data are consistent with lower-concentration electronic CD results and additionally indicate increased helical stability at higher concentrations. VCD amide I data for the 22mer (n = 4) in D2O indicate that the peptide undergoes a transition from a highly helical conformation at 5 degrees C to a dominant random coil structure at approximately 45 degrees C with a Tm of approximately 25 degrees C (effective midpoint). Factor analysis of the thermal data showed that three principal components were required to describe both the VCD and FTIR data for the n = 4 peptide in D2O. The transition is characterized by a gradual loss of contribution from a spectral component representing the alpha-helical fraction. The third component is evidence of an optically detected intermediate conformation best viewed as a mixed coil-helix structure resulting from end fraying of the helical peptide as the temperature is increased. The nature of the junction between the interior helix and frayed ends is not determined by these data and could involve local (phi and psi) angles mimicking a 310-helix that would provide consistency with ESR and NMR results from Millhauser and co-workers.
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Affiliation(s)
- G Yoder
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061, USA
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Dong A, Kery V, Matsuura J, Manning MC, Kraus JP, Carpenter JF. Secondary structure of recombinant human cystathionine beta-synthase in aqueous solution: effect of ligand binding and proteolytic truncation. Arch Biochem Biophys 1997; 344:125-32. [PMID: 9244389 DOI: 10.1006/abbi.1997.0202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The secondary structural composition and substrate-induced conformational changes of recombinant human cystathionine beta-synthase (CBS) in aqueous solution have been investigated in its full-length form (tetramer of 63-kDa subunits) by Fourier transform infrared (FT-IR) and circular dichroism (CD) spectroscopies. In addition, structural comparison of a proteolytic truncated form (dimer of 45-kDa subunits) to that of the full-length enzyme has also been carried out. Second-derivative and Fourier self-deconvolutional enhanced infrared spectra revealed amide I band components ascribed to beta-sheet (1689, 1638, and 1627 cm(-1)), alpha-helix (1658 cm(-1)), beta-turn (1679 and 1668 cm(-1)), and unordered (1651 cm(-1)) structures in the spectra of the full-length enzyme. Quantitative analysis of FT-IR and CD spectra reveals that the full-length enzyme consists of about 48-53% beta-sheet, 25-30% alpha-helix, 8-10% turn, and 10-19% unordered structures. Under constraint of the spectroscopic data, theoretical prediction of locations of these secondary structural elements using Garnier's method shows that human CBS may contain a beta-sheet/alpha-helix/beta-sheet core structure. Second-derivative spectrum of the truncated enzyme exhibited all the major spectral features that are present in the full-length enzyme, indicating a preservation of the core structure of the enzyme. Significant differences were observed between the infrared spectra of the enzymes with or without the substrate, serine, indicating a substrate-induced conformational change in the enzyme, which did not result in a change in overall composition of secondary structural content based on quantitative analysis of FT-IR and far-UV CD spectra.
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Affiliation(s)
- A Dong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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Pancoska P, Fabian H, Yoder G, Baumruk V, Keiderling TA. Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example. Biochemistry 1996; 35:13094-106. [PMID: 8855946 DOI: 10.1021/bi961178u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel descriptor for protein structure is examined here that goes beyond predictions of the average fractional components (FC) of a few conformational types and represents the number and interconnection of segments of continuous, well-defined secondary structural elements such as alpha-helices and beta-sheets. This matrix descriptor can be predicted from optical spectra using neural network methods. The new matrix plus traditional FC descriptors can be quickly and generally obtained to provide a level of detail not previously derived from optical spectra and a discrimination between proteins that might otherwise be viewed as being very similar using just the FC descriptor. As an example of its potential utilization, this matrix descriptor approach was applied to an analysis of both the native state and the reversible thermal denaturation of ribonuclease T1 in H2O. Analyses of the FTIR spectral data indicate initial loss of the major helical segment at 50-55 degrees C but with little accompanying change in the number of sheet segments or the sheet FC values. Circular dichroism (CD) and vibrational CD data are also used to support this interpretation based on FC changes with temperature. Parallel analysis of the corresponding data for this protein in D2O demonstrates that the method is sensitive to the match between the degree of H-D exchange used to prepare samples for the unknown and the reference data set.
