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Cao J, Geng Z, Ma X, Wen J, Yin Y, Wang Z. Evidence for inhibition of HIF-1α prolyl hydroxylase 3 activity by four biologically active tetraazamacrocycles. Org Biomol Chem 2012; 10:3913-23. [PMID: 22481471 DOI: 10.1039/c2ob07076f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Hypoxia inducible factor 1 (HIF-1) is central to the hypoxic response in mammals. HIF-1α prolyl hydroxylase 3 (PHD3) degrades HIF through the hydroxylation of HIF-1α. Inhibition of PHD3 activity is crucial for up-regulating HIF-1α levels, thereby acting as HIF-dependent diseases therapy. Macrocyclic polyamines which display high stability on iron-chelating may well inhibit the enzyme activity. Thus inhibition and interaction on catalytic PHD3 by four biologically active tetraazamacrocycles (1-4), which have two types of parent rings to chelate iron(ii) dissimilarly, were studied. The apparent IC(50) values of 2.56, 1.91, 5.29 and 2.44 μM, respectively, showed good inhibition potency of the four compounds. K(I) values were 7.86, 3.69, 1.59 and 2.92 μM for 1-4, respectively. Different inhibition actions of the two groups of compounds were identified. Circular dichroism (CD) and fluorescence spectrometries proved that one type of compound has significant effects on protein conformation while another type does not. Computational methodology was constructed to employ the equilibrium geometry of enzyme active site with the presence of substrate competitive inhibitor. Iron(ii) coordination in the active site by inhibitors of this kind induces conformational change of the enzyme and blocks substrate binding.
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Affiliation(s)
- Jing Cao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P R China
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2
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3
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Sanyal SC, Bhattacharyya D, Das Gupta C. The folding of dimeric cytoplasmic malate dehydrogenase. Equilibrium and kinetic studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3856-66. [PMID: 12153583 DOI: 10.1046/j.1432-1033.2002.03085.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Porcine heart cytoplasmic malate dehydrogenase (s-MDH) is a dimeric protein (2 x 35 kDa). We have studied equilibrium unfolding and refolding of s-MDH using activity assay, fluorescence, far-UV and near-UV circular dichroism (CD) spectroscopy, hydrophobic probe-1-anilino-8-napthalene sulfonic acid binding, dynamic light scattering, and chromatographic (HPLC) techniques. The unfolding and refolding transitions are reversible and show the presence of two equilibrium intermediate states. The first one is a compact monomer (MC) formed immediately after subunit dissociation and the second one is an expanded monomer (ME), which is little less compact than the native monomer and has most of the characteristic features of a 'molten globule' state. The equilibrium transition is fitted in the model: 2U <--> 2M(E) <--> 2M(C) <--> D. The time course of kinetics of self- refolding of s-MDH revealed two parallel folding pathways [Rudolph, R., Fuchs, I. & Jaenicke, R. (1986) Biochemistry 25, 1662-1669]. The major pathway (70%) is 2U-->2M*-->2M-->D, the rate limiting step being the isomerization of the monomers (K1 = 1.7 x 10(-3) s(-1)). The minor pathway (30%) involves an association step leading to the incorrectly folding dimers, prior to the very slow D*-->D folding step. In this study, we have characterized the folding-assembly pathway of dimeric s-MDH. Our kinetic and equilibrium experiments indicate that the folding of s-MDH involves the formation of two folding intermediates. However, whether the equilibrium intermediates are equivalent to the kinetic ones is beyond the scope of this study.
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Affiliation(s)
- Suparna C Sanyal
- Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, Kolkata, India.
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4
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Sheehan D, Carey K, O'Sullivan S. Design of emulsification peptides. ADVANCES IN FOOD AND NUTRITION RESEARCH 1998; 42:93-129. [PMID: 9597726 DOI: 10.1016/s1043-4526(08)60094-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- D Sheehan
- Department of Biochemistry, University College, Cork, Ireland
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5
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Fiori S, Mammi S, Peggion E, Rovero P, Pegoraro S, Revoltella RP. Conformation of four peptides corresponding to the α-helical segments of human GM–CSF. J Pept Sci 1997. [DOI: 10.1002/(sici)1099-1387(199709)3:5<336::aid-psc109>3.0.co;2-t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Fiori S, Mammi S, Peggion E, Rovero P, Pegoraro S, Revoltella RP. Conformation of four peptides corresponding to the alpha-helical segments of human GM-CSF. J Pept Sci 1997; 3:336-46. [PMID: 9391908 DOI: 10.1002/(sici)1099-1387(199709)3:5%3c336::aid-psc109%3e3.0.co;2-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The conformation of segments corresponding to the four alpha-helical stretches found in human granulocyte-macrophage colony-stimulating factor was studied in water solution in the presence of different amounts of 2,2,2-trifluoroethanol (TFE). The CD spectra reveal the onset of secondary structure upon addition of TFE. The final amount of helical conformation varies among the four peptides. In all cases, the conformational transition is complete before 50% TFE (v/v). 1H-NMR studies were conducted at this solvent composition, leading to the assignment of all the resonances and to the definition of the secondary structure for all four fragments.
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Affiliation(s)
- S Fiori
- University of Padova, Department of Organic Chemistry, CNR, Italy
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7
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Tokmakov AA, Sato KI, Fukami Y. Phosphorylation-sensitive secondary structure in a synthetic peptide corresponding to the activation loop of MAP kinase. Biochem Biophys Res Commun 1997; 236:243-7. [PMID: 9240417 DOI: 10.1006/bbrc.1997.6941] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A 26-amino acid long synthetic peptide corresponding to the activation loop of Xenopus MAP kinase (MAPK), termed IDA (Inter-DFG-APE) MAPK peptide, was found to efficiently inhibit the immunoprecipitation of the enzyme with anti-IDA MAPK serum. The value of half-inhibition concentration (100 nM) indicates that the IDA peptide and native MAPK activation loop are virtually indistinguishable in terms of antibody recognition. On the other hand, the Tyr-phosphorylated form of the peptide exerted its inhibitory action at around one order higher concentration. Shorter nonapeptides covering the epitope sequence of anti-IDA MAPK antibody could also affect the immunoprecipitation but at much higher concentrations (half-inhibition concentration approximately 100 microM) and independently of their phosphorylation state. Circular dichroic study revealed that a secondary structure could be readily induced with the aid of trifluoroethanol in the unphosphorylated and, to a less extent, in the Tyr-phosphorylated IDA MAPK peptide but not in the shorter nonapeptides. These results suggest that the secondary structure similar to that of the unphosphorylated activation loop of MAPK can be formed in the IDA MAPK peptide and may be lost upon its Tyr-phosphorylation.