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Affiliation(s)
- P Pancoska
- Department of Chemistry, University of Illinois at Chicago 60607-7061, USA
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21
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Conformational study of some milk proteins. Comparison of the results of electronic circular dichroism and vibrational circular dichroism. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0302-4598(96)01932-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Jiang H, Song Z, Ling M, Yang S, Du Z. FTIR studies of recombinant human granulocyte-macrophage colony-stimulating factor in aqueous solutions: secondary structure, disulfide reduction and thermal behavior. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1294:121-8. [PMID: 8645729 DOI: 10.1016/0167-4838(96)00002-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR) has been used to investigate the secondary structure, disulfide reduction and thermal behavior of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) in aqueous solutions. The contributions of amino-acid side-chain groups to the amide I bands of rhGM-CSF in H2O and in D2O solutions were carefully scrutinized, as 40% of the total 127 amino-acid residues of rhGM-CSF is side-chain absorptive (asparagine, glutamine, etc.). The FTIR results indicated that rhGM-CSF is composed of 46% alpha-helix, 7% beta-sheet, 23% turn and 24% loop/irregular structures which are in good agreement with the X-ray diffractional data. Reduction of rhGM-CSF with dithiothreitol caused apparent unfolding of the native conformation followed by the time-dependent increase of beta-aggregation bands which arose at 1622 and 1693 cm(-1) in H2O, 1613 and 1684 cm(-1) in D2O solutions. The result also showed that tertiary structure can change independently of the secondary structure. Thermal denaturation of rhGM-CSF took place at 55 to 70 degrees C and the denatured protein adopted an irregular structure as revealed by the FTIR spectra. The thermal denaturation did not show the formation of intermolecular beta-aggregates which is typical of most thermal denatured proteins. Moreover, it is partly reversible, indicating a special thermal stability of rhGM-CSF.
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Affiliation(s)
- H Jiang
- National Center of Biomedical Analysis, Beijing, People's Republic of China
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23
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Chan HK, Ongpipattanakul B, Au-Yeung J. Aggregation of rhDNase occurred during the compression of KBr pellets used for FTIR spectroscopy. Pharm Res 1996; 13:238-42. [PMID: 8932443 DOI: 10.1023/a:1016091030928] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE To determine if a protein changes when it is compressed into a KBr pellet for FTIR spectroscopy measurement in the solid state, using recombinant human deoxyribonuclease I (rhDNase) as an example. METHODS Lyophilized rhDNase with KBr compressed at different pressures were analyzed by FTIR spectroscopy, size exclusion HPLC and enzymatic activity assay. Different protein/KBr weight ratios and residual water contents were studied for their possible effects on aggregation. RESULTS Depending on the pressure, a loss of enzymatic activity accompanied by an increase in soluble high molecular weight aggregates of the protein (up to approximately 15%) was demonstrated. Aggregation was reduced to less than 5% by a suitable dilution of the protein in KBr (1 in 1000). In contrast, water content variability (1-11 wt. %) did not affect aggregation. CONCLUSIONS The findings emphasize the importance to examine for protein integrity when using the KBr method for FTIR sample preparation. Protein aggregation may be minimized by optimizing the sample preparation condition such as changing the protein/KBr weight ratio.
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Affiliation(s)
- H K Chan
- Department of Pharmaceutical Research and Development, Genentech, Inc., South San Francisco, California 94080, USA
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24
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Raimbault C, Couthon F, Vial C, Buchet R. Effects of pH and KCl on the conformations of creatine kinase from rabbit muscle. Infrared, circular dichroic and fluorescence studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 234:570-8. [PMID: 8536705 DOI: 10.1111/j.1432-1033.1995.570_b.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The activity loss of creatine kinase (CK), observed at low pH (midpoint was 4.8) corresponded to the monomerization of the dimeric protein and was correlated with structural changes. The acid-induced unfolding was not complete at this pH, as probed by circular dichroic (CD) and fluorescence methods. Further decrease of pH, led to a second transition (midpoint was pH 3.5). The loss of activity was irreversible at pH 4.8 (< 20% native activity was recovered) while it was almost fully reversible (> 90% of native activity was recovered) for the enzyme incubated at pH 0.9-2.5. The amount of intermolecular beta-sheets (monitored with the 1620 cm-1 infrared component band) was maximal when the enzyme was incubated at pH 4.8, as a consequence of protein aggregation, while it was minimal at extremes of pH and at low ionic strength. Acid-induced and alkaline-induced denaturations promoted different structural changes, leading to distinct partially unfolded conformational states. The addition of KCl (from 0.05 M to 0.5 M) to an acidic solution of monomeric creatine kinase (pH 1.6) resulted in a highly cooperative transition from the partially unfolded conformation (UA) to the more compact conformation (A) with the properties of a molten globule, as probed by CD spectra and by fluorescence. The formation of intermolecular beta-sheets in the compact conformation was observed by infrared spectroscopy, indicating formation of unstable aggregates.
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Affiliation(s)
- C Raimbault
- Laboratoire de Physico-Chimie Biologique, Université Claude Bernard, Lyon 1, CNRS URA, France
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25
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Pancoska P, Bitto E, Janota V, Urbanova M, Gupta VP, Keiderling TA. Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure. Protein Sci 1995; 4:1384-401. [PMID: 7670380 PMCID: PMC2143158 DOI: 10.1002/pro.5560040713] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide II to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and II bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for alpha-helix, and the combined VCD (amide I' + II) predicts the beta-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.
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Affiliation(s)
- P Pancoska
- Department of Chemistry, University of Illinois at Chicago 60607-7061, USA
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26
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de La Fournière L, Nosjean O, Buchet R, Roux B. Thermal and pH stabilities of alkaline phosphatase from bovine intestinal mucosa: a FTIR study. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1248:186-92. [PMID: 7748901 DOI: 10.1016/0167-4838(95)00020-u] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The inactivation of alkaline phosphatase (AP) from bovine intestinal mucosa caused by lowering the p2H from 10.4 to 5.4 or by increasing the temperature from 25 degrees C to 70 degrees C were not followed by significant FTIR changes, indicating that the native conformation of AP was preserved under these conditions. Further decrease of p2H from 5.4 to 3.4 leaded to small infrared spectral changes of AP in the amide I' and amide II regions that were similar to the infrared spectral changes of AP induced by raising the temperature from 70 degrees C to 80 degrees C. The increase of temperature from 70 degrees C to 80 degrees C promoted the formation of intermolecular beta-sheets at the expense of some alpha-helix structures as evidenced by the appearance of the 1684 cm-1 and 1620 cm-1 component bands and the disappearance of the 1651-1657 cm-1 component band. This conformational change was followed by a sharp increase of the 2H/H exchange rate. CD spectra confirmed the FTIR results and were very sensitive to the variation of alpha-helix content while FTIR spectra were more receptive to the changes of beta-sheet structures.