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Affiliation(s)
- A A Tokmakov
- Graduate School of Science and Technology, Biosignal Research Center, Kobe University, Nada, Japan.
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8
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Hagolle N, Relkin P, Dalgleish D, Launay B. Transition temperatures of heat-induced structural changes in ovalbumin solutions at acid and neutral pH. Food Hydrocoll 1997. [DOI: 10.1016/s0268-005x(97)80061-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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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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Dickerson JE, Lou MF, Gracy RW. Ascorbic acid mediated alteration of alpha-crystallin secondary structure. Curr Eye Res 1995; 14:163-6. [PMID: 7768109 DOI: 10.3109/02713689508999929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glycation, the non-enzymatic addition of sugar or other carbonyl compounds to the amino groups of a protein, has been shown to occur with a variety of sugars and a diverse group of proteins. This type of alteration is believed to be an important component of aging for lens proteins and perhaps in cataractogenesis. Glycation has been shown to alter function and spectroscopic techniques have shown that in many cases conformational changes have occurred. Circular dichroism spectroscopy has documented modifications to alpha-crystallin tertiary structure induced by glucose and glucose 6-phosphate but generally no change to secondary structure. Ascorbate and is oxidized derivative dehydroascorbate have been shown to be powerful glycating agents as well as forming cross-links between peptide chains. In this study, alpha-crystallin incubated with ascorbic acid for one or two wk shows significant incorporation of ascorbate, non-reducible cross-links between the protein chains and altered CD spectra in the far UV region indicative of secondary structure modification.
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Affiliation(s)
- J E Dickerson
- Cataract Research Group, Alcon Laboratories, Inc., Fort Worth, TX 76134, USA
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11
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Bloemendal M, Johnson WC. Structural information on proteins from circular dichroism spectroscopy possibilities and limitations. PHARMACEUTICAL BIOTECHNOLOGY 1995; 7:65-100. [PMID: 8564023 DOI: 10.1007/978-1-4899-1079-0_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M Bloemendal
- Department of Protein and Molecular Biology, Royal Free Hospital School of Medicine, London, England
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12
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Svendsen I, Nicolova D, Goshev I, Genov N. Primary structure, spectroscopic and inhibitory properties of a two-chain trypsin inhibitor from the seeds of charlock (Sinapis arvensis L), a member of the napin protein family. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:425-30. [PMID: 8070965 DOI: 10.1111/j.1399-3011.1994.tb00540.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A protein with inhibitory activity toward trypsin has been isolated from Sinapis arvensis L (charlock). It has a molecular weight of 15,500 and consists of two chains connected by disulfide bonds. The amino acid sequence was determined and showed that it belongs to the napin family of storage proteins. CD studies showed an alpha-helix content of 12% and a beta-structure of about 50%.
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Affiliation(s)
- I Svendsen
- Department of Chemistry, Carlsberg Laboratory, Copenhagen Valby, Denmark
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13
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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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14
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Carey K, Kelly S, Price N, O'Sullivan D, Sheehan D. Two amphiphilic, synthetic peptides display strong emulsification properties. Food Chem 1994. [DOI: 10.1016/0308-8146(94)90097-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Tessari M, Foffani MT, Mammi S, Peggion E. Conformation and interactions of uteroglobin fragments 4-14 and 49-65 in aqueous solution containing surfactant micelles. Biopolymers 1993; 33:1877-87. [PMID: 8268412 DOI: 10.1002/bip.360331213] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The conformation of two fragments of rabbit uteroglobin is described. The peptides are PRFAHVIENLL and PQTTRENIMKLTEKIVK, corresponding to helices I and IV in the crystal structure. CD shows that both peptides interact with sodium dodecyl sulfate (SDS) micelles and change their conformation to an alpha-helix. The helical content estimated from the CD band at 222 nm is about 40% in each peptide. Surface tension measurements show that both peptides lower the critical micellar concentration (cmc) of SDS, with a more dramatic effect in the case of helix I. This peptide by itself acts as a surfactant, and is able to interact with SDS even below the observed cmc, forming beta aggregates. Proton magnetic resonance (1H-nmr) suggests that flexible helices are present. The longest helical stretches compatible with 1H-nmr data extend from Phe6 to Leu14 for helix I and from Arg53 to Ile63 for helix IV.
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Affiliation(s)
- M Tessari
- Department of Organic Chemistry, University of Padova, Italy
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16
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Kelly SM, Duncan D, Price NC. Unfolding and refolding of the NAD(+)-dependent isocitrate dehydrogenase from yeast. Int J Biol Macromol 1993; 15:75-9. [PMID: 8485106 DOI: 10.1016/0141-8130(93)90001-3] [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: 01/31/2023]
Abstract
The unfolding of the NAD(+)-dependent isocitrate dehydrogenase from yeast in guanidinium chloride (GdnHCl) has been monitored by changes in c.d. and fluorescence. Major structural changes occur over the range of GdnHCl concentrations from 0.5 to 1.5 M, although loss of catalytic activity is complete at 0.3 M. After incubation in GdnHCl, activity can be regained on dilution; however, the extent of this regain is dependent on the initial concentration of GdnHCl and is very small at a concentration of 2 M or above. Under these conditions there is only limited regain of the secondary and tertiary structure of the enzyme. Considerably more structure and activity can be regained if the concentration of GdnHCl is lowered by dialysis. The implications of these results for the folding and assembly of the enzyme are discussed.
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Affiliation(s)
- S M Kelly
- Department of Biological and Molecular Sciences, University of Stirling, Scotland, UK
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17
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Price NC, Kelly SM, Thomson GJ, Coggins JR, Wood S, auf der Mauer A. The unfolding and attempted refolding of the bacterial chaperone protein groEL (cpn60). BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1161:52-8. [PMID: 8093666 DOI: 10.1016/0167-4838(93)90195-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The unfolding of the bacterial chaperone protein groEL (cpn60) in solutions of guanidinium chloride (GdnHCl) has been studied. From the results of CD, fluorescence and light scattering, it is clear that major structural transitions in the protein occur over the range 1.0-1.5 M GdnHCl. The ATPase activity of the protein is lost at lower concentrations (0.75 M). After denaturation in concentrations of GdnHCl above 1.5 M, removal of the denaturing agent by dialysis results in very nearly complete regain of secondary structure (as judged by CD), but not the regain of correct tertiary or quaternary structure, or ATPase activity. The product was shown to be very sensitive to proteolysis by thermolysin, unlike the native protein, and not to show enhanced binding of ANS, a characteristic property of the 'molten globule' state of proteins. The results are discussed in relation to current information concerning the assembly of the groEL protein.
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Affiliation(s)
- N C Price
- Department of Biological and Molecular Sciences, University of Stirling, UK
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18
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Lebeche D, Kaminer B. Characterization of a calsequestrin-like protein from sea-urchin eggs. Biochem J 1992; 287 ( Pt 3):741-7. [PMID: 1445238 PMCID: PMC1133070 DOI: 10.1042/bj2870741] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Following our studies on the identification of a calsequestrin-like protein (CSLP) from sea-urchin eggs [Oberdorf, Lebeche, Head & Kaminer (1988) J. Biol Chem. 263, 6806-6809], we have characterized its Ca(2+)-binding properties and identified it as a glycoprotein. The molecule binds 23 mol of Ca2+/mol of protein, as determined by equilibrium dialysis. This is in the range reported for cardiac calsequestrin but is about half the binding capacity of striated muscle calsequestrin. The affinities of the CSLP for Ca2+ are decreased by increasing KCl concentrations (20-250 mM) and the presence of Mg2+ (3 mM) in the medium: the half-maximal binding values varied from 1.62 to 5.77 mM. Hill coefficients indicated mild co-operativity in the Ca2+ binding. Ca2+ (1-8 mM)-induced u.v. difference spectra and intrinsic fluorescence changes suggest a net exposure of aromatic residues to an aqueous environment. C.d. measurements showed minor Ca(2+)-induced changes in alpha-helical and beta-sheet content of less than 10%. These spectral changes are distinctly different from those found in muscle calsequestrin. Immunoblotting studies showed that the CSLP is distinct from calreticulin, a low-affinity Ca(2+)-binding protein.
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Affiliation(s)
- D Lebeche
- Department of Physiology, Boston University School of Medicine, MA 02118
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19
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Duff KC, Kelly SM, Price NC, Bradshaw JP. The secondary structure of influenza A M2 transmembrane domain. A circular dichroism study. FEBS Lett 1992; 311:256-8. [PMID: 1397324 DOI: 10.1016/0014-5793(92)81114-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using circular dichroism, this study investigated the secondary structure of the influenza A M2 transmembrane domain. When reconstituted into 1,2-dioleoyl-sn-glycero-3-phosphocholine liposomes, the M2 transmembrane domain was found to adopt a predominantly alpha-helical secondary structure which was unaffected by both temperature and the addition of 1-aminoadamantane hydrochloride. Reconstitution into 1,2-dioleoyl-sn-glycero-3-phosphoglycerol liposomes resulted in a marked decrease in helical content.
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Affiliation(s)
- K C Duff
- Department of Biochemistry, University of Edinburgh Medical School, Scotland, UK
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20
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Bañó MC, Braco L, Abad C. A semi-empirical approach for the simulation of circular dichroism spectra of gramicidin A in a model membrane. Biophys J 1992; 63:70-7. [PMID: 1384735 PMCID: PMC1262125 DOI: 10.1016/s0006-3495(92)81590-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In an extension of our previous work (Bañó, M. C., Braco, L., and Abad, C. 1991. Biochemistry. 30:886-94), the kinetics of dissociation of gramicidin A double-stranded dimers into beta 6.3-helical monomers in small unilamellar vesicles prepared following different protocols, were investigated using in combination circular dichroism (CD) and high-performance liquid chromatography (HPLC). The analysis of the data from both techniques according to a two-component model strongly supports that any given CD pattern of gramicidin incorporated in the phospholipid bilayer can be deconvoluted essentially as a linear combination of the reference subspectra calculated for the double-stranded dimer and the helical monomer. An HPLC-based, semi-empirical approach is proposed for the simulation of gramicidin CD curves in the model membrane used, and it is shown that the congruence between theoretical and experimental spectra is very satisfactory.
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Affiliation(s)
- M C Bañó
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Spain
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21
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Coussons PJ, Price NC, Kelly SM, Smith B, Sawyer L. Transglutaminase catalyses the modification of glutamine side chains in the C-terminal region of bovine beta-lactoglobulin. Biochem J 1992; 283 ( Pt 3):803-6. [PMID: 1350436 PMCID: PMC1130957 DOI: 10.1042/bj2830803] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The transglutaminase-catalysed incorporation of primary amines (putrescine and monodansylcadaverine) into bovine beta-lactoglobulin has been studied. In the presence of 1 mM-dithiothreitol between 1 and 2 mol of amine can be incorporated per mol of beta-lactoglobulin subunit. There is very little incorporation of amines in the absence of reducing agent. By isolating and sequencing the modified peptides, the sites of modification have been identified as Gln-159 (preferred) and Gln-155. C.d. has been used to study the structure of beta-lactoglobulin over a range of pH values and in the presence or absence of dithiothreitol. The results are discussed in terms of the X-ray-crystallographically determined structure of beta-lactoglobulin.
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Affiliation(s)
- P J Coussons
- Department of Biological and Molecular Sciences, University of Stirling, Scotland, U.K
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22
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Vrbjar N, Kean KT, Szabo A, Senak L, Mendelsohn R, Keough KM. Sarcoplasmic reticulum from rabbit and winter flounder: temperature-dependence of protein conformation and lipid motion. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1107:1-11. [PMID: 1535511 DOI: 10.1016/0005-2736(92)90322-d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A comparative study of lipids and proteins in sarcoplasmic reticulum (SR) from rabbit and flounder has been undertaken. The protein/phospholipid ratio (w/w) was 3:1 in flounder SR (FSR) and 2.2:1 in rabbit SR (RSR). Both membranes had similar contents of PC (70%) and PI (6%). PE constituted 15% in RSR and 21% in FSR. PS and sphingomyelin were minor components of both SR (less than 4%). There were differences in the unsaturated chains of the total lipid extracts, PC, PE, and PI between FSR and RSR. RSR was high in linoleate and arachidonate while FSR contained substantial amounts of eicosapentaenoate and docosahexaenoate. FTIR spectroscopy revealed that the lipids of both membranes did not undergo a phase transition between 0 and 50 degrees C. The lipids were in the liquid-crystalline state at physiological temperatures and underwent monotonic increases in conformational disorder as the temperature was raised. CD spectra indicated higher content of alpha-helical structure of proteins in RSR than in FSR. Increasing temperature caused diminution of alpha-helix content. Relatively large decreases in ellipticity were observed between 20 degrees C and 40 degrees C for FSR and 30 degrees C and 60 degrees C for RSR. Measurements of intrinsic tryptophan fluorescence as a function of temperature gave similar results for membrane proteins in both FSR and RSR. The rate of change of tryptophan fluorescence and fluorescence lifetimes was constant over the temperature ranges studied, and no abrupt shifts in fluorescence occurred in the temperature regions where ellipticity decreased rapidly.