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Affiliation(s)
- L de La Fournière
- Université Claude Bernard-LYON I, CNRS URA 1535, Laboratoire de Physico-Chimie Biologique, Villeurbanne, France
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27
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Dong A, Prestrelski SJ, Allison SD, Carpenter JF. Infrared spectroscopic studies of lyophilization- and temperature-induced protein aggregation. J Pharm Sci 1995; 84:415-24. [PMID: 7629730 DOI: 10.1002/jps.2600840407] [Citation(s) in RCA: 383] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent studies have clearly demonstrated that Fourier transform IR spectroscopy can be a powerful tool for the study of protein stabilization during freeze-drying and for optimizing approaches to prevent lyophilization-induced protein aggregation. The purpose of the current review is to provide an overview of these topics, as well as an introduction to the study of protein secondary structure with IR spectroscopy. We will start with a general summary of the theories and practices for processing and interpreting protein IR spectra. We will then review the current literature on the use of IR spectroscopy to study protein structure and the effects of stabilizers during lyophilization. Next we will concentrate specifically on protein aggregation. The bulk of the research and the key assignments of spectral features in protein aggregates come from studies of the effects of high and low temperature on proteins. Therefore, we will first consider this topic. Finally, we will summarize the recent theoretical and applied work on lyophilization-induced aggregation.
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Affiliation(s)
- A Dong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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28
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Bell AF, Ford SJ, Hecht L, Wilson G, Barron LD. Vibrational Raman optical activity of glycoproteins. Int J Biol Macromol 1994; 16:277-8. [PMID: 7893631 DOI: 10.1016/0141-8130(94)90033-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This paper reports the first vibrational Raman optical activity (ROA) spectrum of a glycoprotein. The sample, orosomucoid (alpha 1-acid glycoprotein), shows ROA bands characteristic of a high beta-sheet content together with new bands which could be specific for the carbohydrate and its association with the protein. Our results suggest that ROA spectra of intact glycoproteins may contain information about both protein and carbohydrate conformation and the mutual influence on each other's stability and conformation.
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Affiliation(s)
- A F Bell
- Chemistry Department, The University, Glasgow, UK
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29
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Keiderling TA, Wang B, Urbanova M, Pancoska P, Dukor RK. Empirical studies of protein secondary structure by vibrational circular dichroism and related techniques. Alpha-lactalbumin and lysozyme as examples. Faraday Discuss 1994:263-85; discussion 311-26. [PMID: 7549541 DOI: 10.1039/fd9949900263] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Vibrational circular dichroism (VCD) has been shown to be sensitive to secondary structure in proteins and peptides and has been used as the basis for quantitative secondary-structure-prediction algorithms. However, the accuracy of these algorithms is not matched by the apparent qualitative sensitivity of the VCD spectra. This report provides examples of the use of VCD to follow structural change spectrally and to clarify the qualitative nature of the structural changes underlying the spectral variation. The VCD spectra and the complementary UV electronic CD (ECD) and FTIR spectra of alpha-lactalbumin (LA) have been studied as a function of pH, denaturation, Ca2+ ion and solvent conditions for several species. Spectral data for lysozyme were compared with those of LA because of their very similar crystal structures. In fact, these proteins in D2O-based pH 7 solution have quite different spectra using these optical techniques. Even for the LA proteins, the human differs from the bovine and goat species. Furthermore, under low pH conditions, where the LAs are in a reversibly denatured, molten globule form, the spectra are more similar, species variation is minimal and the spectral differences from lysozyme are in fact smaller. Our data are consistent with native, pH 7, alpha-lactalbumin having a less well organized structure than lysozyme, possibly in a dynamic sense. Conversely, in the low-pH, molten globule form of LA, tertiary structure is lost which could relax constraints that might distort the helical segments in the native form. The differences between the interpretation of our results and those from X-ray and NMR data may be due to motional sampling of various geometries in LA which all contribute to the spectral signatures seen in optical spectra but whose contributions are washed out in NMR or frozen out in the crystal structure. Part of this flexibility may relate to the rather large 3(10)-helical content in the LA protein structure. Fluctionality may have specific functional effects, perhaps allowing LA to bind better to beta-galactosyl transferase and form the biologically active lactose synthetase complex.
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Affiliation(s)
- T A Keiderling
- Department of Chemistry, University of Illinois at Chicago m/c 111 60607-7061, USA
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