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Affiliation(s)
- N Vrbjar
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Canada
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23
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Mammi S, Foffani MT, Improta S, Tessari M, Schievano E, Peggion E. Conformation of uteroglobin fragments. Biopolymers 1992; 32:341-6. [PMID: 1623129 DOI: 10.1002/bip.360320408] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The conformation of three fragments of uteroglobin in aqueous solution and in the presence of SDS micelles is described. Two of these fragments correspond to helix II and helix III of uteroglobin, the crystal structure of which is made of four helices. The third peptide comprises helices II and III, with the connecting beta-turn. While helix II does not interact strongly with the micelles, helix III adopts a rather clear alpha-helix in this system. The elongation of helix III with the addition of helix II at the N-terminus somewhat stabilizes the ordered structure. It is possible that the beta-turn found in the crystal is also present in solution.
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Affiliation(s)
- S Mammi
- Department of Organic Chemistry, University of Padova, Italy
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24
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Kleanthous C, Deka R, Davis K, Kelly SM, Cooper A, Harding SE, Price NC, Hawkins AR, Coggins JR. A comparison of the enzymological and biophysical properties of two distinct classes of dehydroquinase enzymes. Biochem J 1992; 282 ( Pt 3):687-95. [PMID: 1554351 PMCID: PMC1130842 DOI: 10.1042/bj2820687] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper compares the biophysical and mechanistic properties of a typical type I dehydroquinase (DHQase), from the biosynthetic shikimate pathway of Escherichia coli, and a typical type II DHQase, from the quinate pathway of Aspergillus nidulans. C.d. shows that the two proteins have different secondary-structure compositions; the type I enzyme contains approx. 50% alpha-helix while the type II enzyme contains approx. 75% alpha-helix. The stability of the two types of DHQase was compared by denaturant-induced unfolding, as monitored by c.d., and by differential scanning calorimetry. The type II enzyme unfolds at concentrations of denaturant 4-fold greater than the type I and through a series of discrete transitions, while the type I enzyme unfolds in a single transition. These differences in conformational stability were also evident from the calorimetric experiments which show that type I DHQase unfolds as a single co-operative dimer at 57 degrees C whereas the type II enzyme unfolds above 82 degrees C and through a series of transitions suggesting higher orders of structure than that seen for the type I enzyme. Sedimentation and Mr analysis of both proteins by analytical ultracentrifugation is consistent with the unfolding data. The type I DHQase exists predominantly as a dimer with Mr = 46,000 +/- 2000 (a weighted average affected by the presence of monomer) and has a sedimentation coefficient s0(20,w) = 4.12 (+/- 0.08) S whereas the type II enzyme is a dodecamer, weight-average Mr = 190,000 +/- 10,000 and has a sedimentation coefficient, s0(20,w) = 9.96 (+/- 0.21) S. Although both enzymes have reactive histidine residues in the active site and can be inactivated by diethyl pyrocarbonate, the possibility that these structurally dissimilar enzymes catalyse the same dehydration reaction by the same catalytic mechanism is deemed unlikely by three criteria: (1) they have very different pH/log kcat. profiles and pH optima; (2) imine intermediates, which are known to play a central role in the mechanism of type I enzymes, could not be detected (by borohydride reduction) in the type II enzyme; (3) unlike Schiff's base-forming type I enzymes, there are no conserved lysine residues in type II amino acid sequences.
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Affiliation(s)
- C Kleanthous
- Department of Biochemistry, University of Glasgow, U.K
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25
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Toumadje A, Alcorn SW, Johnson WC. Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures. Anal Biochem 1992; 200:321-31. [PMID: 1632496 DOI: 10.1016/0003-2697(92)90473-k] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The CD spectra for 10 proteins with known secondary structure have been extended from 178 to 168 nm. Combined with the data for 6 other proteins investigated previously, this produces a basis set of 16 proteins, which can be used to analyze CD spectra for secondary structure. Extending the spectra adds another CD band to the data and increases the information content from the equivalent of five to six. Analyzing the CD for each of the 16 proteins in the basis set with the 15 other proteins shows a modest improvement in the prediction of secondary structure with the extended CD spectra.
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Affiliation(s)
- A Toumadje
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-6503
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26
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Arteaga G, Nakai S. Thermal denaturation of Turkey breast myosin under different conditions: Effect of temperature and pH, and reversibility of the denaturation. Meat Sci 1992; 31:191-200. [DOI: 10.1016/0309-1740(92)90038-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/1990] [Revised: 10/17/1990] [Accepted: 11/05/1990] [Indexed: 10/27/2022]
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27
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Conformation of one- and two-chain high molecular weight urokinase analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92834-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Walker M, Stevens L, Duncan D, Price NC, Kelly SM. A comparative study of the structure of egg-white riboflavin binding protein from the domestic fowl and Japanese quail. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1991; 100:77-81. [PMID: 1756622 DOI: 10.1016/0305-0491(91)90088-u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1. The riboflavin binding proteins from domestic fowl and Japanese quail have been isolated and their structures compared by circular dichroism, fluorescence and peptide mapping. 2. The two proteins have similar secondary structures, but differ in their tertiary structures as reflected in the environments of aromatic amino acid side chains. 3. Differences in amino acid sequence between the proteins are indicated by the digestion patterns obtained with thermolysin, chymotrypsin and V8 proteinase from Staphylococcus aureus. Both proteins are resistant to digestion by trypsin.
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Affiliation(s)
- M Walker
- Department of Biological and Molecular Sciences, University of Stirling, Scotland, UK
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29
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Ghetti A, Bolognesi M, Cobianchi F, Morandi C. Modeling by homology of RNA binding domain in A1 hnRNP protein. FEBS Lett 1990; 277:272-6. [PMID: 2176620 DOI: 10.1016/0014-5793(90)80863-e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Eukaryotic nuclear RNA binding proteins share a common sequence motif thought to be implicated in RNA binding. One of the two domains present in A1 hnRNP protein, has been modelled by homology in order to make a prediction of the main features of the RNA binding site. Acylphosphatase (EC 3.6.1.7) was selected as template for the modeling experiment. The predicted RNA binding site is a beta-sheet containing the two RNP consensus sequences as well as lysines and arginines conserved among the family.
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Affiliation(s)
- A Ghetti
- Instituto di Scienze Biologiche, Università di Verona, Italy
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30
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Peter ME, Reiser CO, Schirmer NK, Kiefhaber T, Ott G, Grillenbeck NW, Sprinzl M. Interaction of the isolated domain II/III of Thermus thermophilus elongation factor Tu with the nucleotide exchange factor EF-Ts. Nucleic Acids Res 1990; 18:6889-93. [PMID: 2263451 PMCID: PMC332746 DOI: 10.1093/nar/18.23.6889] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The middle and C-terminal domain (domain II/III) of elongation factor Tu from Thermus thermophilus lacking the GTP/GDP binding domain have been prepared by treating nucleotide-free protein with Staphylococcus aureus V8 protease. The isolated domain II/III of EF-Tu has a compact structure and high resistance against tryptic treatment and thermal denaturation. As demonstrated by circular dichroism spectroscopy, the isolated domain II/III does not contain any alpha-helical structure. Nucleotide exchange factor, EF-Ts, was found to interact with domain II/III, whereas the binding of aminoacyl-tRNA, GDP and GTP to this EF-Tu fragment could not be detected.
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Affiliation(s)
- M E Peter
- Laboratorium für Biochemie, Universität Bayreuth, FRG
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31
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Edwards RA, Jacobson AL, Huber RE. Thermal denaturation of beta-galactosidase and of two site-specific mutants. Biochemistry 1990; 29:11001-8. [PMID: 2125499 DOI: 10.1021/bi00501a019] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The thermal denaturation of wild-type beta-galactosidase and two beta-galactosidases with substitutions at the active site was studied by kinetics, differential scanning calorimetry, electrophoresis, molecular exclusion chromatography, and circular dichroism. From the results, a model is developed for thermal denaturation of beta-galactosidase which includes the reversible dissociation of ligands, reversible formation of an inactive tetramer, irreversible dissociation of the inactive tetramer to inactive monomers, and subsequent aggregation of inactive monomers to dimers and larger aggregates. Under some conditions, partial reversibility of the activity loss could be demonstrated, and several intermediates in the thermal denaturation process were trapped by quenching and observed by electrophoresis and molecular exclusion chromatography. The ligands Mg2+ and phenylethyl thio-beta-D-galactoside increase the stability of beta-galactosidase to heat denaturation by shifting the ligand binding equilibrium according to Le Chatelier's principle, thus decreasing the concentration of the ligand-free tetramer which can proceed to subsequent steps. Circular dichroism results indicated that beta-galactosidase is dominated by beta-sheet with lower amounts of alpha-helix. Large changes in secondary structure begin to occur only after activity has been lost. Single amino acid changes at the active site can have significant effects on thermal stability of beta-galactosidases. Some of the effects result from increased thermal stability of the ligand-free enzyme itself. Other effects result from changes in ligand binding, but the magnitude of the resulting changes in stability is not related to the strength of ligand binding in a simple fashion.
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Affiliation(s)
- R A Edwards
- Division of Biochemistry, Faculty of Science, University of Calgary, Alberta, Canada
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32
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Scheibe R, Rudolph R, Reng W, Jaenicke R. Structural and catalytic properties of oxidized and reduced chloroplast NADP-malate dehydrogenase upon denaturation and renaturation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 189:581-7. [PMID: 2351138 DOI: 10.1111/j.1432-1033.1990.tb15526.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chloroplast NADP-dependent malate dehydrogenase exists in two interconvertible forms: the inactive disulfide-containing form and the active dithiol form. No major difference in secondary structure or conformation was found between the oxidized and the reduced enzyme as determined by circular dichroism and intrinsic protein fluorescence. The guanidine/HCl-dependent unfolding of the enzyme is characterized by two transition midpoints: those of the reduced enzyme are lower by about 0.2 M guanidine/HCl compared to the oxidized enzyme. As shown by analytical ultracentrifugation, there was no effect of guanidine/HCl concentrations up to 0.25 M on the quaternary structure of the enzyme in its oxidized and reduced forms: both sedimentation coefficient (S20,w = 4.9 +/- 0.1 S) and sedimentation equilibrium (75 +/- 3 kDa) yield the dimer. In the oxidized state the enzyme undergoes guanidine-dependent dissociation to the monomer with a midpoint of transition at 0.5 M. The kinetics of unfolding were found to be significantly faster for the reduced than for the oxidized enzyme. Renaturation and reactivation of reduced enzyme was more rapid and occurred with higher yields (100%) than for the oxidized enzyme (60-80% yield). Furthermore, the effect of denaturants on catalytic activity, and reductive activation of the oxidized form, were studied. Both increase in protein fluorescence and a stimulatory effect on the activities at low guanidine/HCl concentrations were observed for the oxidized and the reduced form of the enzyme. Denaturants increase the rate of reductive activation of NADP-malate dehydrogenase.
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Affiliation(s)
- R Scheibe
- Lehrstuhl Pflanzenphysiologie, Universität Bayreuth, Federal Republic of Germany
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33
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Mangel WF, Lin BH, Ramakrishnan V. Characterization of an extremely large, ligand-induced conformational change in plasminogen. Science 1990; 248:69-73. [PMID: 2108500 DOI: 10.1126/science.2108500] [Citation(s) in RCA: 164] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Native human plasminogen has a radius of gyration of 39 angstroms. Upon occupation of a weak lysine binding site, the radius of gyration increases to 56 angstroms, an extremely large ligand-induced conformational change. There are no intermediate conformational states between the closed and open form. The conformational chang is not accompanied by a change in secondary structure, hence the closed conformation is formed by interaction between domains that is abolished upon conversion to the open form. This reversible change in conformation, in which the shape of the protein changes from that best described by a prolate ellipsoid to a flexible structure best described by a Debye random coil, is physiologically relevant because a weak lysine binding site regulates the activation of plasminogen.
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Affiliation(s)
- W F Mangel
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973
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34
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Wrzosek A, Famulski KS, Lehotsky J, Pikuła S. Conformational changes of (Ca2+-Mg2+)-ATPase of erythrocyte plasma membrane caused by calmodulin and phosphatidylserine as revealed by circular dichroism and fluorescence studies. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 986:263-70. [PMID: 2531612 DOI: 10.1016/0005-2736(89)90476-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two spectroscopic techniques, circular dichroism and steady-state fluorescence, were employed in order to study conformational changes of the purified, detergent-solubilized (Ca2+-Mg2+)-ATPase of porcine erythrocyte ghost membranes. Circular dichroism (CD) spectra in the peptide region were obtained from the purified (Ca2+-Mg2+)-ATPase of porcine erythrocyte ghost membranes with the aim to investigate the secondary structure of the enzyme in the presence of calmodulin (CaM) or phosphatidylserine (PS), as well as in the E1 and E2 states. The E1 conformation was stabilized by 10 microM free Ca2+, while the E2 conformation was stabilized by 0.1 mM ethylene glycol bis(2-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA). It was found that the E1 and E2 states of the enzyme strikingly differed in their secondary structure (66% and 46% of calculated alpha-helix content, respectively). In the presence of Ca2+, PS decreased the helical content of the ATPase to 61%, while CaM to 55%. Quenching of intrinsic fluorescence of (Ca2+-Mg2+)-ATPase by acrylamide, performed in the presence of Ca2+, gave evidence for a single class of tryptophan residues with Stern-Volmer constant (KSV) of 10 M-1. Accessibility of tryptophan residues varied depending on the conformational status of the enzyme. Addition of PS and CaM decreased the KSV value to 7.6 M-1 and 8.5 M-1, respectively. In the absence of Ca2+, KSV was 7.0 M-1. KI and CsCl were less effective as quenchers. The fluorescence energy transfer between (Ca2+-Mg2+)-ATPase tryptophan residues and dansyl derivative of covalently labeled CaM occurred in the presence of EGTA, but was further promoted by Ca2+. It is concluded that the interaction of CaM and PS with (Ca2+-Mg2+)-ATPase results in different conformational states of the enzyme. CD and fluorescence spectroscopy allowed to distinguish these states from the E1 and E2 conformational forms of the ATPase.
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Affiliation(s)
- A Wrzosek
- Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
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35
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Svendsen IB, Nicolova D, Goshev I, Genov N. Isolation and characterization of a trypsin inhibitor from the seeds of kohlrabi (Brassica napus var. rapifera) belonging to the napin family of storage proteins. CARLSBERG RESEARCH COMMUNICATIONS 1989; 54:231-9. [PMID: 2490369 DOI: 10.1007/bf02910458] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A trypsin inhibitor with a Km of 5 x 10(-5) M has been isolated from kohlrabi (Brassica napus var. rapifera). Subtilisin DY is inhibited only weakly and chymotrypsin not at all. The inhibitor is closely related to napin as determined by amino acid sequence analysis which also showed the inhibitor to be polymorphous. The inhibitor has been further characterized by means of molecular weight determination using SDS gel-electrophoresis and by amino acid analysis, fluorimetry as well as circular dichroism. A simplified method for purification of napins is given.
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Affiliation(s)
- I B Svendsen
- Department of Chemistry, Carlsberg Laboratory, Copenhagen Valby
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36
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Barden JA, Kemp BE. NMR study of a 34-residue N-terminal fragment of the parathyroid-hormone-related protein secreted during humoral hypercalcemia of malignancy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 184:379-94. [PMID: 2792105 DOI: 10.1111/j.1432-1033.1989.tb15030.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The proton resonances of the biologically active peptide parathyroid-hormone-related protein (residues 1-34) were assigned using one-dimensional spin-decoupling techniques, two-dimensional correlated spectroscopy and by comparing the spectra of the peptides 1-20, 1-25, 1-29, 7-34 and 15-34. The conformation of 1-34 was determined using one- and two-dimensional nuclear Overhauser enhancement spectroscopy in the rotating frame. Amide proton temperature coefficients, vicinal coupling constants and circular dichroic spectra helped reveal a surprisingly compact structure with residues 3-9 forming alpha-helix, type-I beta-turns between residues 10-13 and 16-19 and several interactions between the N-terminal residues and the C-terminal residues. Of these latter, the strongest appeared to be between Asp-10 and Phe-22. One peptide surface in the deduced model presents multiple positive charges, while the opposite surface has a hydrophobic character possibly functioning to exclude water from the binding interface and enhancing the binding constant.
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Affiliation(s)
- J A Barden
- Department of Anatomy, University of Sydney, NSW, Australia
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37
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Abdul-Razzak KK, Denton ML, Cox DJ, Reeck GR. Isolation and characterization of folded fragments released by Staphylococcal aureus proteinase from the non-histone chromosomal protein HMG-1. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 996:125-31. [PMID: 2736255 DOI: 10.1016/0167-4838(89)90104-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
HMG-1 was isolated from newborn calf thymus without exposure to overt denaturing conditions. The purified protein was digested under several solvent conditions with the proteinase (endoproteinase GluC) from Staphylococcus aureus strain V8. We found that the preferred site of attack by the enzyme on HMG-1 was influenced markedly by ionic strength and temperature. In 0.35 M NaCl/50 mM Tris-phosphate (pH 7.8) at 37 degrees C, cleavage near the junction between the A and B domains is predominant, as previously reported by Carballo et al. (EMBO J. 2 (1983) 1759-1764). However, in 50 mM Tris-phosphate (pH 7.8) lacking NaCl and at 0 degrees C, cleavage between the B and C domains strongly predominates. Three major products of the digestions were purified and characterized. The fragment consisting of domains B and C was found by circular dichroism to contain a substantial amount of helix. This re-emphasizes the importance of avoiding overt denaturing conditions when working with members of the HMG-1 family.
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Affiliation(s)
- K K Abdul-Razzak
- Department of Biochemistry, Kansas State University, Manhattan 66506
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38
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Jordi W, Zhou LX, Pilon M, Demel RA, de Kruijff B. The importance of the amino terminus of the mitochondrial precursor protein apocytochrome c for translocation across model membranes. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94175-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Lin TH, Quinn TP, Grandgenett D, Walsh MT. Secondary structural analysis of retrovirus integrase: characterization by circular dichroism and empirical prediction methods. Proteins 1989; 5:156-65. [PMID: 2546146 DOI: 10.1002/prot.340050210] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The retrovirus integrase (IN) protein is essential for integration of viral DNA into host DNA. The secondary structure of the purified IN protein from avian myeloblastosis virus was investigated by both circular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least-squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou-Fasman, Garnier-Osguthorpe-Robson, Nishikawa-Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn-Finkelstein method. Among all of the methods used, the Nishikawa-Ooi prediction gave the closest match in the composition of secondary structure to the CD result, although the other methods each correctly predicted one or more secondary structural group. Most of the alpha-helix and beta-sheet states predicted by the Ptitsyn-Finkelstein method were in accord with the Nishikawa-Ooi method. Secondary structural predictions by the Nishikawa-Ooi method were extended further to include IN proteins from four phylogenetic distinct retroviruses. The structural relationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.
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Affiliation(s)
- T H Lin
- Institute for Molecular Virology, St. Louis University, Missouri 63110
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40
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Manning MC. Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review. J Pharm Biomed Anal 1989; 7:1103-19. [PMID: 2490370 DOI: 10.1016/0731-7085(89)80049-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recombinant DNA technology has made possible the large-scale production of proteins for pharmaceutical applications. As a result, there has been a renaissance in methodology which can provide information on the structural stability and character of these materials. Circular dichroism (CD) spectroscopy, with its sensitivity to the secondary structure adopted by the polypeptide chain, is a powerful tool in this regard. Quantitative analysis of the CD spectra of proteins is now wide-spread, aided by the availability of such algorithms on commercial instrumentation. However, there are basic assumptions made when conducting these calculations, many of which have not been addressed or summarized. Some of these assumptions are independent of the selection of basis spectra and the algorithm employed. These assumptions are listed and the available data concerning their validity is presented and discussed.
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Affiliation(s)
- M C Manning
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence 66045
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41
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Beals JM, Castellino FJ. Circular dichroism analysis of the secondary structures of bovine blood coagulation factor IX, factor X, and prothrombin. JOURNAL OF PROTEIN CHEMISTRY 1988; 7:593-612. [PMID: 3255380 DOI: 10.1007/bf01024877] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Analysis of the far-ultraviolet circular dichroism spectrum of bovine blood coagulation factor IX reveals the presence of approximately 14% helical structures 26% beta-sheets, 20% beta-turns, and 40% coils. These values are essentially the same for the activation products of this zymogen, factor IX alpha alpha and factor IX alpha beta. Similar analysis for bovine factor X permits calculation of these secondary structural as approximately 11% helices, 31% beta-structures, 22% beta-turns, and 36% random structures. Bovine prothrombin contains approximately 12% helical structures, 35% beta-structures, 24% beta-turns, and 29% coils. None of these values is substantially altered as a result of increase of the pH from 7.4 to 10.5, or upon addition of Ca2+ to a concentration of at least 20 mM. Analysis of the near-ultraviolet spectra of factor IX and prothrombin suggests that several aromatic amino acid residues and the disulfide bond present in their gamma-carboxyglutamic acid-containing regions are exposed to solvent and are perturbed by the above pH adjustment and Ca2+ addition. Similar effects are observed in the case of factor X; in addition, the Trp residue at the amino terminus of the heavy chain appears to be influenced by the above pH alteration. The results reported in this paper show that these vitamin K-dependent blood coagulation proteins are similar in their ordered secondary structures, which are dominated by beta-sheets and beta-turns. Their overall secondary structures are not influenced by Ca2+ binding and are stable to alkaline pH changes. However, these same environmental alterations appear to be effective probes of aromatic residues in the gamma-carboxyglutamic acid regions.
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Affiliation(s)
- J M Beals
- Department of Chemistry, University of Notre Dame, Indiana 46556
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42
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Shanmugasundaram T, Kumar GK, Wood HG. Involvement of tryptophan residues at the coenzyme A binding site of carbon monoxide dehydrogenase from Clostridium thermoaceticum. Biochemistry 1988; 27:6499-503. [PMID: 3219350 DOI: 10.1021/bi00417a045] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Carbon monoxide dehydrogenase (CODH) from Clostridium thermoaceticum plays a central role in the newly discovered acetyl-CoA pathway [Wood, H.G., Ragsdale, S.W., & Pezacka, E. (1986) FEMS Microbiol. Rev. 39, 345-362]. The enzyme catalyzes the formation of acetyl-CoA from methyl, carbonyl, and CoA groups, and it has specific binding sites for these moieties. In this study, we have determined the role of tryptophans at these subsites. N-Bromosuccinimide (NBS) oxidation of the exposed and reactive tryptophans (5 out of a total of approximately 20) of CODH at pH 5.5 results in the partial inactivation of the exchange reaction (approximately 50%) involving carbon monoxide and the carbonyl group of the acetyl-CoA. Also, about 70% of the acetyl-CoA synthesis was abolished as a result of NBS modification. The presence of CoA (10 microM) produced complete protection against the partial inhibition of the exchange activity and the overall synthesis of acetyl-CoA caused by NBS. Additionally, none of the exposed tryptophans of CODH was modified in the presence of CoA. Ligands such as the methyl or the carbonyl groups did not afford protection against these inactivations or the modification of the exposed tryptophans. A significant fraction of the accessible fluorescence of CODH was shielded in the presence of CoA against acrylamide quenching. On the basis of these observations, it appears that certain tryptophans are involved at or near the CoA binding site of CODH.
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Affiliation(s)
- T Shanmugasundaram
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
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43
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Hennessey JP, Scarborough GA. Secondary structure of the Neurospora crassa plasma membrane H+-ATPase as estimated by circular dichroism. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69044-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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44
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Abstract
The molecular mechanisms responsible for the unusual stability of enzymes isolated from thermophilic microorganisms are much more complex and subtle than was originally thought. In particular, a general mechanism cannot be proposed, since individual enzymes can be stabilized by specific molecular interactions and forces. The results of studies on thermophilic enzymes obtained in recent years in our laboratory will be summarized, with particular emphasis being placed on those obtained with thermolysin, a stable metalloendopeptidase isolated from Bacillus thermoproteolyticus. Fragmentation of thermolysin by limited proteolysis by added protease (subtilisin) or autolysis mediated by heat or the ion-chelating agent EDTA leads to quite selective peptide bond fissions, allowing isolation of 'nicked' thermolysin species. Correlation of the sites of proteolytic cleavage with the known three-dimensional structure of thermolysin allowed us to infer some of the key characteristics of the structure, folding, dynamics and stability of the thermolysin molecule. The potential utility of these and other studies on thermophilic enzymes in devising strategies for enhancing the stability of mesophilic enzymes using genetic engineering techniques is discussed.
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Affiliation(s)
- A Fontana
- Department of Organic Chemistry, Biopolymer Research Centre of CNR, University of Padua, Italy
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45
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Yada RY, Jackman RL, Nakai S. Secondary structure prediction and determination of proteins--a review. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1988; 31:98-108. [PMID: 3284835 DOI: 10.1111/j.1399-3011.1988.tb00011.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.
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Affiliation(s)
- R Y Yada
- Department of Food Science, University of Guelph, Ontario, Canada
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46
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Teeter MM, Whitlow M. Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins. Proteins 1988; 4:262-73. [PMID: 3253736 DOI: 10.1002/prot.340040405] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin. The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945A resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S.W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W.C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (alpha 1- and beta-purothionin, phoratoxin A and B, and viscotoxin A3 and B). The new program SEQ (pronounced "seek") was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location. Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.
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Affiliation(s)
- M M Teeter
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02167
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47
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Horwitz J, Bok D. Conformational properties of the main intrinsic polypeptide (MIP26) isolated from lens plasma membranes. Biochemistry 1987; 26:8092-8. [PMID: 3442647 DOI: 10.1021/bi00399a012] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The conformational properties of the main intrinsic polypeptide (MIP26) isolated from lens plasma membranes were studied by using near- and far-ultraviolet circular dichroism. The far-ultraviolet spectrum of MIP26 solubilized with octyl beta-D-glucopyranoside indicates an alpha-helical content of approximately 50% and a beta-structure content of approximately 20%. A detergent-free membrane suspension of MIP26 produced a typically distorted far-ultraviolet spectrum which was caused by differential light scattering and absorption flattening. However, decreasing the size of the membrane fragments by sonication produced a far-ultraviolet spectrum free of distortion, and with a rotatory strength profile similar to that obtained for MIP26 solubilized with octyl beta-D-glucopyranoside. This implies similar secondary structure properties for the protein in both the suspension and the sugar detergent. The cleavage of MIP26 with Staphylococcus aureus protease, which results in removal of a 5-kilodalton peptide and which mimics the age-dependent posttranslational changes that take place in the lens, did not significantly affect the conformation of the core protein as judged by the near-ultraviolet circular dichroism spectra.
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Affiliation(s)
- J Horwitz
- Jules Stein Eye Institute, University of California, Los Angeles, School of Medicine 90024-1771
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48
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Manavalan P, Johnson WC. Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal Biochem 1987; 167:76-85. [PMID: 3434802 DOI: 10.1016/0003-2697(87)90135-7] [Citation(s) in RCA: 565] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A new procedure based on the statistical method of "variable selection" is used to predict the secondary structure of proteins from circular dichroism spectra. Variable selection adds the flexibility found in the Provencher and Glöckner method (S. W. Provencher and J. Glöckner, 1981, Biochemistry 20, 33-37) to the method of Hennessey and Johnson (J. P. Hennessey and W. C. Johnson, 1981, Biochemistry 20, 1085-1094). Two analytical methods are presented for choosing a solution from the series generated by the Provencher and Glöckner method, and this improves the technique. All three methods are compared and it is shown that both the variable selection method and the improved Provencher and Glöckner methods have equivalent reliability superior to the original Hennessey and Johnson method. For the new variable selection method, correlation coefficients calculated between X-ray structure and predicted secondary structures for data measured to 178 nm are: 0.97 for alpha-helix, 0.75 for beta-sheet, 0.50 for beta-turn, and 0.89 for other structures. Although the variable selection method improves the analysis of circular dichroism data truncated at 190 nm, data measured to 178 nm gives superior results. It is shown that improving the fit to the measured CD beyond the accuracy of the data can result in poorer analyses.
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Affiliation(s)
- P Manavalan
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331
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49
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Chong GL, Reeck GR. Interaction of trypsin, beta-factor XIIa, and plasma kallikrein with a trypsin inhibitor isolated from barley seeds: a comparison with the corn inhibitor of activated Hageman factor. Thromb Res 1987; 48:211-21. [PMID: 3501175 DOI: 10.1016/0049-3848(87)90418-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A trypsin inhibitor was purified from barley seeds by a modification of published procedures. We determined the dissociation constant, Ki, for the complexes of the barley inhibitor with trypsin, beta-Factor XIIa, and plasma kallikrein. We compared these constants for those of the same enzymes with the corn Hageman Factor inhibitor, which is a homolog of the barley inhibitor. The strength of interaction of the barley inhibitor with the three enzymes was: trypsin greater than beta-Factor XIIa greater than plasma kallikrein. In contrast, the corn inhibitor inhibits beta-Factor XIIa most strongly and does not inhibit plasma kallikrein at all. A possible structural basis for the difference in inhibition specificity is discussed.
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Affiliation(s)
- G L Chong
- Department of Biochemistry, Kansas State University, Manhattan
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50
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Johnson CM, Price NC. Denaturation and renaturation of the monomeric phosphoglycerate mutase from Schizosaccharomyces pombe. Biochem J 1987; 245:525-30. [PMID: 2822024 PMCID: PMC1148153 DOI: 10.1042/bj2450525] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The denaturation by guanidinium chloride of the monomeric phosphoglycerate mutase from Schizosaccharomyces pombe was studied. The loss in activity broadly parallels the changes in protein structure detected by fluorescence and c.d. Renaturation can be brought about by dilution of the denaturing agent. These processes were compared with those in the enzymes from baker's yeast and rabbit muscle, which are tetrameric and dimeric respectively. The effects of the cofactor 2,3-bisphosphoglycerate on the structure and stability of the S. pombe enzyme were also investigated.
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Affiliation(s)
- C M Johnson
- Department of Biological Science, University of Stirling, Scotland, U.K
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